Science.gov

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 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

  15. 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

  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 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

  14. 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

  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. 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.

  1. 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

  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

    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 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

  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. 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

  8. 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

  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 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  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. 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

  8. 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

  9. [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

  10. 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

  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. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  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. 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.

  9. 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

  10. 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

  11. 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

  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. 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.

  16. 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.

  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. [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

  8. 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.

  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. 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

  3. 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.

  4. 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.

  5. 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

  6. 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

  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. 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

  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. 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

  20. 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

  1. 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

  2. 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

  3. 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

  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. 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

  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. 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.

  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. 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

  14. 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.

  15. 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

  16. 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

  17. [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

  18. 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

  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. 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

  8. 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

  9. 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

  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. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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

  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 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. [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

  9. 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

  10. Large-Scale Quantitative Analysis of Painting Arts

    PubMed Central

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

    2014-01-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images – the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances. PMID:25501877

  11. 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

  12. Quantitative Image Analysis of HIV-1 Infection in Lymphoid Tissue

    NASA Astrophysics Data System (ADS)

    Haase, Ashley T.; Henry, Keith; Zupancic, Mary; Sedgewick, Gerald; Faust, Russell A.; Melroe, Holly; Cavert, Winston; Gebhard, Kristin; Staskus, Katherine; Zhang, Zhi-Qiang; Dailey, Peter J.; Balfour, Henry H., Jr.; Erice, Alejo; Perelson, Alan S.

    1996-11-01

    Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productively infected cells Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment.

  13. Large-Scale Quantitative Analysis of Painting Arts

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. A Novel Quantitative Approach to Concept Analysis: The Internomological Network

    PubMed Central

    Cook, Paul F.; Larsen, Kai R.; Sakraida, Teresa J.; Pedro, Leli

    2012-01-01

    Background When a construct such as patients’ transition to self-management of chronic illness is studied by researchers across multiple disciplines, the meaning of key terms can become confused. This results from inherent problems in language where a term can have multiple meanings (polysemy) and different words can mean the same thing (synonymy). Objectives To test a novel quantitative method for clarifying the meaning of constructs by examining the similarity of published contexts in which they are used. Method Published terms related to the concept transition to self-management of chronic illness were analyzed using the internomological network (INN), a type of latent semantic analysis to calculate the mathematical relationships between constructs based on the contexts in which researchers use each term. This novel approach was tested by comparing results to those from concept analysis, a best-practice qualitative approach to clarifying meanings of terms. By comparing results of the two methods, the best synonyms of transition to self-management, as well as key antecedent, attribute, and consequence terms, were identified. Results Results from INN analysis were consistent with those from concept analysis. The potential synonyms self-management, transition, and adaptation had the greatest utility. Adaptation was the clearest overall synonym, but had lower cross-disciplinary use. The terms coping and readiness had more circumscribed meanings. The INN analysis confirmed key features of transition to self-management, and suggested related concepts not found by the previous review. Discussion The INN analysis is a promising novel methodology that allows researchers to quantify the semantic relationships between constructs. The method works across disciplinary boundaries, and may help to integrate the diverse literature on self-management of chronic illness. PMID:22592387

  15. A quantitative histological analysis of the dilated ureter of childhood.

    PubMed

    Lee, B R; Partin, A W; Epstein, J I; Quinlan, D M; Gosling, J A; Gearhart, J P

    1992-11-01

    A quantitative histological study of the dilated ureter of childhood was performed on 26 ureters. The specimens were from 15 male and 11 female patients 10 days to 12 years old (mean age 2.0 years). A color image analysis system was used to examine and compare collagen and smooth muscle components of the muscularis layers to normal control ureters of similar age. In comparing primary obstructed (12) to primary refluxing (14) megaureters and control ureters (6), there was a statistically different collagen-to-smooth muscle ratio (p < 0.001) between the primary obstructed and primary refluxing megaureter groups. For patients with primary refluxing megaureter there was a 2-fold increase in the tissue matrix ratio of collagen-to-smooth muscle when compared to patients with primary obstructed megaureter. In the primary obstructed megaureters the amount of collagen and smooth muscle was not statistically different from controls (p > 0.01). The increased tissue matrix ratio of 2.0 +/- 0.35 (collagen-to-smooth muscle) in the refluxing megaureter group compared to 0.78 +/- 0.22 in the obstructed megaureter group and 0.52 +/- 0.12 in controls was found to be due not only to a marked increase in collagen but also a significant decrease in the smooth muscle component of the tissue. Primary obstructed and normal control ureters had similar quantitative amounts of smooth muscle with 60 +/- 5% and 61 +/- 6%, respectively, while refluxing megaureters had only 40 +/- 5% smooth muscle. The percentage collagen was 36 +/- 5 in the obstructed megaureter group and 30 +/- 5 in controls, with refluxing megaureters having 58 +/- 5% collagen on analysis. Our findings emphasize the significant differences in the structural components (collagen and smooth muscle) of the dilated ureter of childhood, and provide us with further insight into the pathological nature of these dilated ureters and their surgical repair. PMID:1433552

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

    PubMed

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

    2016-08-01

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

  17. Quantitative Medical Image Analysis for Clinical Development of Therapeutics

    NASA Astrophysics Data System (ADS)

    Analoui, Mostafa

    There has been significant progress in development of therapeutics for prevention and management of several disease areas in recent years, leading to increased average life expectancy, as well as of quality of life, globally. However, due to complexity of addressing a number of medical needs and financial burden of development of new class of therapeutics, there is a need for better tools for decision making and validation of efficacy and safety of new compounds. Numerous biological markers (biomarkers) have been proposed either as adjunct to current clinical endpoints or as surrogates. Imaging biomarkers are among rapidly increasing biomarkers, being examined to expedite effective and rational drug development. Clinical imaging often involves a complex set of multi-modality data sets that require rapid and objective analysis, independent of reviewer's bias and training. In this chapter, an overview of imaging biomarkers for drug development is offered, along with challenges that necessitate quantitative and objective image analysis. Examples of automated and semi-automated analysis approaches are provided, along with technical review of such methods. These examples include the use of 3D MRI for osteoarthritis, ultrasound vascular imaging, and dynamic contrast enhanced MRI for oncology. Additionally, a brief overview of regulatory requirements is discussed. In conclusion, this chapter highlights key challenges and future directions in this area.

  18. Automatic quantitative analysis of cardiac MR perfusion images

    NASA Astrophysics Data System (ADS)

    Breeuwer, Marcel M.; Spreeuwers, Luuk J.; Quist, Marcel J.

    2001-07-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and accurate image analysis methods. This paper focuses on the evaluation of blood perfusion in the myocardium (the heart muscle) from MR images, using contrast-enhanced ECG-triggered MRI. We have developed an automatic quantitative analysis method, which works as follows. First, image registration is used to compensate for translation and rotation of the myocardium over time. Next, the boundaries of the myocardium are detected and for each position within the myocardium a time-intensity profile is constructed. The time interval during which the contrast agent passes for the first time through the left ventricle and the myocardium is detected and various parameters are measured from the time-intensity profiles in this interval. The measured parameters are visualized as color overlays on the original images. Analysis results are stored, so that they can later on be compared for different stress levels of the heart. The method is described in detail in this paper and preliminary validation results are presented.

  19. Temporal-resolved characterization of laser-induced plasma for spectrochemical analysis of gas shales

    NASA Astrophysics Data System (ADS)

    Xu, Tao; Zhang, Yong; Zhang, Ming; He, Yi; Yu, Qiaoling; Duan, Yixiang

    2016-07-01

    Optical emission of laser ablation plasma on a shale target surface provides sensitive laser-induced breakdown spectrometry (LIBS) detection of major, minor or trace elements. An exploratory study for the characterization of the plasma induced on shale materials was carried out with the aim to trigger a crucial step towards the quantitative LIBS measurement. In this work, the experimental strategies that optimize the plasma generation on a pressed shale pellet surface are presented. The temporal evolution properties of the plasma induced by ns Nd:YAG laser pulse at the fundamental wavelength in air were investigated using time-resolved space-integrated optical emission spectroscopy. The electron density as well as the temperatures of the plasma were diagnosed as functions of the decay time for the bulk plasma analysis. In particular, the values of time-resolved atomic and ionic temperatures of shale elements, such as Fe, Mg, Ca, and Ti, were extracted from the well-known Boltzmann or Saha-Boltzmann plot method. Further comparison of these temperatures validated the local thermodynamic equilibrium (LTE) within specific interval of the delay time. In addition, the temporal behaviors of the signal-to-noise ratio of shale elements, including Si, Al, Fe, Ca, Mg, Ba, Li, Ti, K, Na, Sr, V, Cr, and Ni, revealed the coincidence of their maximum values with LIBS LTE condition in the time frame, providing practical implications for an optimized LIBS detection of shale elements. Analytical performance of LIBS was further evaluated with the linear calibration procedure for the most concerned trace elements of Sr, V, Cr, and Ni present in different shales. Their limits of detection obtained are elementally dependent and can be lower than tens of parts per million with the present LIBS experimental configurations. However, the occurrence of saturation effect for the calibration curve is still observable with the increasing trace element content, indicating that, due to the

  20. An approach for quantitative image quality analysis for CT

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  1. A temporal examination of the planktonic and biofilm proteome of whole cell Pseudomonas aeruginosa PAO1 using quantitative mass spectrometry.

    PubMed

    Park, Amber J; Murphy, Kathleen; Krieger, Jonathan R; Brewer, Dyanne; Taylor, Paul; Habash, Marc; Khursigara, Cezar M

    2014-04-01

    Chronic polymicrobial lung infections are the chief complication in patients with cystic fibrosis. The dominant pathogen in late-stage disease is Pseudomonas aeruginosa, which forms recalcitrant, structured communities known as biofilms. Many aspects of biofilm biology are poorly understood; consequently, effective treatment of these infections is limited, and cystic fibrosis remains fatal. Here we combined in-solution protein digestion of triplicate growth-matched samples with a high-performance mass spectrometry platform to provide the most comprehensive proteomic dataset known to date for whole cell P. aeruginosa PAO1 grown in biofilm cultures. Our analysis included protein-protein interaction networks and PseudoCAP functional information for unique and significantly modulated proteins at three different time points. Secondary analysis of a subgroup of proteins using extracted ion currents validated the spectral counting data of 1884 high-confidence proteins. In this paper we demonstrate a greater representation of proteins related to metabolism, DNA stability, and molecular activity in planktonically grown P. aeruginosa PAO1. In addition, several virulence-related proteins were increased during planktonic growth, including multiple proteins encoded by the pyoverdine locus, uncharacterized proteins with sequence similarity to mammalian cell entry protein, and a member of the hemagglutinin family of adhesins, HecA. Conversely, biofilm samples contained an uncharacterized protein with sequence similarity to an adhesion protein with self-association characteristics (AidA). Increased levels of several phenazine biosynthetic proteins, an uncharacterized protein with sequence similarity to a metallo-beta-lactamase, and lower levels of the drug target gyrA support the putative characteristics of in situ P. aeruginosa infections, including competitive fitness and antibiotic resistance. This quantitative whole cell approach advances the existing P. aeruginosa

  2. A Temporal Examination of the Planktonic and Biofilm Proteome of Whole Cell Pseudomonas aeruginosa PAO1 Using Quantitative Mass Spectrometry*

    PubMed Central

    Park, Amber J.; Murphy, Kathleen; Krieger, Jonathan R.; Brewer, Dyanne; Taylor, Paul; Habash, Marc; Khursigara, Cezar M.

    2014-01-01

    Chronic polymicrobial lung infections are the chief complication in patients with cystic fibrosis. The dominant pathogen in late-stage disease is Pseudomonas aeruginosa, which forms recalcitrant, structured communities known as biofilms. Many aspects of biofilm biology are poorly understood; consequently, effective treatment of these infections is limited, and cystic fibrosis remains fatal. Here we combined in-solution protein digestion of triplicate growth-matched samples with a high-performance mass spectrometry platform to provide the most comprehensive proteomic dataset known to date for whole cell P. aeruginosa PAO1 grown in biofilm cultures. Our analysis included protein–protein interaction networks and PseudoCAP functional information for unique and significantly modulated proteins at three different time points. Secondary analysis of a subgroup of proteins using extracted ion currents validated the spectral counting data of 1884 high-confidence proteins. In this paper we demonstrate a greater representation of proteins related to metabolism, DNA stability, and molecular activity in planktonically grown P. aeruginosa PAO1. In addition, several virulence-related proteins were increased during planktonic growth, including multiple proteins encoded by the pyoverdine locus, uncharacterized proteins with sequence similarity to mammalian cell entry protein, and a member of the hemagglutinin family of adhesins, HecA. Conversely, biofilm samples contained an uncharacterized protein with sequence similarity to an adhesion protein with self-association characteristics (AidA). Increased levels of several phenazine biosynthetic proteins, an uncharacterized protein with sequence similarity to a metallo-beta-lactamase, and lower levels of the drug target gyrA support the putative characteristics of in situ P. aeruginosa infections, including competitive fitness and antibiotic resistance. This quantitative whole cell approach advances the existing P. aeruginosa

  3. Variation and diversity in Homo erectus: a 3D geometric morphometric analysis of the temporal bone.

    PubMed

    Terhune, Claire E; Kimbel, William H; Lockwood, Charles A

    2007-07-01

    Although the level of taxonomic diversity within the fossil hominin species Homo erectus (sensu lato) is continually debated, there have been relatively few studies aiming to quantify the morphology of this species. Instead, most researchers have relied on qualitative descriptions or the evaluation of nonmetric characters, which in many cases display continuous variation. Also, only a few studies have used quantitative data to formally test hypotheses regarding the taxonomic composition of the "erectus" hypodigm. Despite these previous analyses, however, and perhaps in part due to these varied approaches for assessing variation within specimens typically referred to H. erectus (sensu lato) and the general lack of rigorous statistical testing of how variation within this taxon is partitioned, there is currently little consensus regarding whether this group is a single species, or whether it should instead be split into separate temporal or geographically delimited taxa. In order to evaluate possible explanations for variation within H. erectus, we tested the general hypothesis that variation within the temporal bone morphology of H. erectus is consistent with that of a single species, using great apes and humans as comparative taxa. Eighteen three-dimensional (3D) landmarks of the temporal bone were digitized on a total of 520 extant and fossil hominid crania. Landmarks were registered by Generalized Procrustes Analysis, and Procrustes distances were calculated for comparisons of individuals within and between the extant taxa. Distances between fossil specimens and between a priori groupings of fossils were then compared to the distances calculated within the extant taxa to assess the variation within the H. erectus sample relative to that of known species, subspecies, and populations. Results of these analyses indicate that shape variation within the entire H. erectus sample is generally higher than extant hominid intraspecific variation, and putative H. ergaster

  4. Analysis of temporal jitter in a copper vapor laser system.

    PubMed

    Durga Praveen Kumar, D; Gantayet, L M; Singh, Sunita; Rawat, A S; Rana, Paramjit; Rajasree, V; Agarwalla, Sandeep K; Chakravarthy, D P

    2012-02-01

    Temporal jitter in a magnetic pulse compression based copper vapor laser (CVL) system is analyzed by considering ripple present in the input dc power supply and ripple present in the magnetic core resetting power supply. It is shown that the jitter is a function of the ratio of operating voltage to the designed voltage, percentage ripple, and the total propagation delay of the magnetic pulse compression circuit. Experimental results from a CVL system operating at a repetition rate of 9 kHz are presented. PMID:22380123

  5. Quantitative analysis of night skyglow amplification under cloudy conditions

    NASA Astrophysics Data System (ADS)

    Kocifaj, Miroslav; Solano Lamphar, Héctor Antonio

    2014-10-01

    The radiance produced by artificial light is a major source of nighttime over-illumination. It can, however, be treated experimentally using ground-based and satellite data. These two types of data complement each other and together have a high information content. For instance, the satellite data enable upward light emissions to be normalized, and this in turn allows skyglow levels at the ground to be modelled under cloudy or overcast conditions. Excessive night lighting imposes an unacceptable burden on nature, humans and professional astronomy. For this reason, there is a pressing need to determine the total amount of downwelling diffuse radiation. Undoubtedly, cloudy periods can cause a significant increase in skyglow as a result of amplification owing to diffuse reflection from clouds. While it is recognized that the amplification factor (AF) varies with cloud cover, the effects of different types of clouds, of atmospheric turbidity and of the geometrical relationships between the positions of an individual observer, the cloud layer, and the light source are in general poorly known. In this paper the AF is quantitatively analysed considering different aerosol optical depths (AODs), urban layout sizes and cloud types with specific albedos and altitudes. The computational results show that the AF peaks near the edges of a city rather than at its centre. In addition, the AF appears to be a decreasing function of AOD, which is particularly important when modelling the skyglow in regions with apparent temporal or seasonal variability of atmospheric turbidity. The findings in this paper will be useful to those designing engineering applications or modelling light pollution, as well as to astronomers and environmental scientists who aim to predict the amplification of skyglow caused by clouds. In addition, the semi-analytical formulae can be used to estimate the AF levels, especially in densely populated metropolitan regions for which detailed computations may be CPU

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

    PubMed

    Siegel, Erin M; Riggs, Bridget M; Delmas, Amber L; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D

    2015-01-01

    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated. PMID:25826459

  7. Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer

    PubMed Central

    Siegel, Erin M.; Riggs, Bridget M.; Delmas, Amber L.; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D.

    2015-01-01

    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97–1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated. PMID:25826459

  8. Research of spatio-temporal analysis of agricultural pest

    NASA Astrophysics Data System (ADS)

    Wang, Changwei; Li, Deren; Hu, Yueming; Wu, Xiaofang; Qi, Yu

    2009-10-01

    The increase of agricultural pest disasters in recent years has become one of major problems in agriculture harvest; how to predict and control the disasters of agricultural pest has thus attracted great research interest. Although a series of works have been done and some achievements have been attained, the knowledge in this area remains limited. The migration of agricultural pest is not only related to the time variation, but also the space; consequently, the population of agricultural pest has complex spatio-temporal characteristics. The space factor and the temporal factor must be considered at the same time in the research of dynamics changes of the pest population. Using plant hoppers as an object of study, this study employed the biological analogy deviation model to study the distribution of pest population in different periods of time in Guangdong Province. It is demonstrated that the population distribution of plant hoppers is not only related to the space location, but also has a certain direction. The result reported here offers help to the monitor, prevention and control of plant hoppers in Guangdong Provinces.

  9. Ontology Driven Analysis of Spatio-temporal Phenomena, Aimed At Spatial Planning And Environmental Forecasting

    NASA Astrophysics Data System (ADS)

    Iwaniak, A.; Łukowicz, J.; Strzelecki, M.; Kaczmarek, I.

    2013-10-01

    Spatial planning is a crucial area for balancing civilization development with environmental protection. Spatial planning has a multidisciplinary nature. It must take into account the dynamics of the processes, which could affect the integrity of the environmental system. That is why we need a new approach to modelling phenomena occurring in space. Such approach is offered by ontologies, based on Description Logic (DL) and related to inference systems. Ontology is a system for the knowledge representation, including conceptual scheme and based on this scheme representation of reality. Ontologies can be enriched with additional logical systems. The authors present a way of building domain ontologies for spatial planning, including the representation of spatio-temporal phenomena. Description Logic is supplemented by structures of temporal logic. As a result, the analysis for exploring the topological relations between spatial objects will be extended to include temporal relationships: coincidence, precedence and succession, cause and effect relationship. Spatio-temporal models with temporal logic structures, encoded in ontologies, could be a subject of inference process, performed by semantic reasoners (reasoner engines). Spatio-temporal representations are offered, by so-called upper ontologies, such as GFO, BFO, OCHRE and others. Temporal structures provided in such ontologies, are useful for the analysis of data obtained from environmental and development monitoring systems and for description and representation of historical phenomena. They allow creating the models and scenarios of expected spatial transformation. They will support analysis for spatial development design, decision-making in spatial planning and forecasting of environmental impact.

  10. Quantitative Analysis Of Acoustic Emission From Rock Fracture Experiments

    NASA Astrophysics Data System (ADS)

    Goodfellow, Sebastian David

    This thesis aims to advance the methods of quantitative acoustic emission (AE) analysis by calibrating sensors, characterizing sources, and applying the results to solve engi- neering problems. In the first part of this thesis, we built a calibration apparatus and successfully calibrated two commercial AE sensors. The ErgoTech sensor was found to have broadband velocity sensitivity and the Panametrics V103 was sensitive to surface normal displacement. These calibration results were applied to two AE data sets from rock fracture experiments in order to characterize the sources of AE events. The first data set was from an in situ rock fracture experiment conducted at the Underground Research Laboratory (URL). The Mine-By experiment was a large scale excavation response test where both AE (10 kHz - 1 MHz) and microseismicity (MS) (1 Hz - 10 kHz) were monitored. Using the calibration information, magnitude, stress drop, dimension and energy were successfully estimated for 21 AE events recorded in the tensile region of the tunnel wall. Magnitudes were in the range -7.5 < Mw < -6.8, which is consistent with other laboratory AE results, and stress drops were within the range commonly observed for induced seismicity in the field (0.1 - 10 MPa). The second data set was AE collected during a true-triaxial deformation experiment, where the objectives were to characterize laboratory AE sources and identify issues related to moving the analysis from ideal in situ conditions to more complex laboratory conditions in terms of the ability to conduct quantitative AE analysis. We found AE magnitudes in the range -7.8 < Mw < -6.7 and as with the in situ data, stress release was within the expected range of 0.1 - 10 MPa. We identified four major challenges to quantitative analysis in the laboratory, which in- hibited our ability to study parameter scaling (M0 ∝ fc -3 scaling). These challenges were 0c (1) limited knowledge of attenuation which we proved was continuously evolving, (2

  11. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling

    PubMed Central

    Jacobs, Kris; Klammer, Martin; Jordan, Nicole; Elschenbroich, Sarah; Parade, Marc; Jacoby, Edgar; Linders, Joannes T. M.; Brehmer, Dirk; Cools, Jan; Daub, Henrik

    2016-01-01

    The four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies. PMID:26745281

  12. Quantitative analysis of bloggers' collective behavior powered by emotions

    NASA Astrophysics Data System (ADS)

    Mitrović, Marija; Paltoglou, Georgios; Tadić, Bosiljka

    2011-02-01

    Large-scale data resulting from users' online interactions provide the ultimate source of information to study emergent social phenomena on the Web. From individual actions of users to observable collective behaviors, different mechanisms involving emotions expressed in the posted text play a role. Here we combine approaches of statistical physics with machine-learning methods of text analysis to study the emergence of emotional behavior among Web users. Mapping the high-resolution data from digg.com onto bipartite networks of users and their comments onto posted stories, we identify user communities centered around certain popular posts and determine emotional contents of the related comments by the emotion classifier developed for this type of text. Applied over different time periods, this framework reveals strong correlations between the excess of negative emotions and the evolution of communities. We observe avalanches of emotional comments exhibiting significant self-organized critical behavior and temporal correlations. To explore the robustness of these critical states, we design a network-automaton model on realistic network connections and several control parameters, which can be inferred from the dataset. Dissemination of emotions by a small fraction of very active users appears to critically tune the collective states.

  13. Inside Single Cells: Quantitative Analysis with Advanced Optics and Nanomaterials

    PubMed Central

    Cui, Yi; Irudayaraj, Joseph

    2014-01-01

    Single cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single cell activity. In order to obtain quantitative information (e.g. molecular quantity, kinetics and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single cell studies both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live cell analysis. Although a considerable proportion of single cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single cell analysis. PMID:25430077

  14. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    SciTech Connect

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-02

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

  15. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    SciTech Connect

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-01

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, and which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

  16. Inside single cells: quantitative analysis with advanced optics and nanomaterials.

    PubMed

    Cui, Yi; Irudayaraj, Joseph

    2015-01-01

    Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis. PMID:25430077

  17. Quantitative genetic analysis of the metabolic syndrome in Hispanic children.

    PubMed

    Butte, Nancy F; Comuzzie, Anthony G; Cole, Shelley A; Mehta, Nitesh R; Cai, Guowen; Tejero, Maria; Bastarrachea, Raul; Smith, E O'Brian

    2005-12-01

    Childhood obesity is associated with a constellation of metabolic derangements including glucose intolerance, hypertension, and dyslipidemia, referred to as metabolic syndrome. The purpose of this study was to investigate genetic and environmental factors contributing to the metabolic syndrome in Hispanic children. Metabolic syndrome, defined as having three or more metabolic risk components, was determined in 1030 Hispanic children, ages 4-19 y, from 319 families enrolled in the VIVA LA FAMILIA study. Anthropometry, body composition by dual energy x-ray absorptiometry, clinical signs, and serum biochemistries were measured using standard techniques. Risk factor analysis and quantitative genetic analysis were performed. Of the overweight children, 20%, or 28% if abnormal liver function is included in the definition, presented with the metabolic syndrome. Odds ratios for the metabolic syndrome were significantly increased by body mass index z-score and fasting serum insulin; independent effects of sex, age, puberty, and body composition were not seen. Heritabilities +/- SE for waist circumference, triglycerides (TG), HDL, systolic blood pressure (SBP), glucose, and alanine aminotransferase (ALT) were highly significant. Pleiotropy (a common set of genes affecting two traits) detected between SBP and waist circumference, SBP and glucose, HDL and waist circumference, ALT and waist circumference, and TG and ALT may underlie the clustering of the components of the metabolic syndrome. Significant heritabilities and pleiotropy seen for the components of the metabolic syndrome indicate a strong genetic contribution to the metabolic syndrome in overweight Hispanic children. PMID:16306201

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

    SciTech Connect

    Charland, P.; Peters, T. |

    1996-10-01

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

  19. Quantitative analysis of noninvasive diagnostic procedures for induction motor drives

    NASA Astrophysics Data System (ADS)

    Eltabach, Mario; Antoni, Jerome; Najjar, Micheline

    2007-10-01

    This paper reports quantitative analyses of spectral fault components in five noninvasive diagnostic procedures that use input electric signals to detect different types of abnormalities in induction motors. Besides the traditional one phase current spectrum analysis "SC", the diagnostic procedures based on spectrum analysis of the instantaneous partial powers " P ab", " P cb", total power " P abc", and the current space vector modulus " csvm" are considered. The aim of this comparison study is to improve the diagnosis tools for detection of electromechanical faults in electrical machines by using the best suitable diagnostic procedure knowing some motor and fault characteristics. Defining a severity factor as the increase in amplitude of the fault characteristic frequency, with respect to the healthy condition, enables us to study the sensitivity of the electrical diagnostic tools. As a result, it is shown that the relationship between the angular displacement of the current side-bands components at frequencies ( f± fosc) is directly related to the type of induction motor faults. It is also proved that the total instantaneous power diagnostic procedure was observed to exhibit the highest values of the detection criterion in case of mechanical faults while in case of electrical ones the most reliable diagnostic procedure is tightly related to the value of the motor power factor angle and the group motor-load inertia. Finally, simulation and experimental results show good agreement with the fault modeling theoretical results.

  20. Semiautomatic Software For Quantitative Analysis Of Cardiac Positron Tomography Studies

    NASA Astrophysics Data System (ADS)

    Ratib, Osman; Bidaut, Luc; Nienaber, Christoph; Krivokapich, Janine; Schelbert, Heinrich R.; Phelps, Michael E.

    1988-06-01

    In order to derive accurate values for true tissue radiotracers concentrations from gated positron emission tomography (PET) images of the heart, which are critical for quantifying noninvasively regional myocardial blood flow and metabolism, appropriate corrections for partial volume effect (PVE) and contamination from adjacent anatomical structures are required. We therefore developed an integrated software package for quantitative analysis of tomographic images which provides for such corrections. A semiautomatic edge detection technique outlines and partitions the myocardium into sectors. Myocardial wall thickness is measured on the images perpendicularly to the detected edges and used to correct for PVE. The programs automatically correct for radioactive decay, activity calibration and cross contaminations for both static and dynamic studies. Parameters derived with these programs include tracer concentrations and their changes over time. They are used for calculating regional metabolic rates and can be further displayed as color coded parametric images. The approach was validated for PET imaging in 11 dog experiments. 2D echocardiograms (Echo) were recorded simultaneously to validate the edge detection and wall thickness measurement techniques. After correction for PVE using automatic WT measurement, regional tissue tracer concentrations derived from PET images correlated well with true tissue concentrations as determined by well counting (r=0.98). These preliminary studies indicate that the developed automatic image analysis technique allows accurate and convenient evaluation of cardiac PET images for the measurement of both, regional tracer tissue concentrations as well as regional myocardial function.

  1. Applying Qualitative Hazard Analysis to Support Quantitative Safety Analysis for Proposed Reduced Wake Separation Conops

    NASA Technical Reports Server (NTRS)

    Shortle, John F.; Allocco, Michael

    2005-01-01

    This paper describes a scenario-driven hazard analysis process to identify, eliminate, and control safety-related risks. Within this process, we develop selective criteria to determine the applicability of applying engineering modeling to hypothesized hazard scenarios. This provides a basis for evaluating and prioritizing the scenarios as candidates for further quantitative analysis. We have applied this methodology to proposed concepts of operations for reduced wake separation for closely spaced parallel runways. For arrivals, the process identified 43 core hazard scenarios. Of these, we classified 12 as appropriate for further quantitative modeling, 24 that should be mitigated through controls, recommendations, and / or procedures (that is, scenarios not appropriate for quantitative modeling), and 7 that have the lowest priority for further analysis.

  2. Timing of omitted events: an analysis of temporal control of inhibitory behavior.

    PubMed

    Denniston, James C; Miller, Ralph R

    2007-02-22

    This paper reviews research designed to investigate the temporal control of inhibitory responding using rats as subjects. One area of investigation has focused on the role of temporal variables in conditioned inhibition produced using Pavlov's [Pavlov, I.P., 1927. Conditioned Reflexes. Oxford University Press, London, 430 pp.] procedure. These studies have found that evidence of conditioned inhibition obtained by negative summation testing is strongest when the conditioned inhibitor signals the omission of the unconditioned stimulus (US) at the same temporal location as a transfer excitor signals presentation of the US [e.g., Barnet, R.C., Miller, R.R., 1996. Temporal encoding as a determinant of inhibitory control. Learn. Motiv. 27, 73-91]. Similarly, retardation of acquisition of behavioral control by a previously inhibitory conditioned stimulus (CS) is maximal when the inhibitory CS is paired with the US at the same temporal location as the inhibitor had previously signaled US omission [Burger, D., Denniston, J.C., Miller, R.R., 2001. Temporal coding in condition inhibition: retardation tests. Anim. Learn. Behav. 29, 281-290]. Other lines of research designed to assess the associative structure of temporal control of inhibition [e.g., Denniston, J.C., Blaisdell, A.P., Miller, R.R., 2004. Temporal control in conditioned inhibition: analysis of associative structure of inhibition. J. Exp. Psychol. Anim. Behav. Process. 30, 190-202] are reviewed, as is the assessment of temporal control of inhibition produced through extinction [Denniston, J.C., Miller, R.R., 2003. The role of temporal variables in inhibition produced through extinction. Learn. Behav. 31, 35-48]. These collective observations are discussed in terms of the temporal coding hypothesis [Matzel, L.D., Held, F.P., Miller, R.R., 1988. Reexamination of simultaneous and backward conditioning: Implications for contiguity theory. Learn. Motiv. 19, 317-344]. PMID:17194549

  3. Spatio-temporal analysis of the cerebral spontaneous oscillation

    NASA Astrophysics Data System (ADS)

    Choi, Jee H.; Wolf, Martin; Toronov, Vladislav Y.; Michalos, Antonios; Gratton, Enrico

    2004-05-01

    Cerebral vasomotion was studied on the human brain in vivo by use of multi-optode frequency domain near-infrared spectroscopy (NIRS). Vasomotion is a spontaneous oscillation with a frequency of 0.1 Hz in the arterial flow. We investigated (1) the fluctuations of cerebral hemodynamics on the dynamical characteristics of cerebral vasomotion and (2) the dynamical coupling between vasomotion in the skin and brain. We found that (1) vasomotion is temporal coherent at least for about 3 min; (2) vasomotion observed from NIRS is low-dimensional chaotic with its fractal dimension of about 4.5; (3) vasomotion is spatially coherent with coherence length of about 1 - 2 cm but cerebral vasomotion is dynamically independent from vasomotion in the skin.

  4. Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

    PubMed

    Kerepesi, Csaba; Grolmusz, Vince

    2016-05-01

    DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet-a webserver implementation of AMPHORA2-, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under

  5. Rapid inorganic ion analysis using quantitative microchip capillary electrophoresis.

    PubMed

    Vrouwe, Elwin X; Luttge, Regina; Olthuis, Wouter; van den Berg, Albert

    2006-01-13

    Rapid quantitative microchip capillary electrophoresis (CE) for online monitoring of drinking water enabling inorganic ion separation in less than 15 s is presented. Comparing cationic and anionic standards at different concentrations the analysis of cationic species resulted in non-linear calibration curves. We interpret this effect as a variation in the volume of the injected sample plug caused by changes of the electroosmotic flow (EOF) due to the strong interaction of bivalent cations with the glass surface. This explanation is supported by the observation of severe peak tailing. Conducting microchip CE analysis in a glass microchannel, optimized conditions are received for the cationic species K+, Na+, Ca2+, Mg2+ using a background electrolyte consisting of 30 mmol/L histidine and 2-(N-morpholino)ethanesulfonic acid, containing 0.5 mmol/L potassium chloride to reduce surface interaction and 4 mmol/L tartaric acid as a complexing agent resulting in a pH-value of 5.8. Applying reversed EOF co-migration for the anionic species Cl-, SO42- and HCO3- optimized separation occurs in a background electrolyte consisting of 10 mmol/L 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) and 10 mmol/L HEPES sodium salt, containing 0.05 mmol/L CTAB (cetyltrimethylammonium bromide) resulting in a pH-value of 7.5. The detection limits are 20 micromol/L for the monovalent cationic and anionic species and 10 micromol/L for the divalent species. These values make the method very suitable for many applications including the analysis of abundant ions in tap water as demonstrated in this paper. PMID:16310794

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

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

  8. Advanced spatio-temporal filtering techniques for photogrammetric image sequence analysis in civil engineering material testing

    NASA Astrophysics Data System (ADS)

    Liebold, F.; Maas, H.-G.

    2016-01-01

    The paper shows advanced spatial, temporal and spatio-temporal filtering techniques which may be used to reduce noise effects in photogrammetric image sequence analysis tasks and tools. As a practical example, the techniques are validated in a photogrammetric spatio-temporal crack detection and analysis tool applied in load tests in civil engineering material testing. The load test technique is based on monocular image sequences of a test object under varying load conditions. The first image of a sequence is defined as a reference image under zero load, wherein interest points are determined and connected in a triangular irregular network structure. For each epoch, these triangles are compared to the reference image triangles to search for deformations. The result of the feature point tracking and triangle comparison process is a spatio-temporally resolved strain value field, wherein cracks can be detected, located and measured via local discrepancies. The strains can be visualized as a color-coded map. In order to improve the measuring system and to reduce noise, the strain values of each triangle must be treated in a filtering process. The paper shows the results of various filter techniques in the spatial and in the temporal domain as well as spatio-temporal filtering techniques applied to these data. The best results were obtained by a bilateral filter in the spatial domain and by a spatio-temporal EOF (empirical orthogonal function) filtering technique.

  9. Dynamics and spatio-temporal variability of environmental factors in Eastern Australia using functional principal component analysis

    USGS Publications Warehouse

    Szabo, J.K.; Fedriani, E.M.; Segovia-Gonzalez, M. M.; Astheimer, L.B.; Hooper, M.J.

    2010-01-01

    This paper introduces a new technique in ecology to analyze spatial and temporal variability in environmental variables. By using simple statistics, we explore the relations between abiotic and biotic variables that influence animal distributions. However, spatial and temporal variability in rainfall, a key variable in ecological studies, can cause difficulties to any basic model including time evolution. The study was of a landscape scale (three million square kilometers in eastern Australia), mainly over the period of 19982004. We simultaneously considered qualitative spatial (soil and habitat types) and quantitative temporal (rainfall) variables in a Geographical Information System environment. In addition to some techniques commonly used in ecology, we applied a new method, Functional Principal Component Analysis, which proved to be very suitable for this case, as it explained more than 97% of the total variance of the rainfall data, providing us with substitute variables that are easier to manage and are even able to explain rainfall patterns. The main variable came from a habitat classification that showed strong correlations with rainfall values and soil types. ?? 2010 World Scientific Publishing Company.

  10. Gibbs distribution analysis of temporal correlations structure in retina ganglion cells

    PubMed Central

    Vasquez, J. C.; Marre, O.; Palacios, A.G.; Berry, M.J.; Cessac, B.

    2012-01-01

    We present a method to estimate Gibbs distributions with spatio-temporal constraints on spike trains statistics. We apply this method to spike trains recorded from ganglion cells of the salamander retina, in response to natural movies. Our analysis, restricted to a few neurons, performs more accurately than pairwise synchronization models (Ising) or the 1-time step Markov models (Marre et al. (2009)) to describe the statistics of spatio-temporal spike patterns and emphasizes the role of higher order spatio-temporal interactions. PMID:22115900

  11. Temporal statistical analysis of laser speckle images and its application to retinal blood-flow imaging.

    PubMed

    Cheng, Haiying; Yan, Yumei; Duong, Timothy Q

    2008-07-01

    Temporal-statistical analysis of laser-speckle image (TS-LSI) preserves the original spatial resolution, in contrast to conventional spatial-statistical analysis (SS-LSI). Concerns have been raised regarding the temporal independency of TS-LSI signals and its insensitivity toward stationary-speckle contamination. Our results from flow phantoms and in vivo rat retinas demonstrated that the TS-LSI signals are temporally statistically independent and TS-LSI minimizes stationary-speckle contamination. The latter is because the stationary speckle is "non-random" and thus non-ergodic where the temporal average of stationary speckle needs not equal its spatial ensemble average. TS-LSI detects blood flow in smaller blood vessels and is less susceptible to stationary-speckle artifacts. PMID:18607429

  12. Teaching Quantitative Literacy through a Regression Analysis of Exam Performance

    ERIC Educational Resources Information Center

    Lindner, Andrew M.

    2012-01-01

    Quantitative literacy is increasingly essential for both informed citizenship and a variety of careers. Though regression is one of the most common methods in quantitative sociology, it is rarely taught until late in students' college careers. In this article, the author describes a classroom-based activity introducing students to regression…

  13. Separation and quantitative analysis of alkyl sulfate ethoxymers by HPLC.

    PubMed

    Morvan, Julien; Hubert-Roux, Marie; Agasse, Valérie; Cardinael, Pascal; Barbot, Florence; Decock, Gautier; Bouillon, Jean-Philippe

    2008-01-01

    Separation of alkyl sulfate ethoxymers is investigated on various high-performance liquid chromatography (HPLC) stationary phases: Acclaim C18 Surfactant, Surfactant C8, and Hypercarb. For a fixed alkyl chain length, ethoxymers are eluted in the order of increasing number of ethoxylated units on Acclaim C18 Surfactant, whereas a reversed elution order is observed on Surfactant C8 and Hypercarb. Moreover, on an Acclaim C18 Surfactant column, non-ethoxylated compounds are eluted in their ethoxymers distribution and the use of sodium acetate additive in mobile phase leads to a co-elution of ethoxymers. HPLC stationary phases dedicated to surfactants analysis are evaluated by means of the Tanaka test. Surfactant C8 presents a great silanol activity whereas Acclaim C18 Surfactant shows a high steric selectivity. For alkyl sulfates, linearity of the calibration curve and limits of detection and quantitation are evaluated. The amount of sodium laureth sulfate raw material found in commercial body product is in agreement with the specification of the manufacturer. PMID:19007494

  14. Copulation patterns in captive hamadryas baboons: a quantitative analysis.

    PubMed

    Nitsch, Florian; Stueckle, Sabine; Stahl, Daniel; Zinner, Dietmar

    2011-10-01

    For primates, as for many other vertebrates, copulation which results in ejaculation is a prerequisite for reproduction. The probability of ejaculation is affected by various physiological and social factors, for example reproductive state of male and female and operational sex-ratio. In this paper, we present quantitative and qualitative data on patterns of sexual behaviour in a captive group of hamadryas baboons (Papio hamadryas), a species with a polygynous-monandric mating system. We observed more than 700 copulations and analysed factors that can affect the probability of ejaculation. Multilevel logistic regression analysis and Akaike's information criterion (AIC) model selection procedures revealed that the probability of successful copulation increased as the size of female sexual swellings increased, indicating increased probability of ovulation, and as the number of females per one-male unit (OMU) decreased. In contrast, occurrence of female copulation calls, sex of the copulation initiator, and previous male aggression toward females did not affect the probability of ejaculation. Synchrony of oestrus cycles also had no effect (most likely because the sample size was too small). We also observed 29 extra-group copulations by two non-adult males. Our results indicate that male hamadryas baboons copulated more successfully around the time of ovulation and that males in large OMUs with many females may be confronted by time or energy-allocation problems. PMID:21710159

  15. Quantitative analysis of protein dynamics during asymmetric cell division.

    PubMed

    Mayer, Bernd; Emery, Gregory; Berdnik, Daniela; Wirtz-Peitz, Frederik; Knoblich, Juergen A

    2005-10-25

    In dividing Drosophila sensory organ precursor (SOP) cells, the fate determinant Numb and its associated adaptor protein Pon localize asymmetrically and segregate into the anterior daughter cell, where Numb influences cell fate by repressing Notch signaling. Asymmetric localization of both proteins requires the protein kinase aPKC and its substrate Lethal (2) giant larvae (Lgl). Because both Numb and Pon localization require actin and myosin, lateral transport along the cell cortex has been proposed as a possible mechanism for their asymmetric distribution. Here, we use quantitative live analysis of GFP-Pon and Numb-GFP fluorescence and fluorescence recovery after photobleaching (FRAP) to characterize the dynamics of Numb and Pon localization during SOP division. We demonstrate that Numb and Pon rapidly exchange between a cytoplasmic pool and the cell cortex and that preferential recruitment from the cytoplasm is responsible for their asymmetric distribution during mitosis. Expression of a constitutively active form of aPKC impairs membrane recruitment of GFP-Pon. This defect can be rescued by coexpression of nonphosphorylatable Lgl, indicating that Lgl is the main target of aPKC. We propose that a high-affinity binding site is asymmetrically distributed by aPKC and Lgl and is responsible for asymmetric localization of cell-fate determinants during mitosis. PMID:16243032

  16. Hyperspectral imaging and quantitative analysis for prostate cancer detection

    PubMed Central

    Akbari, Hamed; Halig, Luma V.; Schuster, David M.; Osunkoya, Adeboye; Master, Viraj; Nieh, Peter T.; Chen, Georgia Z.

    2012-01-01

    Abstract. Hyperspectral imaging (HSI) is an emerging modality for various medical applications. Its spectroscopic data might be able to be used to noninvasively detect cancer. Quantitative analysis is often necessary in order to differentiate healthy from diseased tissue. We propose the use of an advanced image processing and classification method in order to analyze hyperspectral image data for prostate cancer detection. The spectral signatures were extracted and evaluated in both cancerous and normal tissue. Least squares support vector machines were developed and evaluated for classifying hyperspectral data in order to enhance the detection of cancer tissue. This method was used to detect prostate cancer in tumor-bearing mice and on pathology slides. Spatially resolved images were created to highlight the differences of the reflectance properties of cancer versus those of normal tissue. Preliminary results with 11 mice showed that the sensitivity and specificity of the hyperspectral image classification method are 92.8% to 2.0% and 96.9% to 1.3%, respectively. Therefore, this imaging method may be able to help physicians to dissect malignant regions with a safe margin and to evaluate the tumor bed after resection. This pilot study may lead to advances in the optical diagnosis of prostate cancer using HSI technology. PMID:22894488

  17. Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

    PubMed Central

    de la Fuente, Ildefonso Martínez

    2010-01-01

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

  18. Hyperspectral imaging and quantitative analysis for prostate cancer detection

    NASA Astrophysics Data System (ADS)

    Akbari, Hamed; Halig, Luma V.; Schuster, David M.; Osunkoya, Adeboye; Master, Viraj; Nieh, Peter T.; Chen, Georgia Z.; Fei, Baowei

    2012-07-01

    Hyperspectral imaging (HSI) is an emerging modality for various medical applications. Its spectroscopic data might be able to be used to noninvasively detect cancer. Quantitative analysis is often necessary in order to differentiate healthy from diseased tissue. We propose the use of an advanced image processing and classification method in order to analyze hyperspectral image data for prostate cancer detection. The spectral signatures were extracted and evaluated in both cancerous and normal tissue. Least squares support vector machines were developed and evaluated for classifying hyperspectral data in order to enhance the detection of cancer tissue. This method was used to detect prostate cancer in tumor-bearing mice and on pathology slides. Spatially resolved images were created to highlight the differences of the reflectance properties of cancer versus those of normal tissue. Preliminary results with 11 mice showed that the sensitivity and specificity of the hyperspectral image classification method are 92.8% to 2.0% and 96.9% to 1.3%, respectively. Therefore, this imaging method may be able to help physicians to dissect malignant regions with a safe margin and to evaluate the tumor bed after resection. This pilot study may lead to advances in the optical diagnosis of prostate cancer using HSI technology.

  19. Quantitative phase imaging applied to laser damage detection and analysis.

    PubMed

    Douti, Dam-Bé L; Chrayteh, Mhamad; Aknoun, Sherazade; Doualle, Thomas; Hecquet, Christophe; Monneret, Serge; Gallais, Laurent

    2015-10-01

    We investigate phase imaging as a measurement method for laser damage detection and analysis of laser-induced modification of optical materials. Experiments have been conducted with a wavefront sensor based on lateral shearing interferometry associated with a high-magnification optical microscope. The system has been used for the in-line observation of optical thin films and bulk samples, laser irradiated in two different conditions: 500 fs pulses at 343 and 1030 nm, and millisecond to second irradiation with a CO2 laser at 10.6 μm. We investigate the measurement of the laser-induced damage threshold of optical material by detection and phase changes and show that the technique realizes high sensitivity with different optical path measurements lower than 1 nm. Additionally, the quantitative information on the refractive index or surface modification of the samples under test that is provided by the system has been compared to classical metrology instruments used for laser damage or laser ablation characterization (an atomic force microscope, a differential interference contrast microscope, and an optical surface profiler). An accurate in-line measurement of the morphology of laser-ablated sites, from few nanometers to hundred microns in depth, is shown. PMID:26479612

  20. Quantitative SERS sensors for environmental analysis of naphthalene.

    PubMed

    Péron, O; Rinnert, E; Toury, T; Lamy de la Chapelle, M; Compère, C

    2011-03-01

    In the investigation of chemical pollutants, such as PAHs (Polycyclic Aromatic Hydrocarbons) at low concentration in aqueous medium, Surface-Enhanced Raman Scattering (SERS) stands for an alternative to the inherent low cross-section of normal Raman scattering. Indeed, SERS is a very sensitive spectroscopic technique due to the excitation of the surface plasmon modes of the nanostructured metallic film. The surface of quartz substrates was coated with a hydrophobic film obtained by silanization and subsequently reacted with polystyrene (PS) beads coated with gold nanoparticles. The hydrophobic surface of the SERS substrates pre-concentrates non-polar molecules such as naphthalene. Under laser excitation, the SERS-active substrates allow the detection and the identification of the target molecules localized close to the gold nanoparticles. The morphology of the SERS substrates based on polystyrene beads surrounded by gold nanoparticles was characterized by scanning electron microscopy (SEM). Furthermore, the Raman fingerprint of the polystyrene stands for an internal spectral reference. To this extent, an innovative method to detect and to quantify organic molecules, as naphthalene in the range of 1 to 20 ppm, in aqueous media was carried out. Such SERS-active substrates tend towards an application as quantitative SERS sensors for the environmental analysis of naphthalene. PMID:21165476

  1. Quantitative analysis of flagellar proteins in Drosophila sperm tails.

    PubMed

    Mendes Maia, Teresa; Paul-Gilloteaux, Perrine; Basto, Renata

    2015-01-01

    The cilium has a well-defined structure, which can still accommodate some morphological and molecular composition diversity to suit the functional requirements of different cell types. The sperm flagellum of the fruit fly Drosophila melanogaster appears as a good model to study the genetic regulation of axoneme assembly and motility, due to the wealth of genetic tools publically available for this organism. In addition, the fruit fly's sperm flagellum displays quite a long axoneme (∼1.8mm), which may facilitate both histological and biochemical analyses. Here, we present a protocol for imaging and quantitatively analyze proteins, which associate with the fly differentiating, and mature sperm flagella. We will use as an example the quantification of tubulin polyglycylation in wild-type testes and in Bug22 mutant testes, which present defects in the deposition of this posttranslational modification. During sperm biogenesis, flagella appear tightly bundled, which makes it more challenging to get accurate measurements of protein levels from immunostained specimens. The method we present is based on the use of a novel semiautomated, macro installed in the image processing software ImageJ. It allows to measure fluorescence levels in closely associated sperm tails, through an exact distinction between positive and background signals, and provides background-corrected pixel intensity values that can directly be used for data analysis. PMID:25837396

  2. Quantitative Financial Analysis of Alternative Energy Efficiency Shareholder Incentive Mechanisms

    SciTech Connect

    Cappers, Peter; Goldman, Charles; Chait, Michele; Edgar, George; Schlegel, Jeff; Shirley, Wayne

    2008-08-03

    Rising energy prices and climate change are central issues in the debate about our nation's energy policy. Many are demanding increased energy efficiency as a way to help reduce greenhouse gas emissions and lower the total cost of electricity and energy services for consumers and businesses. Yet, as the National Action Plan on Energy Efficiency (NAPEE) pointed out, many utilities continue to shy away from seriously expanding their energy efficiency program offerings because they claim there is insufficient profit-motivation, or even a financial disincentive, when compared to supply-side investments. With the recent introduction of Duke Energy's Save-a-Watt incentive mechanism and ongoing discussions about decoupling, regulators and policymakers are now faced with an expanded and diverse landscape of financial incentive mechanisms, Determining the 'right' way forward to promote deep and sustainable demand side resource programs is challenging. Due to the renaissance that energy efficiency is currently experiencing, many want to better understand the tradeoffs in stakeholder benefits between these alternative incentive structures before aggressively embarking on a path for which course corrections can be time-consuming and costly. Using a prototypical Southwest utility and a publicly available financial model, we show how various stakeholders (e.g. shareholders, ratepayers, etc.) are affected by these different types of shareholder incentive mechanisms under varying assumptions about program portfolios. This quantitative analysis compares the financial consequences associated with a wide range of alternative incentive structures. The results will help regulators and policymakers better understand the financial implications of DSR program incentive regulation.

  3. Quantitative analysis of biomedical samples using synchrotron radiation microbeams

    NASA Astrophysics Data System (ADS)

    Ektessabi, Ali; Shikine, Shunsuke; Yoshida, Sohei

    2001-07-01

    X-ray fluorescence (XRF) using a synchrotron radiation (SR) microbeam was applied to investigate distributions and concentrations of elements in single neurons of patients with neurodegenerative diseases. In this paper we introduce a computer code that has been developed to quantify the trace elements and matrix elements at the single cell level. This computer code has been used in studies of several important neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD) and parkinsonism-dementia complex (PDC), as well as in basic biological experiments to determine the elemental changes in cells due to incorporation of foreign metal elements. The substantial nigra (SN) tissue obtained from the autopsy specimens of patients with Guamanian parkinsonism-dementia complex (PDC) and control cases were examined. Quantitative XRF analysis showed that neuromelanin granules of Parkinsonian SN contained higher levels of Fe than those of the control. The concentrations were in the ranges of 2300-3100 ppm and 2000-2400 ppm respectively. On the contrary, Zn and Ni in neuromelanin granules of SN tissue from the PDC case were lower than those of the control. Especially Zn was less than 40 ppm in SN tissue from the PDC case while it was 560-810 ppm in the control. These changes are considered to be closely related to the neuro-degeneration and cell death.

  4. Hyperspectral imaging and quantitative analysis for prostate cancer detection.

    PubMed

    Akbari, Hamed; Halig, Luma V; Schuster, David M; Osunkoya, Adeboye; Master, Viraj; Nieh, Peter T; Chen, Georgia Z; Fei, Baowei

    2012-07-01

    Hyperspectral imaging (HSI) is an emerging modality for various medical applications. Its spectroscopic data might be able to be used to noninvasively detect cancer. Quantitative analysis is often necessary in order to differentiate healthy from diseased tissue. We propose the use of an advanced image processing and classification method in order to analyze hyperspectral image data for prostate cancer detection. The spectral signatures were extracted and evaluated in both cancerous and normal tissue. Least squares support vector machines were developed and evaluated for classifying hyperspectral data in order to enhance the detection of cancer tissue. This method was used to detect prostate cancer in tumor-bearing mice and on pathology slides. Spatially resolved images were created to highlight the differences of the reflectance properties of cancer versus those of normal tissue. Preliminary results with 11 mice showed that the sensitivity and specificity of the hyperspectral image classification method are 92.8% to 2.0% and 96.9% to 1.3%, respectively. Therefore, this imaging method may be able to help physicians to dissect malignant regions with a safe margin and to evaluate the tumor bed after resection. This pilot study may lead to advances in the optical diagnosis of prostate cancer using HSI technology. PMID:22894488

  5. Quantitative image analysis of HIV-1 infection in lymphoid tissue

    SciTech Connect

    Haase, A.T.; Zupancic, M.; Cavert, W.

    1996-11-08

    Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy. A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productivity infected cells. Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment. 22 refs., 2 figs., 2 tabs.

  6. Quantitative trait locus analysis for hemostasis and thrombosis

    PubMed Central

    Sa, Qila; Hart, Erika; Hill, Annie E.; Nadeau, Joseph H.

    2009-01-01

    Susceptibility to thrombosis varies in human populations as well as many in inbred mouse strains. The objective of this study was to characterize the genetic control of thrombotic risk on three chromosomes. Previously, utilizing a tail-bleeding/rebleeding assay as a surrogate of hemostasis and thrombosis function, three mouse chromosome substitution strains (CSS) (B6-Chr5A/J, Chr11A/J, Chr17A/J) were identified (Hmtb1, Hmtb2, Hmtb3). The tailbleeding/rebleeding assay is widely used and distinguishes mice with genetic defects in blood clot formation or dissolution. In the present study, quantitative trait locus (QTL) analysis revealed a significant locus for rebleeding (clot stability) time (time between cessation of initial bleeding and start of the second bleeding) on chromosome 5, suggestive loci for bleeding time (time between start of bleeding and cessation of bleeding) also on chromosomes 5, and two suggestive loci for clot stability on chromosome 17 and one on chromosome 11. The three CSS and the parent A/J had elevated clot stability time. There was no interaction of genes on chromosome 11 with genes on chromosome 5 or chromosome 17. On chromosome 17, twenty-three candidate genes were identified in synteny with previously identified loci for thrombotic risk on human chromosome 18. Thus, we have identified new QTLs and candidate genes not previously known to influence thrombotic risk. PMID:18787898

  7. Fault detection in digital and analog circuits using an i(DD) temporal analysis technique

    NASA Technical Reports Server (NTRS)

    Beasley, J.; Magallanes, D.; Vridhagiri, A.; Ramamurthy, Hema; Deyong, Mark

    1993-01-01

    An i(sub DD) temporal analysis technique which is used to detect defects (faults) and fabrication variations in both digital and analog IC's by pulsing the power supply rails and analyzing the temporal data obtained from the resulting transient rail currents is presented. A simple bias voltage is required for all the inputs, to excite the defects. Data from hardware tests supporting this technique are presented.

  8. Temporal and Spatial Analysis of Monogenetic Volcanic Fields

    NASA Astrophysics Data System (ADS)

    Kiyosugi, Koji

    Achieving an understanding of the nature of monogenetic volcanic fields depends on identification of the spatial and temporal patterns of volcanism in these fields, and their relationships to structures mapped in the shallow crust and inferred in the deep crust and mantle through interpretation of geochemical, radiometric and geophysical data. We investigate the spatial and temporal distributions of volcanism in the Abu Monogenetic Volcano Group, Southwest Japan. E-W elongated volcano distribution, which is identified by a nonparametric kernel method, is found to be consistent with the spatial extent of P-wave velocity anomalies in the lower crust and upper mantle, supporting the idea that the spatial density map of volcanic vents reflects the geometry of a mantle diapir. Estimated basalt supply to the lower crust is constant. This observation and the spatial distribution of volcanic vents suggest stability of magma productivity and essentially constant two-dimensional size of the source mantle diapir. We mapped conduits, dike segments, and sills in the San Rafael sub-volcanic field, Utah, where the shallowest part of a Pliocene magmatic system is exceptionally well exposed. The distribution of conduits matches the major features of dike distribution, including development of clusters and distribution of outliers. The comparison of San Rafael conduit distribution and the distributions of volcanoes in several recently active volcanic fields supports the use of statistical models, such as nonparametric kernel methods, in probabilistic hazard assessment for distributed volcanism. We developed a new recurrence rate calculation method that uses a Monte Carlo procedure to better reflect and understand the impact of uncertainties of radiometric age determinations on uncertainty of recurrence rate estimates for volcanic activity in the Abu, Yucca Mountain Region, and Izu-Tobu volcanic fields. Results suggest that the recurrence rates of volcanic fields can change by more

  9. Communication about vaccinations in Italian websites: a quantitative analysis.

    PubMed

    Tafuri, Silvio; Gallone, Maria S; Gallone, Maria F; Zorico, Ivan; Aiello, Valeria; Germinario, Cinzia

    2014-01-01

    Babies' parents and people who look for information about vaccination often visit anti-vaccine movement's websites, blogs by naturopathic physicians or natural and alternative medicine practitioners. The aim of this work is to provide a quantitative analysis on the type of information available to Italian people regarding vaccination and a quality analysis of websites retrieved through our searches. A quality score was created to evaluate the technical level of websites. A research was performed through Yahoo, Google, and MSN using the keywords "vaccine" and "vaccination," with the function "OR" in order to identify the most frequently used websites. The 2 keywords were input in Italian, and the first 15 pages retrieved by each search engine were analyzed. 149 websites were selected through this methodology. Fifty-three per cent of the websites belonged to associations, groups, or scientific companies, 32.2% (n = 48) consisted of a personal blog and 14.8% (n = 22) belonged to some of the National Health System offices. Among all analyzed websites, 15.4% (n = 23) came from anti-vaccine movement groups. 37.6% reported webmaster name, 67.8% webmaster e-mail, 28.6% indicated the date of the last update and 46.6% the author's name. The quality score for government sites was higher on average than anti-vaccine websites; although, government sites don't use Web 2.0 functions, as the forums.: National Health System institutions who have to promote vaccination cannot avoid investing in web communication because it cannot be managed by private efforts but must be the result of Public Health, private and scientific association, and social movement synergy. PMID:24607988

  10. Quantitative Analysis of Human Cancer Cell Extravasation Using Intravital Imaging.

    PubMed

    Willetts, Lian; Bond, David; Stoletov, Konstantin; Lewis, John D

    2016-01-01

    Metastasis, or the spread of cancer cells from a primary tumor to distant sites, is the leading cause of cancer-associated death. Metastasis is a complex multi-step process comprised of invasion, intravasation, survival in circulation, extravasation, and formation of metastatic colonies. Currently, in vitro assays are limited in their ability to investigate these intricate processes and do not faithfully reflect metastasis as it occurs in vivo. Traditional in vivo models of metastasis are limited by their ability to visualize the seemingly sporadic behavior of where and when cancer cells spread (Reymond et al., Nat Rev Cancer 13:858-870, 2013). The avian embryo model of metastasis is a powerful platform to study many of the critical steps in the metastatic cascade including the migration, extravasation, and invasion of human cancer cells in vivo (Sung et al., Nat Commun 6:7164, 2015; Leong et al., Cell Rep 8, 1558-1570, 2014; Kain et al., Dev Dyn 243:216-28, 2014; Leong et al., Nat Protoc 5:1406-17, 2010; Zijlstra et al., Cancer Cell 13:221-234, 2008; Palmer et al., J Vis Exp 51:2815, 2011). The chicken chorioallantoic membrane (CAM) is a readily accessible and well-vascularized tissue that surrounds the developing embryo. When the chicken embryo is grown in a shell-less, ex ovo environment, the nearly transparent CAM provides an ideal environment for high-resolution fluorescent microcopy approaches. In this model, the embryonic chicken vasculature and labeled cancer cells can be visualized simultaneously to investigate specific steps in the metastatic cascade including extravasation. When combined with the proper image analysis tools, the ex ovo chicken embryo model offers a cost-effective and high-throughput platform for the quantitative analysis of tumor cell metastasis in a physiologically relevant in vivo setting. Here we discuss detailed procedures to quantify cancer cell extravasation in the shell-less chicken embryo model with advanced fluorescence

  11. Higher-order aggregate networks in the analysis of temporal networks: path structures and centralities

    NASA Astrophysics Data System (ADS)

    Scholtes, Ingo; Wider, Nicolas; Garas, Antonios

    2016-03-01

    Despite recent advances in the study of temporal networks, the analysis of time-stamped network data is still a fundamental challenge. In particular, recent studies have shown that correlations in the ordering of links crucially alter causal topologies of temporal networks, thus invalidating analyses based on static, time-aggregated representations of time-stamped data. These findings not only highlight an important dimension of complexity in temporal networks, but also call for new network-analytic methods suitable to analyze complex systems with time-varying topologies. Addressing this open challenge, here we introduce a novel framework for the study of path-based centralities in temporal networks. Studying betweenness, closeness and reach centrality, we first show than an application of these measures to time-aggregated, static representations of temporal networks yields misleading results about the actual importance of nodes. To overcome this problem, we define path-based centralities in higher-order aggregate networks, a recently proposed generalization of the commonly used static representation of time-stamped data. Using data on six empirical temporal networks, we show that the resulting higher-order measures better capture the true, temporal centralities of nodes. Our results demonstrate that higher-order aggregate networks constitute a powerful abstraction, with broad perspectives for the design of new, computationally efficient data mining techniques for time-stamped relational data.

  12. Analysis of SWOT spatial and temporal samplings over continents

    NASA Astrophysics Data System (ADS)

    Biancamaria, Sylvain; Lamy, Alain; Mognard, Nelly

    2014-05-01

    The future Surface Water and Ocean Topography (SWOT) satellite mission, collaboratively developed by NASA, CNES and CSA, is a joint oceanography/continental hydrology mission planned for launch in 2020. In June 2013, a new SWOT orbit has been selected with a 77.6° inclination, a 21 days repeat cycle and a 891 km altitude. The main satellite payload (a Ka-band SAR Interferometer), will provide 2D maps of water elevation, mask and slope over two swaths, both having a 50 km extent. These two swaths will be separated by a 20 km nadir gap. Most of the studies concerning SWOT published since 2007 have considered a former orbit with a 78° inclination, 22 day repeat orbit and a 970 km altitude and a 60 km extent for each swath. None of them have studied the newly selected orbit and the impact of the 20 km nadir gap on the spatial coverage has not been much explored. The purpose of the work presented here is to investigate the spatial and temporal coverage given this new orbit and the actual swath extent (2*50 km swaths with the 20 km nadir gap in between) and compare it to the former SWOT configuration. It is shown that the new configuration will have almost no impact on the computation of monthly averages, however it will impact the spatial coverage. Because of the nadir gap, the orbit repeatitivity and the swaths extent, 3.6% of the continental surfaces in between 78°S and 78°N will never be observed by SWOT (which was previously equal to 2.2% with the former SWOT configuration). The equatorial regions will be the most impacted, as uncovered area could go up to ~14% locally, whereas it never exceeded 9% with the previous SWOT configuration.

  13. Quantitative analysis of LISA pathfinder test-mass noise

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  14. Global migration and the changing distribution of sickle haemoglobin: a quantitative study of temporal trends between 1960 and 2000

    PubMed Central

    Piel, Frédéric B; Tatem, Andrew J; Huang, Zhuojie; Gupta, Sunetra; Williams, Thomas N; Weatherall, David J

    2014-01-01

    Summary Background Changes in the geographical distribution of genetic disorders are often thought to happen slowly, especially when compared with infectious diseases. Whereas mutations, genetic drift, and natural selection take place over many generations, epidemics can spread through large populations within a few days or weeks. Nevertheless, population movements can interfere with these processes, and few studies have been done of their effect on genetic disorders. We aimed to investigate the effect of global migration on the distribution of the sickle-cell gene—the most common and clinically significant haemoglobin structural variant. Methods For each country, we extracted data from the World Bank's Global Bilateral Migration Database about international human migrations between 1960 and 2000. We combined this information with evidence-based estimates of national HbS allele frequencies, generated within a Bayesian geostatistical framework, to analyse temporal changes in the net numbers of migrants, and classified countries with an index summarising these temporal trends. Findings The number of international migrants increased from 92·6 million in 1960, to 165·2 million in 2000. The estimated global number of migrants with HbS increased from about 1·6 million in 1960, to 3·6 million in 2000. This increase was largely due to an increase in the number of migrants from countries with HbS allele frequencies higher than 10%, from 3·1 million in 1960, to 14·2 million in 2000. Additionally, the mean number of countries of origin for each destination country increased from 70 (SE 46) in 1960, to 98 (48) in 2000, showing an increasing diversity in the network of international migrations between countries. Our index of change map shows a patchy distribution of the magnitude of temporal changes, with the highest positive and negative values scattered across all continents. Interpretation Global human population movements have had a substantial effect on the

  15. Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

    PubMed Central

    De la Fuente, Ildefonso M.; Cortes, Jesus M.

    2012-01-01

    The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis. PMID:22393350

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

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

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

  17. Quantitative analysis of harmonic convergence in mosquito auditory interactions

    PubMed Central

    Aldersley, Andrew; Champneys, Alan; Robert, Daniel

    2016-01-01

    This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the ‘harmonic convergence’ phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male–female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male–male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry. PMID:27053654

  18. Quantitative analysis of harmonic convergence in mosquito auditory interactions.

    PubMed

    Aldersley, Andrew; Champneys, Alan; Homer, Martin; Robert, Daniel

    2016-04-01

    This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the 'harmonic convergence' phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male-female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male-male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry. PMID:27053654

  19. Analysis of quantitative phase detection based on optical information processing

    NASA Astrophysics Data System (ADS)

    Tao, Wang; Tu, Jiang-Chen; Chun, Kuang-Tao; Yu, Han-Wang; Xin, Du

    2009-07-01

    Phase object exists widely in nature, such as biological cells, optical components, atmospheric flow field and so on. The phase detection of objects has great significance in the basic research, nondestructive testing, aerospace, military weapons and other areas. The usual methods of phase object detection include interference method, grating method, schlieren method, and phase-contrast method etc. These methods have their own advantages, but they also have some disadvantages on detecting precision, environmental requirements, cost, detection rate, detection range, detection linearity in various applications, even the most sophisticated method-phase contrast method mainly used in microscopic structure, lacks quantitative analysis of the size of the phase of the object and the relationship between the image contrast and the optical system. In this paper, various phase detection means and the characteristics of different applications are analyzed based on the optical information processing, and a phase detection system based on optical filtering is formed. Firstly the frequency spectrum of the phase object is achieved by Fourier transform lens in the system, then the frequency spectrum is changed reasonably by the filter, at last the image which can represent the phase distribution through light intensity is achieved by the inverse Fourier transform. The advantages and disadvantages of the common used filters such as 1/4 wavelength phase filter, high-pass filter and edge filter are analyzed, and their phase resolution is analyzed in the same optical information processing system, and the factors impacting phase resolution are pointed out. The paper draws a conclusion that there exists an optimal filter which makes the detect accuracy best for any application. At last, we discussed how to design an optimal filter through which the ability of the phase testing of optical information processing system can be improved most.

  20. Descriptive Quantitative Analysis of Rearfoot Alignment Radiographic Parameters.

    PubMed

    Meyr, Andrew J; Wagoner, Matthew R

    2015-01-01

    Although the radiographic parameters of the transverse talocalcaneal angle (tTCA), calcaneocuboid angle (CCA), talar head uncovering (THU), calcaneal inclination angle (CIA), talar declination angle (TDA), lateral talar-first metatarsal angle (lTFA), and lateral talocalcaneal angle (lTCA) form the basis of the preoperative evaluation and procedure selection for pes planovalgus deformity, the so-called normal values of these measurements are not well-established. The objectives of the present study were to retrospectively evaluate the descriptive statistics of these radiographic parameters (tTCA, CCA, THU, CIA, TDA, lTFA, and lTCA) in a large population, and, second, to determine an objective basis for defining "normal" versus "abnormal" measurements. As a secondary outcome, the relationship of these variables to the body mass index was assessed. Anteroposterior and lateral foot radiographs from 250 consecutive patients without a history of previous foot and ankle surgery and/or trauma were evaluated. The results revealed a mean measurement of 24.12°, 13.20°, 74.32%, 16.41°, 26.64°, 8.37°, and 43.41° for the tTCA, CCA, THU, CIA, TDA, lTFA, and lTCA, respectively. These were generally in line with the reported historical normal values. Descriptive statistical analysis demonstrated that the tTCA, THU, and TDA met the standards to be considered normally distributed but that the CCA, CIA, lTFA, and lTCA demonstrated data characteristics of both parametric and nonparametric distributions. Furthermore, only the CIA (R = -0.2428) and lTCA (R = -0.2449) demonstrated substantial correlation with the body mass index. No differentiations in deformity progression were observed when the radiographic parameters were plotted against each other to lead to a quantitative basis for defining "normal" versus "abnormal" measurements. PMID:26002682

  1. Automatic quantitative analysis of experimental primary and secondary retinal neurodegeneration: implications for optic neuropathies

    PubMed Central

    Davis, B M; Guo, L; Brenton, J; Langley, L; Normando, E M; Cordeiro, M F

    2016-01-01

    Secondary neurodegeneration is thought to play an important role in the pathology of neurodegenerative disease, which potential therapies may target. However, the quantitative assessment of the degree of secondary neurodegeneration is difficult. The present study describes a novel algorithm from which estimates of primary and secondary degeneration are computed using well-established rodent models of partial optic nerve transection (pONT) and ocular hypertension (OHT). Brn3-labelled retinal ganglion cells (RGCs) were identified in whole-retinal mounts from which RGC density, nearest neighbour distances and regularity indices were determined. The spatial distribution and rate of RGC loss were assessed and the percentage of primary and secondary degeneration in each non-overlapping segment was calculated. Mean RGC number (82 592±681) and RGC density (1695±23.3 RGC/mm2) in naïve eyes were comparable with previous studies, with an average decline in RGC density of 71±17 and 23±5% over the time course of pONT and OHT models, respectively. Spatial analysis revealed greatest RGC loss in the superior and central retina in pONT, but significant RGC loss in the inferior retina from 3 days post model induction. In comparison, there was no significant difference between superior and inferior retina after OHT induction, and RGC loss occurred mainly along the superior/inferior axis (~30%) versus the nasal–temporal axis (~15%). Intriguingly, a significant loss of RGCs was also observed in contralateral eyes in experimental OHT. In conclusion, a novel algorithm to automatically segment Brn3a-labelled retinal whole-mounts into non-overlapping segments is described, which enables automated spatial and temporal segmentation of RGCs, revealing heterogeneity in the spatial distribution of primary and secondary degenerative processes. This method provides an attractive means to rapidly determine the efficacy of neuroprotective therapies with implications for any

  2. Large-scale temporal analysis of computer and information science

    NASA Astrophysics Data System (ADS)

    Soos, Sandor; Kampis, George; Gulyás, László

    2013-09-01

    The main aim of the project reported in this paper was twofold. One of the primary goals was to produce an extensive source of network data for bibliometric analyses of field dynamics in the case of Computer and Information Science. To this end, we rendered the raw material of the DBLP computer and infoscience bibliography into a comprehensive collection of dynamic network data, promptly available for further statistical analysis. The other goal was to demonstrate the value of our data source via its use in mapping Computer and Information Science (CIS). An analysis of the evolution of CIS was performed in terms of collaboration (co-authorship) network dynamics. Dynamic network analysis covered three quarters of the XX. century (76 years, from 1936 to date). Network evolution was described both at the macro- and the mezo level (in terms of community characteristics). Results show that the development of CIS followed what appears to be a universal pattern of growing into a "mature" discipline.

  3. Quantitative PCR analysis of salivary pathogen burden in periodontitis

    PubMed Central

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

    2015-01-01

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

  4. Temporal geospatial analysis of secondary school students’ examination performance

    NASA Astrophysics Data System (ADS)

    Nik Abd Kadir, ND; Adnan, NA

    2016-06-01

    Malaysia's Ministry of Education has improved the organization of the data to have the geographical information system (GIS) school database. However, no further analysis is done using geospatial analysis tool. Mapping has emerged as a communication tool and becomes effective way to publish the digital and statistical data such as school performance results. The objective of this study is to analyse secondary school student performance of science and mathematics scores of the Sijil Pelajaran Malaysia Examination result in the year 2010 to 2014 for the Kelantan's state schools with the aid of GIS software and geospatial analysis. The school performance according to school grade point average (GPA) from Grade A to Grade G were interpolated and mapped and query analysis using geospatial tools able to be done. This study will be beneficial to the education sector to analyse student performance not only in Kelantan but to the whole Malaysia and this will be a good method to publish in map towards better planning and decision making to prepare young Malaysians for the challenges of education system and performance.

  5. Temporal Distributions of Problem Behavior Based on Scatter Plot Analysis.

    ERIC Educational Resources Information Center

    Kahng, SungWoo; Iwata, Brian A.; Fischer, Sonya M.; Page, Terry J.; Treadwell, Kimberli R. H.; Williams, Don E.; Smith, Richard G.

    1998-01-01

    A large-scale analysis was conducted of problem behavior by observing 20 individuals living in residential facilities. Data were converted into scatter plot formats. When the data were transformed into aggregate "control charts," 12 of 15 sets of data revealed 30-minute intervals during which problem behavior was more likely to occur. (Author/CR)

  6. Temporal Land Cover Analysis for Net Ecosystem Improvement

    SciTech Connect

    Ke, Yinghai; Coleman, Andre M.; Diefenderfer, Heida L.

    2013-04-09

    We delineated 8 watersheds contributing to previously defined river reaches within the 1,468-km2 historical floodplain of the tidally influenced lower Columbia River and estuary. We assessed land-cover change at the watershed, reach, and restoration site scales by reclassifying remote-sensing data from the National Oceanic and Atmospheric Administration Coastal Change Analysis Program’s land cover/land change product into forest, wetland, and urban categories. The analysis showed a 198.3 km2 loss of forest cover during the first 6 years of the Columbia Estuary Ecosystem Restoration Program, 2001–2006. Total measured urbanization in the contributing watersheds of the estuary during the full 1996-2006 change analysis period was 48.4 km2. Trends in forest gain/loss and urbanization differed between watersheds. Wetland gains and losses were within the margin of error of the satellite imagery analysis. No significant land cover change was measured at restoration sites, although it was visible in aerial imagery, therefore, the 30-m land-cover product may not be appropriate for assessment of early-stage wetland restoration. These findings suggest that floodplain restoration sites in reaches downstream of watersheds with decreasing forest cover will be subject to increased sediment loads, and those downstream of urbanization will experience effects of increased impervious surfaces on hydrologic processes.

  7. Towards a temporal network analysis of interactive WiFi users

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Wang, Lin; Zhang, Yi-Qing; Li, Xiang

    2012-06-01

    Complex networks are used to depict topological features of complex systems. The structure of a network characterizes the interactions among elements of the system, and facilitates the study of many dynamical processes taking place on it. In previous investigations, the topological infrastructure underlying dynamical systems is simplified as a static and invariable skeleton. However, this assumption cannot cover the temporal features of many time-evolution networks, whose components are evolving and mutating. In this letter, utilizing the log data of WiFi users in a Chinese university campus, we infuse the temporal dimension into the construction of dynamical human contact network. By quantitative comparison with the traditional aggregation approach, we find that the temporal contact network differs in many features, e.g., the reachability, the path length distribution. We conclude that the correlation between temporal path length and duration is not only determined by their definitions, but also influenced by the micro-dynamical features of human activities under certain social circumstance as well. The time order of individuals' interaction events plays a critical role in understanding many dynamical processes via human close proximity interactions studied in this letter. Besides, our study also provides a promising measure to identify the potential superspreaders by distinguishing the nodes functioning as the relay hub. The first two authors contributed equally to this paper.

  8. Temporal variations in ozone concentrations derived from Principal Component Analysis

    NASA Astrophysics Data System (ADS)

    Yonemura, S.; Kawashima, S.; Matsueda, H.; Sawa, Y.; Inoue, S.; Tanimoto, H.

    2008-03-01

    The application of principal components and cluster analysis to vertical ozone concentration profiles in Tsukuba, Japan, has been explored. Average monthly profiles and profiles of the ratio between standard deviation and the absolute ozone concentration (SDPR) of 1 km data were calculated from the original ozone concentration data. Mean (first) and gradient (second) components explained more than 80% of the variation in both the 0-6 km tropospheric and 11-20 km troposphere-stratosphere (interspheric) layers. The principal components analysis not only reproduced the expected inverse relationship between mean ozone concentration and tropopause height ( r 2 = 0.41) and that in the tropospheric layer this is larger in spring and summer, but also yielded new information as follows. The larger gradient component score in summer for the interspheric layer points to the seasonal variation of the troposphere-stratosphere exchange. The minimum SDPR was at about 3 km in the tropospheric layer and the maximum was at about 17 km in the interspheric layer. The tropospheric SDPR mean component score was larger in summer, possibly reflecting the mixing of Pacific maritime air masses with urban air masses. The cluster analysis of the monthly ozone profiles for the 1970s and 2000s revealed different patterns for winter and summer. The month of May was part of the winter pattern in the 1970s but part of the summer pattern during the 2000s. This statistically detected change likely reflects the influence of global warming. Thus, these two statistical analysis techniques can be powerful tools for identifying features of ozone concentration profiles.

  9. Kir4.1-mediated spatial buffering of K+: Experimental challenges in determination of its temporal and quantitative contribution to K+ clearance in the brain

    PubMed Central

    Larsen, Brian Roland; MacAulay, Nanna

    2014-01-01

    Neuronal activity results in release of K+ into the extracellular space of the central nervous system. If the excess K+ is allowed to accumulate, neuronal firing will be compromised by the ensuing neuronal membrane depolarization. The surrounding glial cells are involved in clearing K+ from the extracellular space by molecular mechanism(s), the identity of which have been a matter of controversy for over half a century. Kir4.1-mediated spatial buffering of K+ has been promoted as a major contributor to K+ removal although its quantitative and temporal contribution has remained undefined. We discuss the biophysical and experimental challenges regarding determination of the contribution of Kir4.1 to extracellular K+ management during neuronal activity. It is concluded that 1) the geometry of the experimental preparation is crucial for detection of Kir4.1-mediated spatial buffering and 2) Kir4.1 enacts spatial buffering of K+ during but not after neuronal activity. PMID:25483287

  10. Statistical methods for temporal and space–time analysis of community composition data†

    PubMed Central

    Legendre, Pierre; Gauthier, Olivier

    2014-01-01

    This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran's eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix. PMID:24430848

  11. Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

    ERIC Educational Resources Information Center

    Hill, Devon W.; And Others

    1988-01-01

    Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

  12. Hydrological drought types in cold climates: quantitative analysis of causing factors and qualitative survey of impacts

    NASA Astrophysics Data System (ADS)

    Van Loon, A. F.; Ploum, S. W.; Parajka, J.; Fleig, A. K.; Garnier, E.; Laaha, G.; Van Lanen, H. A. J.

    2015-04-01

    For drought management and prediction, knowledge of causing factors and socio-economic impacts of hydrological droughts is crucial. Propagation of meteorological conditions in the hydrological cycle results in different hydrological drought types that require separate analysis. In addition to the existing hydrological drought typology, we here define two new drought types related to snow and ice. A snowmelt drought is a deficiency in the snowmelt discharge peak in spring in snow-influenced basins and a glaciermelt drought is a deficiency in the glaciermelt discharge peak in summer in glacierised basins. In 21 catchments in Austria and Norway we studied the meteorological conditions in the seasons preceding and at the time of snowmelt and glaciermelt drought events. Snowmelt droughts in Norway were mainly controlled by below-average winter precipitation, while in Austria both temperature and precipitation played a role. For glaciermelt droughts, the effect of below-average summer air temperature was dominant, both in Austria and Norway. Subsequently, we investigated the impacts of temperature-related drought types (i.e. snowmelt and glaciermelt drought, but also cold and warm snow season drought and rain-to-snow-season drought). In historical archives and drought databases for the US and Europe many impacts were found that can be attributed to these temperature-related hydrological drought types, mainly in the agriculture and electricity production (hydropower) sectors. However, drawing conclusions on the frequency of occurrence of different drought types from reported impacts is difficult, mainly because of reporting biases and the inevitably limited spatial and temporal scales of the information. Finally, this study shows that complete integration of quantitative analysis of causing factors and qualitative analysis of impacts of temperature-related droughts is not yet possible. Analysis of selected events, however, points out that it can be a promising research

  13. Integrated Analysis and Tools for Land Subsidence Surveying and Monitoring: a Semi-Quantitative Approach

    NASA Astrophysics Data System (ADS)

    Mosconi, A.; Pozzoli, A.; Meroni, A.; Gagliano, S.

    2015-10-01

    This paper presents an integrated approach for land subsidence monitoring using measures coming from different sensors. Eni S.p.A., the main Italian oil and gas company, constantly surveys the land with all the state of the art and innovative techniques, and a method able to integrate the results is an important and actual topic. Nowadays the world is a multi-sensor platform, and measure integration is strictly necessary. Combining the different data sources should be done in a clever way, taking advantages from the best performances of each technique. An integrated analysis allows the interpretation of simultaneous temporal series of data, coming from different sources, and try to separate subsidence contributions. With this purpose Exelis VIS in collaboration with Eni S.p.A. customize PISAV (Permanent Interferometric Scatterometer Analysis and Visualization), an ENVI extension able to capitalize on and combine all the different data collected in the surveys. In this article are presented some significant examples to show the potential of this tool in oil and gas activity: a hydrocarbon storage field where the comparison between SAR and production volumes emphasise a correlation between the two measures in few steps; and a hydrocarbon production field with the Satellite Survey Unit (S.S.U.), where SAR, CGPS, piezometers and assestimeters measure in the same area at the same time, giving the opportunity to analyse data contextually. In the integrated analysis performed with PISAV not always a mathematical rigorous study is possible, and a semi-quantitative approach is the only method for results interpretation. As a result, in the first test case strong correlation between injected hydrocarbon volume and vertical displacement were highlighted; in the second one the integrated analysis has different advantages in monitoring the land subsidence: permits a first qualitative "differentiation" of the natural and anthropic component of subsidence, and also gives more

  14. Quantitative analysis of localized surface plasmons based on molecular probing.

    PubMed

    Deeb, Claire; Bachelot, Renaud; Plain, Jérôme; Baudrion, Anne-Laure; Jradi, Safi; Bouhelier, Alexandre; Soppera, Olivier; Jain, Prashant K; Huang, Libai; Ecoffet, Carole; Balan, Lavinia; Royer, Pascal

    2010-08-24

    We report on the quantitative characterization of the plasmonic optical near-field of a single silver nanoparticle. Our approach relies on nanoscale molecular molding of the confined electromagnetic field by photoactivated molecules. We were able to directly image the dipolar profile of the near-field distribution with a resolution better than 10 nm and to quantify the near-field depth and its enhancement factor. A single nanoparticle spectral signature was also assessed. This quantitative characterization constitutes a prerequisite for developing nanophotonic applications. PMID:20687536

  15. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    PubMed

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-01-01

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  16. Tools for the Quantitative Analysis of Sedimentation Boundaries Detected by Fluorescence Optical Analytical Ultracentrifugation

    PubMed Central

    Zhao, Huaying; Casillas, Ernesto; Shroff, Hari; Patterson, George H.; Schuck, Peter

    2013-01-01

    Fluorescence optical detection in sedimentation velocity analytical ultracentrifugation allows the study of macromolecules at nanomolar concentrations and below. This has significant promise, for example, for the study of systems of high-affinity protein interactions. Here we describe adaptations of the direct boundary modeling analysis approach implemented in the software SEDFIT that were developed to accommodate unique characteristics of the confocal fluorescence detection system. These include spatial gradients of signal intensity due to scanner movements out of the plane of rotation, temporal intensity drifts due to instability of the laser and fluorophores, and masking of the finite excitation and detection cone by the sample holder. In an extensive series of experiments with enhanced green fluorescent protein ranging from low nanomolar to low micromolar concentrations, we show that the experimental data provide sufficient information to determine the parameters required for first-order approximation of the impact of these effects on the recorded data. Systematic deviations of fluorescence optical sedimentation velocity data analyzed using conventional sedimentation models developed for absorbance and interference optics are largely removed after these adaptations, resulting in excellent fits that highlight the high precision of fluorescence sedimentation velocity data, thus allowing a more detailed quantitative interpretation of the signal boundaries that is otherwise not possible for this system. PMID:24204779

  17. Dynamics of natural killer cell receptor revealed by quantitative analysis of photoswitchable protein.

    PubMed

    Pageon, Sophie V; Aquino, Gerardo; Lagrue, Kathryn; Köhler, Karsten; Endres, Robert G; Davis, Daniel M

    2013-11-01

    Natural Killer (NK) cell activation is dynamically regulated by numerous activating and inhibitory surface receptors that accumulate at the immune synapse. Quantitative analysis of receptor dynamics has been limited by methodologies that rely on indirect measurements such as fluorescence recovery after photobleaching. Here, we report an apparently novel approach to study how proteins traffic to and from the immune synapse using NK cell receptors tagged with the photoswitchable fluorescent protein tdEosFP, which can be irreversibly photoswitched from a green to red fluorescent state by ultraviolet light. Thus, after a localized switching event, the movement of the photoswitched molecules can be temporally and spatially resolved by monitoring fluorescence in two regions of interest. By comparing images with mathematical models, we evaluated the diffusion coefficient of the receptor KIR2DL1 (0.23 ± 0.06 μm(2) s(-1)) and assessed how synapse formation affects receptor dynamics. Our data conclude that the inhibitory NK cell receptor KIR2DL1 is continually trafficked into the synapse, and remains surprisingly stable there. Unexpectedly, however, in NK cells forming synapses with multiple target cells simultaneously, KIR2DL1 at one synapse can relocate to another synapse. Thus, our results reveal a previously undetected intersynaptic exchange of protein. PMID:24209843

  18. Quantitative analysis for lumen and media-adventitia border detection in intravascular ultrasound images

    NASA Astrophysics Data System (ADS)

    Wang, Ling; Yu, Daoyin; Chen, Xiaodong; An, Zhiyong

    2008-12-01

    Therosclerosis causes partial or total obstruction of human arteries. Early quantitative analysis and accurate assessment of plaque position and volume are essential for the selection of the appropriate treatment. Several imaging techniques can be used for the estimation of the severity of the disease in vivo. Intravascular ultrasound (IVUS) is a commonly used diagnostic tool, which provides real-time visualization of plaque morphology and detection of typical plaque components, such as calcium, quantification of plaque eccentricity and wall thickness. In this paper, we firstly used a spatio-temporal filter to reduce the effect of speckles and enhance the image. Then we translated the problem of image segmentation to the problem of the minimum resolution of energy function. using an improved deformable models, we detected the border of lumen and media-adventitia in sequential intravascular ultrasound frames, and optimized it by dynamic programming. Finally, through the identification of the internal and external elastic lamina and the plaque-lumen interface, we figured out the parameter of plaque load, maximal and minimal diameters of the internal and external elastic lamina and so on. The obtained results demonstrate that our method is statistically accurate, reproducible, and capable to identify the regions of interest in sequences of IVUS frames.

  19. A new quantitative method for gunshot residue analysis by ion beam analysis.

    PubMed

    Christopher, Matthew E; Warmenhoeven, John-William; Romolo, Francesco S; Donghi, Matteo; Webb, Roger P; Jeynes, Christopher; Ward, Neil I; Kirkby, Karen J; Bailey, Melanie J

    2013-08-21

    Imaging and analyzing gunshot residue (GSR) particles using the scanning electron microscope equipped with an energy dispersive X-ray spectrometer (SEM-EDS) is a standard technique that can provide important forensic evidence, but the discrimination power of this technique is limited due to low sensitivity to trace elements and difficulties in obtaining quantitative results from small particles. A new, faster method using a scanning proton microbeam and Particle Induced X-ray Emission (μ-PIXE), together with Elastic Backscattering Spectrometry (EBS) is presented for the non-destructive, quantitative analysis of the elemental composition of single GSR particles. In this study, the GSR particles were all Pb, Ba, Sb. The precision of the method is assessed. The grouping behaviour of different makes of ammunition is determined using multivariate analysis. The protocol correctly groups the cartridges studied here, with a confidence >99%, irrespective of the firearm or population of particles selected. PMID:23775063

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

    ERIC Educational Resources Information Center

    Boose, David L.

    2014-01-01

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

  1. MOLD SPECIFIC QUANTITATIVE PCR: THE EMERGING STANDARD IN MOLD ANALYSIS

    EPA Science Inventory

    Today I will talk about the use of quantitative or Real time PCR for the standardized identification and quantification of molds. There are probably at least 100,000 species of molds or fungi. But there are actually about 100 typically found indoors. Some pose a threat to human...

  2. Features of the Quantitative Analysis in Moessbauer Spectroscopy

    SciTech Connect

    Semenov, V. G.; Panchuk, V. V.; Irkaev, S. M.

    2010-07-13

    The results describing the effect of different factors on errors in quantitative determination of the phase composition of studied substances by Moessbauer spectroscopy absorption are presented, and the ways of using them are suggested. The effectiveness of the suggested methods is verified by an example of analyzing standard and unknown compositions.

  3. Quantitative and Qualitative Analysis of Biomarkers in Fusarium verticillioides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, a combination HPLC-DART-TOF-MS system was utilized to identify and quantitatively analyze carbohydrates in wild type and mutant strains of Fusarium verticillioides. Carbohydrate fractions were isolated from F. verticillioides cellular extracts by HPLC using a cation-exchange size-excl...

  4. Quantitative Analysis of Radionuclides in Process and Environmental Samples

    SciTech Connect

    Boni, A.L.

    2003-02-21

    An analytical method was developed for the radiochemical separation and quantitative recovery of ruthenium, zirconium, niobium, neptunium, cobalt, iron, zinc, strontium, rare earths, chromium and cesium from a wide variety of natural materials. This paper discusses this analytical method, based on the anion exchange properties of the various radionuclides, although both ion exchange and precipitation techniques are incorporated.

  5. Ictal Spread of Medial Temporal Lobe Seizures With and Without Secondary Generalization: An Intracranial EEG Analysis

    PubMed Central

    Yoo, Ji Yeoun; Farooque, Pue; Chen, William; Youngblood, Mark W.; Zaveri, Hitten P.; Gerrard, Jason L.; Spencer, Dennis D.; Hirsch, Lawrence J.; Blumenfeld, Hal

    2013-01-01

    Summary Objective Secondary generalization of seizures has devastating consequences for patient safety and quality of life. The aim of this intracranial EEG (icEEG) study was to investigate the differences in onset and propagation patterns of temporal lobe seizures that remained focal vs. those with secondary generalization in order to better understand the mechanism of secondary generalization. Methods A total of 39 seizures were analyzed in 9 patients who met the following criteria: 1) icEEG-video monitoring with at least 1 secondarily generalized tonic clonic seizure (GTC), 2) pathologically proven hippocampal sclerosis, and 3) no seizures for at least 1 year after anteromedial temporal lobe resection. Seizures were classified as focal or secondary generalized by behavioral analysis of video. Onset and propagation patterns were compared by analysis of icEEG. Results We obtained data from 22 focal seizures without generalization (FS), and 17 GTC. Seizure onset patterns did not differ between FS and GTCs, but there were differences in later propagation. All seizures started with low voltage fast activity except 7 seizures in one patient (6 FS, 1 GTC), which started with sharply contoured theta activity. 15 of 39 seizures started from the hippocampus and 24 seizures (including 6 seizures in a patient without hippocampal contacts) started from other medial temporal lobe areas. We observed involvement or more prominent activation of the posterior-lateral temporal regions in GTCs prior to propagation to the other cortical regions, vs. FS which had no involvement or less prominent activation of the posterior lateral temporal cortex. Occipital contacts were not involved at the time of clinical secondary generalization. Significance The posterior-lateral temporal cortex may serve as an important “gateway” controlling propagation of medial temporal lobe seizures to other cortical regions. Identifying the mechanisms of secondary generalization of focal seizures may

  6. Assessing temporal variations in connectivity through suspended sediment hysteresis analysis

    NASA Astrophysics Data System (ADS)

    Sherriff, Sophie; Rowan, John; Fenton, Owen; Jordan, Phil; Melland, Alice; Mellander, Per-Erik; hUallacháin, Daire Ó.

    2016-04-01

    Connectivity provides a valuable concept for understanding catchment-scale sediment dynamics. In intensive agricultural catchments, land management through tillage, high livestock densities and extensive land drainage practices significantly change hydromorphological behaviour and alter sediment supply and downstream delivery. Analysis of suspended sediment-discharge hysteresis has offered insights into sediment dynamics but typically on a limited selection of events. Greater availability of continuous high-resolution discharge and turbidity data and qualitative hysteresis metrics enables assessment of sediment dynamics during more events and over time. This paper assesses the utility of this approach to explore seasonal variations in connectivity. Data were collected from three small (c. 10 km2) intensive agricultural catchments in Ireland with contrasting morphologies, soil types, land use patterns and management practices, and are broadly defined as low-permeability supporting grassland, moderate-permeability supporting arable and high-permeability supporting arable. Suspended sediment concentration (using calibrated turbidity measurements) and discharge data were collected at 10-min resolution from each catchment outlet and precipitation data were collected from a weather station within each catchment. Event databases (67-90 events per catchment) collated information on sediment export metrics, hysteresis category (e.g., clockwise, anti-clockwise, no hysteresis), numeric hysteresis index, and potential hydro-meteorological controls on sediment transport including precipitation amount, duration, intensity, stream flow and antecedent soil moisture and rainfall. Statistical analysis of potential controls on sediment export was undertaken using Pearson's correlation coefficient on separate hysteresis categories in each catchment. Sediment hysteresis fluctuations through time were subsequently assessed using the hysteresis index. Results showed the numeric

  7. Spatio-temporal network analysis for studying climate patterns

    NASA Astrophysics Data System (ADS)

    Fountalis, Ilias; Bracco, Annalisa; Dovrolis, Constantine

    2014-02-01

    A fast, robust and scalable methodology to examine, quantify, and visualize climate patterns and their relationships is proposed. It is based on a set of notions, algorithms and metrics used in the study of graphs, referred to as complex network analysis. The goals of this approach are to explain known climate phenomena in terms of an underlying network structure and to uncover regional and global linkages in the climate system, while comparing general circulation models outputs with observations. The proposed method is based on a two-layer network representation. At the first layer, gridded climate data are used to identify "areas", i.e., geographical regions that are highly homogeneous in terms of the given climate variable. At the second layer, the identified areas are interconnected with links of varying strength, forming a global climate network. This paper describes the climate network inference and related network metrics, and compares network properties for different sea surface temperature reanalyses and precipitation data sets, and for a small sample of CMIP5 outputs.

  8. Temporal analysis of social networks using three-way DEDICOM.

    SciTech Connect

    Bader, Brett William; Harshman, Richard A. (University of Ontario, London, Ontario, Canada); Kolda, Tamara Gibson

    2006-06-01

    DEDICOM is an algebraic model for analyzing intrinsically asymmetric relationships, such as the balance of trade among nations or the flow of information among organizations or individuals. It provides information on latent components in the data that can be regarded as ''properties'' or ''aspects'' of the objects, and it finds a few patterns that can be combined to describe many relationships among these components. When we apply this technique to adjacency matrices arising from directed graphs, we obtain a smaller graph that gives an idealized description of its patterns. Three-way DEDICOM is a higher-order extension of the model that has certain uniqueness properties. It allows for a third mode of the data, such as time, and permits the analysis of semantic graphs. We present an improved algorithm for computing three-way DEDICOM on sparse data and demonstrate it by applying it to the adjacency tensor of a semantic graph with time-labeled edges. Our application uses the Enron email corpus, from which we construct a semantic graph corresponding to email exchanges among Enron personnel over a series of 44 months. Meaningful patterns are recovered in which the representation of asymmetries adds insight into the social networks at Enron.

  9. Analysis of spatial and temporal water pollution patterns in Lake Dianchi using multivariate statistical methods.

    PubMed

    Yang, Yong-Hui; Zhou, Feng; Guo, Huai-Cheng; Sheng, Hu; Liu, Hui; Dao, Xu; He, Cheng-Jie

    2010-11-01

    Various multivariate statistical methods including cluster analysis (CA), discriminant analysis (DA), factor analysis (FA), and principal component analysis (PCA) were used to explain the spatial and temporal patterns of surface water pollution in Lake Dianchi. The dataset, obtained during the period 2003-2007 from the Kunming Environmental Monitoring Center, consisted of 12 variables surveyed monthly at eight sites. The CA grouped the 12 months into two groups, August-September and the remainder, and divided the lake into two regions based on their different physicochemical properties and pollution levels. The DA showed the best results for data reduction and pattern recognition in both temporal and spatial analysis. It calculated four parameters (TEMP, pH, CODMn, and Chl-a) to 85.4% correct assignment in the temporal analysis and three parameters (BOD, NH₄+-N, and TN) to almost 71.7% correct assignment in spatial analysis of the two clusters. The FA/PCA applied to datasets of two special clusters of the lake calculated four factors for each region, capturing 72.5% and 62.5% of the total variance, respectively. Strong loadings included DO, BOD, TN, CODCr, CODMn, NH₄+-N, TP, and EC. In addition, box-whisker plots and GIS further facilitated and supported the multivariate analysis results. PMID:19936953

  10. Exploratory Analysis of Spatial-Temporal Patterns of Air Pollution in the City

    NASA Astrophysics Data System (ADS)

    Champendal, Alexandre; Kanevski, Mikhail; Huguenot, Pierre-Emmanuel; Golay, Jean

    2013-04-01

    Air pollution in the city is an important problem influencing environment, well-being of society, economy, management of urban zones, etc. The problem is extremely difficult due to a very complex distribution of the pollution sources, morphology of the city and dispersion processes leading to multivariate nature of the phenomena and high local spatial-temporal variability. The task of understanding, modelling and prediction of spatial-temporal patterns of air pollution in urban zones is an interesting and challenging topic having many research axes from science-based modelling to geostatistics and data mining. The present research mainly deals with a comprehensive exploratory analysis of spatial-temporal air pollution data using statistical, geostatistical and machine learning tools. This analysis helps to 1) understand and model spatial-temporal correlations using variography, 2) explore the temporal evolution of spatial correlation matrix; 3) analyse and visualize an interconnection between measurement stations using network science tools; 4) quantify the availability and predictability of structured patterns. The real data case study deals with spatial-temporal air pollution data of canton Geneva (2002-2011). Carbon dioxide (NO2) have caught our attention. It has effects on health: nitrogen dioxide can irritate the lungs, effects on plants; NO2 contributes to the phenomenon of acid rain. The negative effects of nitrogen dioxides on plants are reducing the growth, production and pesticide resistance. And finally the effects on materials: nitrogen dioxides increase the corrosion. Well-defined patterns of spatial-temporal correlations were detected. The analysis and visualization of spatial correlation matrix for 91 stations were carried out using the network science tools and high levels of clustering were revealed. Moving Window Correlation Matrix and Spatio-temporal variography methods were applied to define and explore the dynamic of our data. More than just

  11. On the use of radar-based quantitative precipitation estimates for precipitation frequency analysis

    NASA Astrophysics Data System (ADS)

    Eldardiry, Hisham; Habib, Emad; Zhang, Yu

    2015-12-01

    The high spatio-temporal resolutions of radar-based multi-sensor Quantitative Precipitation Estimates (QPEs) makes them a potential complement to the gauge records for engineering design purposes, such as precipitation frequency analysis. The current study investigates three fundamental issues that arise when radar-based QPE products are used in frequency analysis: (a) Effect of sample size due to the typically short records of radar products; (b) Effect of uncertainties present in radar-rainfall estimation algorithms; and (c) Effect of the frequency estimation approach adopted. The study uses a 13-year dataset of hourly, 4 × 4 km2 radar-based over a domain that covers Louisiana, USA. Data-based investigations, as well as synthetic simulations, are performed to quantify the uncertainties associated with the radar-based derived frequencies, and to gain insight into the relative contributions of short record lengths and those from conditional biases in the radar product. Three regional estimation procedures were tested and the results indicate the sensitivity of the radar frequency estimates to the selection of the estimation approach and the impact on the uncertainties of the derived extreme quantiles. The simulation experiments revealed that the relatively short radar records explained the majority of the uncertainty associated with the radar-based quantiles; however, they did not account for any tangible contribution to the systematic underestimation observed between radar- and gauge-based frequency estimates. This underestimation was mostly attributable to the conditional bias inherent in the radar product. Addressing such key outstanding problems in radar-rainfall products is necessary before they can be fully and reliably used for frequency analysis applications.

  12. Temporal Sequence of Hemispheric Network Activation during Semantic Processing: A Functional Network Connectivity Analysis

    ERIC Educational Resources Information Center

    Assaf, Michal; Jagannathan, Kanchana; Calhoun, Vince; Kraut, Michael; Hart, John, Jr.; Pearlson, Godfrey

    2009-01-01

    To explore the temporal sequence of, and the relationship between, the left and right hemispheres (LH and RH) during semantic memory (SM) processing we identified the neural networks involved in the performance of functional MRI semantic object retrieval task (SORT) using group independent component analysis (ICA) in 47 healthy individuals. SORT…

  13. Quantitative analysis of macular contraction in idiopathic epiretinal membrane

    PubMed Central

    2014-01-01

    Background We aimed to quantify the displacement of macular capillaries using infrared fundus photographs and image processing software (ImageJ) in patients with idiopathic epiretinal membrane (ERM) who have undergone vitrectomy and to analyze the correlation between vessel displacement and retinal thickness. Methods This prospective study included 16 patients who underwent vitrectomy for idiopathic ERM. Ophthalmic examination and optical coherence tomography (OCT) were performed before and 3 months after surgery. The length of radial vessel segment included in each area (VLA) and the length from the foveola to the vessel branching point (FBL) depending on the superior, inferior, nasal, and temporal areas of the macula were measured using infrared fundus images and image processing software (ImageJ). Preoperative and postoperative parameters were compared and correlations between VLA, FBL, macular thickness, and visual acuity were assessed. Results The VLA of superior, inferior, and temporal areas showed a significant postoperative reduction. VLA differences showed a positive correlation with differences in macular thickness, which corresponded to the superior, inferior, and temporal areas; however, no correlation was observed in the nasal area. The FBL of the superior and inferior areas was significantly increased postoperatively. A positive correlation was observed between FBL differences and macular thickness differences in the superior area. Postoperative change in VLA and FBL did not show a significant correlation with postoperative best corrected visual acuity (BCVA) and BCVA differences. Conclusions Infrared fundus photographs and image processing software can be useful for quantifying progressive changes in retinal surface distortion after surgical removal of ERM. Macular edema and vascular distortion showed significant improvement after surgery. Furthermore, a correlation was observed between topographic and tomographic changes. PMID:24735324

  14. Quantitative analysis of HSV gene expression during lytic infection

    PubMed Central

    Turner, Anne-Marie W.; Arbuckle, Jesse H.; Kristie, Thomas M.

    2014-01-01

    Herpes Simplex Virus (HSV) is a human pathogen that establishes latency and undergoes periodic reactivation, resulting in chronic recurrent lytic infection. HSV lytic infection is characterized by an organized cascade of three gene classes, however successful transcription and expression of the first, the immediate early class, is critical to the overall success of viral infection. This initial event of lytic infection is also highly dependent on host cell factors. This unit uses RNA interference and small molecule inhibitors to examine the role of host and viral proteins in HSV lytic infection. Methods detailing isolation of viral and host RNA and genomic DNA, followed by quantitative real-time PCR, allow characterization of impacts on viral transcription and replication respectively. Western blot can be used to confirm quantitative PCR results. This combination of protocols represents a starting point for researchers interested in virus-host interactions during HSV lytic infection. PMID:25367270

  15. Quantitative and qualitative HPLC analysis of thermogenic weight loss products.

    PubMed

    Schaneberg, B T; Khan, I A

    2004-11-01

    An HPLC qualitative and quantitative method of seven analytes (caffeine, ephedrine, forskolin, icariin, pseudoephedrine, synephrine, and yohimbine) in thermogenic weight loss preparations available on the market is described in this paper. After 45 min the seven analytes were separated and detected in the acetonitrile: water (80:20) extract. The method uses a Waters XTerra RP18 (5 microm particle size) column as the stationary phase, a gradient mobile phase of water (5.0 mM SDS) and acetonitrile, and a UV detection of 210 nm. The correlation coefficients for the calibration curves and the recovery rates ranged from 0.994 to 0.999 and from 97.45% to 101.05%, respectively. The qualitative and quantitative results are discussed. PMID:15587578

  16. Fluorescent microscopy approaches of quantitative soil microbial analysis

    NASA Astrophysics Data System (ADS)

    Ivanov, Konstantin; Polyanskaya, Lubov

    2015-04-01

    Classical fluorescent microscopy method was used during the last decades in various microbiological studies of terrestrial ecosystems. The method provides representative results and simple application which is allow to use it both as routine part of amplitudinous research and in small-scaled laboratories. Furthermore, depending on research targets a lot of modifications of fluorescent microscopy method were established. Combination and comparison of several approaches is an opportunity of quantitative estimation of microbial community in soil. The first analytical part of the study was dedicated to soil bacterial density estimation by fluorescent microscopy in dynamic of several 30-days experiments. The purpose of research was estimation of changes in soil bacterial community on the different soil horizons under aerobic and anaerobic conditions with adding nutrients in two experimental sets: cellulose and chitin. Was modified the nalidixic acid method for inhibition of DNA division of gram-negative bacteria, and the method provides the quantification of this bacterial group by fluorescent microscopy. Established approach allowed to estimate 3-4 times more cells of gram-negative bacteria in soil. The functions of actinomyces in soil polymer destruction are traditionally considered as dominant in comparison to gram-negative bacterial group. However, quantification of gram-negative bacteria in chernozem and peatland provides underestimation of classical notion for this bacterial group. Chitin introduction had no positive effect to gram-negative bacterial population density changes in chernozem but concurrently this nutrient provided the fast growing dynamics at the first 3 days of experiment both under aerobic and anaerobic conditions. This is confirming chitinolytic activity of gram-negative bacteria in soil organic matter decomposition. At the next part of research modified method for soil gram-negative bacteria quantification was compared to fluorescent in situ

  17. Comprehensive objective maps of macromolecular conformations by quantitative SAXS analysis

    PubMed Central

    Hura, Greg L.; Budworth, Helen; Dyer, Kevin N.; Rambo, Robert P.; Hammel, Michal

    2013-01-01

    Comprehensive perspectives of macromolecular conformations are required to connect structure to biology. Here we present a small angle X-ray scattering (SAXS) Structural Similarity Map (SSM) and Volatility of Ratio (VR) metric providing comprehensive, quantitative and objective (superposition-independent) perspectives on solution state conformations. We validate VR and SSM utility on human MutSβ, a key ABC ATPase and chemotherapeutic target, by revealing MutSβ DNA sculpting and identifying multiple conformational states for biological activity. PMID:23624664

  18. Spatial and Temporal Heterogeneity in High-Grade Serous Ovarian Cancer: A Phylogenetic Analysis

    PubMed Central

    Schwarz, Roland F.; Ng, Charlotte K. Y.; Cooke, Susanna L.; Newman, Scott; Temple, Jillian; Piskorz, Anna M.; Gale, Davina; Sayal, Karen; Murtaza, Muhammed; Baldwin, Peter J.; Rosenfeld, Nitzan; Earl, Helena M.; Sala, Evis; Jimenez-Linan, Mercedes; Parkinson, Christine A.; Markowetz, Florian; Brenton, James D.

    2015-01-01

    Background The major clinical challenge in the treatment of high-grade serous ovarian cancer (HGSOC) is the development of progressive resistance to platinum-based chemotherapy. The objective of this study was to determine whether intra-tumour genetic heterogeneity resulting from clonal evolution and the emergence of subclonal tumour populations in HGSOC was associated with the development of resistant disease. Methods and Findings Evolutionary inference and phylogenetic quantification of heterogeneity was performed using the MEDICC algorithm on high-resolution whole genome copy number profiles and selected genome-wide sequencing of 135 spatially and temporally separated samples from 14 patients with HGSOC who received platinum-based chemotherapy. Samples were obtained from the clinical CTCR-OV03/04 studies, and patients were enrolled between 20 July 2007 and 22 October 2009. Median follow-up of the cohort was 31 mo (interquartile range 22–46 mo), censored after 26 October 2013. Outcome measures were overall survival (OS) and progression-free survival (PFS). There were marked differences in the degree of clonal expansion (CE) between patients (median 0.74, interquartile range 0.66–1.15), and dichotimization by median CE showed worse survival in CE-high cases (PFS 12.7 versus 10.1 mo, p = 0.009; OS 42.6 versus 23.5 mo, p = 0.003). Bootstrap analysis with resampling showed that the 95% confidence intervals for the hazard ratios for PFS and OS in the CE-high group were greater than 1.0. These data support a relationship between heterogeneity and survival but do not precisely determine its effect size. Relapsed tissue was available for two patients in the CE-high group, and phylogenetic analysis showed that the prevalent clonal population at clinical recurrence arose from early divergence events. A subclonal population marked by a NF1 deletion showed a progressive increase in tumour allele fraction during chemotherapy. Conclusions This study demonstrates that

  19. Thalamotemporal impairment in temporal lobe epilepsy: A combined MRI analysis of structure, integrity, and connectivity

    PubMed Central

    Keller, Simon S; O'Muircheartaigh, Jonathan; Traynor, Catherine; Towgood, Karren; Barker, Gareth J; Richardson, Mark P

    2014-01-01

    Objective Thalamic abnormality in temporal lobe epilepsy (TLE) is well known from imaging studies, but evidence is lacking regarding connectivity profiles of the thalamus and their involvement in the disease process. We used a novel multisequence magnetic resonance imaging (MRI) protocol to elucidate the relationship between mesial temporal and thalamic pathology in TLE. Methods For 23 patients with TLE and 23 healthy controls, we performed T1-weighted (for analysis of tissue structure), diffusion tensor imaging (tissue connectivity), and T1 and T2 relaxation (tissue integrity) MRI across the whole brain. We used connectivity-based segmentation to determine connectivity patterns of thalamus to ipsilateral cortical regions (occipital, parietal, prefrontal, postcentral, precentral, and temporal). We subsequently determined volumes, mean tractography streamlines, and mean T1 and T2 relaxometry values for each thalamic segment preferentially connecting to a given cortical region, and of the hippocampus and entorhinal cortex. Results As expected, patients had significant volume reduction and increased T2 relaxation time in ipsilateral hippocampus and entorhinal cortex. There was bilateral volume loss, mean streamline reduction, and T2 increase of the thalamic segment preferentially connected to temporal lobe, corresponding to anterior, dorsomedial, and pulvinar thalamic regions, with no evidence of significant change in any other thalamic segments. Left and right thalamotemporal segment volume and T2 were significantly correlated with volume and T2 of ipsilateral (epileptogenic), but not contralateral (nonepileptogenic), mesial temporal structures. Significance These convergent and robust data indicate that thalamic abnormality in TLE is restricted to the area of the thalamus that is preferentially connected to the epileptogenic temporal lobe. The degree of thalamic pathology is related to the extent of mesial temporal lobe damage in TLE. PMID:24447099

  20. Temporal Variations of Water Productivity in Irrigated Corn: An Analysis of Factors Influencing Yield and Water Use across Central Nebraska

    PubMed Central

    Carr, Tony; Yang, Haishun; Ray, Chittaranjan

    2016-01-01

    Water Productivity (WP) of a crop defines the relationship between the economic or physical yield of the crop and its water use. With this concept it is possible to identify disproportionate water use or water-limited yield gaps and thereby support improvements in agricultural water management. However, too often important qualitative and quantitative environmental factors are not part of a WP analysis and therefore neglect the aspect of maintaining a sustainable agricultural system. In this study, we examine both the physical and economic WP in perspective with temporally changing environmental conditions. The physical WP analysis was performed by comparing simulated maximum attainable corn yields per unit of water using the crop model Hybrid-Maize with observed data from 2005 through 2013 from 108 farm plots in the Central Platte and the Tri Basin Natural Resource Districts of Nebraska. In order to expand the WP analysis on external factors influencing yields, a second model, Maize-N, was used to estimate optimal nitrogen (N)–fertilizer rate for specific fields in the study area. Finally, a vadose zone flow and transport model, HYDRUS-1D for simulating vertical nutrient transport in the soil, was used to estimate locations of nitrogen pulses in the soil profile. The comparison of simulated and observed data revealed that WP was not on an optimal level, mainly due to large amounts of irrigation used in the study area. The further analysis illustrated year-to-year variations of WP during the nine consecutive years, as well as the need to improve fertilizer management to favor WP and environmental quality. In addition, we addressed the negative influence of groundwater depletion on the economic WP through increasing pumping costs. In summary, this study demonstrated that involving temporal variations of WP as well as associated environmental and economic issues can represent a bigger picture of WP that can help to create incentives to sustainably improve

  1. Temporal Variations of Water Productivity in Irrigated Corn: An Analysis of Factors Influencing Yield and Water Use across Central Nebraska.

    PubMed

    Carr, Tony; Yang, Haishun; Ray, Chittaranjan

    2016-01-01

    Water Productivity (WP) of a crop defines the relationship between the economic or physical yield of the crop and its water use. With this concept it is possible to identify disproportionate water use or water-limited yield gaps and thereby support improvements in agricultural water management. However, too often important qualitative and quantitative environmental factors are not part of a WP analysis and therefore neglect the aspect of maintaining a sustainable agricultural system. In this study, we examine both the physical and economic WP in perspective with temporally changing environmental conditions. The physical WP analysis was performed by comparing simulated maximum attainable corn yields per unit of water using the crop model Hybrid-Maize with observed data from 2005 through 2013 from 108 farm plots in the Central Platte and the Tri Basin Natural Resource Districts of Nebraska. In order to expand the WP analysis on external factors influencing yields, a second model, Maize-N, was used to estimate optimal nitrogen (N)-fertilizer rate for specific fields in the study area. Finally, a vadose zone flow and transport model, HYDRUS-1D for simulating vertical nutrient transport in the soil, was used to estimate locations of nitrogen pulses in the soil profile. The comparison of simulated and observed data revealed that WP was not on an optimal level, mainly due to large amounts of irrigation used in the study area. The further analysis illustrated year-to-year variations of WP during the nine consecutive years, as well as the need to improve fertilizer management to favor WP and environmental quality. In addition, we addressed the negative influence of groundwater depletion on the economic WP through increasing pumping costs. In summary, this study demonstrated that involving temporal variations of WP as well as associated environmental and economic issues can represent a bigger picture of WP that can help to create incentives to sustainably improve

  2. Quantitative and dynamic analysis of PTEN phosphorylation by NMR.

    PubMed

    Cordier, Florence; Chaffotte, Alain; Wolff, Nicolas

    2015-05-01

    The dual lipid and protein phosphatase PTEN is a tumor suppressor controlling key biological processes, such as cell growth, proliferation and neuro-survival. Its activity and intracellular trafficking is finely regulated notably by multi-site phosphorylation of its C-terminal tail. The reversible and highly dynamic character of these regulatory events confers a temporal dimension to the cell for triggering crucial decisions. In this review, we describe how a recently developed time-resolved NMR spectroscopy approach unveils the dynamic establishment of the phosphorylation events of PTEN C-terminal tail controlled by CK2 and GSK3β kinases. Two cascades of reactions have been identified, in vitro and in extracts of human neuroblastoma cells. They are triggered independently on two nearby clusters of sites (S380-S385 and S361-S370) and occur on different timescales. In each cascade, the reactions follow an ordered model with a distributive kinetic mechanism. The vision of these cascades as two delay timers activating distinct or time-delayed regulatory responses gives a temporal dimension on PTEN regulation and is discussed in relation to the known functional roles of each cluster. PMID:25449899

  3. Fractal dimension-bound spatio-temporal analysis of digital mammograms

    NASA Astrophysics Data System (ADS)

    Shanmugavadivu, P.; Sivakumar, V.; Sudhir, Rashmi

    2016-02-01

    A new Fractal Dimension-based diagnosis technique for the change detection and time-series analysis of masses in the temporal digital mammogram is presented in this paper. As the digital mammograms are confirmed as a reliable source for the prognosis of breast cancer, the demand for the development of precise computer aided detection techniques is constantly on the increase. This formed the basis for the development of this method using Fractal geometry, which is an efficient mathematical approach that deals with self-similar and irregular geometric objects called fractals. This work comprises of the detection of spatial masses using Fractal Hurst bound enhancement and segmentation of those temporal masses using Fractal Thresholding. The consultant radiologist's assessment of mass lesions forms the baseline for comparison and validation of the detected masses. Further, this research work performs temporal analysis of mass lesions, detected from the mammograms of the current and the respective prior view using the principle of Fractal Dimension. The precision of Fractal-dimension based temporal texture analysis of malignant masses of digital mammograms subsequently attributes to their characterization.

  4. Design and performance analysis of high-order optical temporal differentiator with twin-core fiber

    NASA Astrophysics Data System (ADS)

    You, Haidong; Ning, Tigang; Li, Jing; Jian, Wei; Wen, Xiaodong; Pei, Li

    2013-08-01

    A simple and general approach for implementing all-fiber high-order optical temporal differentiator based on twin-core fiber (TCF) is presented and demonstrated. Specifically, the core 2 (or core 1) of the TCF should be cut in N sections with the same length for achieving N'th-order optical temporal differentiator, which can be considered to consist of N cascaded first-order optical temporal differentiators based on TCF. Our simulations show that the proposed approach can provide optical operation bandwidths in the several THz regime, which is capable of accurately processing time features as short as subpicoseconds. Performance analysis results show a good accuracy calculating the high-order time differentiation of the optical signal launched at core 2 (or core 1).

  5. An Adaptive Organization Method of Geovideo Data for Spatio-Temporal Association Analysis

    NASA Astrophysics Data System (ADS)

    Wu, C.; Zhu, Q.; Zhang, Y. T.; Du, Z. Q.; Zhou, Y.; Xie, X.; He, F.

    2015-07-01

    Public security incidents have been increasingly challenging to address with their new features, including large-scale mobility, multi-stage dynamic evolution, spatio-temporal concurrency and uncertainty in the complex urban environment, which require spatio-temporal association analysis among multiple regional video data for global cognition. However, the existing video data organizational methods that view video as a property of the spatial object or position in space dissever the spatio-temporal relationship of scattered video shots captured from multiple video channels, limit the query functions on interactive retrieval between a camera and its video clips and hinder the comprehensive management of event-related scattered video shots. GeoVideo, which maps video frames onto a geographic space, is a new approach to represent the geographic world, promote security monitoring in a spatial perspective and provide a highly feasible solution to this problem. This paper analyzes the large-scale personnel mobility in public safety events and proposes a multi-level, event-related organization method with massive GeoVideo data by spatio-temporal trajectory. This paper designs a unified object identify(ID) structure to implicitly store the spatio-temporal relationship of scattered video clips and support the distributed storage management of massive cases. Finally, the validity and feasibility of this method are demonstrated through suspect tracking experiments.

  6. An Inexpensive Electrodeposition Device and Its Use in a Quantitative Analysis Laboratory Exercise

    ERIC Educational Resources Information Center

    Parker, Richard H.

    2011-01-01

    An experimental procedure, using an apparatus that is easy to construct, was developed to incorporate a quantitative electrogravimetric determination of the solution nickel content into an undergraduate or advanced high school quantitative analysis laboratory. This procedure produces results comparable to the procedure used for the gravimetric…

  7. Spatial and temporal statistical analysis of a ground-water level network, Broward County, Florida

    USGS Publications Warehouse

    Swain, E.D.; Sonenshein, R.S.

    1994-01-01

    The U.S. Geological Survey has developed a method to evaluate the spatial and temporal statistics of a continuous ground-water level recorder network in Broward County, Florida. Because the Broward County network is sparse for most spatial statistics, a technique has been developed to define polygons for each well that represent the area monitored by the well within specified criteria. The boundaries of these "confidence polygons" are defined by the endpoints of radial lines oriented toward the other wells. The lengths of these lines are determined as the statistically estimated distances to the points at which ground-water levels can be predicted within specirfied criteria. The confidence polygons indicate: (1) the areal coverage of the network, (2) locations where data are unavailable, and (3) areas of redundant data collection. Comparison with data from a noncontinuous recorder well indicates that the confidence polygons are a good represen- tation of areal coverages. The temporal analysis utilizes statistical techniques similar to those used in the spatial method, defining variations in time rather than in space. Consequently, instead of defining radial distances to points, time intervals are defined over which water-level values can be predicted within a specified confidence. These "temporal confidence intervals" correspond to maximum allowable periods between field measure- ments. To combine all results from the analyses, a single coefficient reflecting the spatial and temporal results has been developed. The coefficient is referred to as the Spatial and Temporal Adequacy and Redundancy Evaluation (STARE) and is determined by three factors: the size of the confidence polygon, the number of times the well is part of a redundant pair, and the temporal confidence interval. This coefficient and the individual results of each analysis are used in evaluating the present network and determining future management decisions.

  8. Quantitative analysis of single amino acid variant peptides associated with pancreatic cancer in serum by an isobaric labeling quantitative method.

    PubMed

    Nie, Song; Yin, Haidi; Tan, Zhijing; Anderson, Michelle A; Ruffin, Mack T; Simeone, Diane M; Lubman, David M

    2014-12-01

    Single amino acid variations are highly associated with many human diseases. The direct detection of peptides containing single amino acid variants (SAAVs) derived from nonsynonymous single nucleotide polymorphisms (SNPs) in serum can provide unique opportunities for SAAV associated biomarker discovery. In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls. The largest number of SAAV peptides to date in serum including 96 unique variant peptides were quantified in this quantitative analysis, of which five variant peptides showed a statistically significant difference between pancreatic cancer and other controls (p-value < 0.05). Significant differences in the variant peptide SDNCEDTPEAGYFAVAVVK from serotransferrin were detected between pancreatic cancer and controls, which was further validated by selected reaction monitoring (SRM) analysis. The novel biomarker panel obtained by combining α-1-antichymotrypsin (AACT), Thrombospondin-1 (THBS1) and this variant peptide showed an excellent diagnostic performance in discriminating pancreatic cancer from healthy controls (AUC = 0.98) and chronic pancreatitis (AUC = 0.90). These results suggest that large-scale analysis of SAAV peptides in serum may provide a new direction for biomarker discovery research. PMID:25393578

  9. Quantitative analysis of a wind energy conversion model

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    A rotor of 12 cm diameter is attached to a precision electric motor, used as a generator, to make a model wind turbine. Output power of the generator is measured in a wind tunnel with up to 15 m s-1 air velocity. The maximum power is 3.4 W, the power conversion factor from kinetic to electric energy is cp = 0.15. The v3 power law is confirmed. The model illustrates several technically important features of industrial wind turbines quantitatively.

  10. Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.

    PubMed

    Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O

    2013-06-01

    Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. PMID:23523366

  11. Mining biomedical time series by combining structural analysis and temporal abstractions.

    PubMed Central

    Bellazzi, R.; Magni, P.; Larizza, C.; De Nicolao, G.; Riva, A.; Stefanelli, M.

    1998-01-01

    This paper describes the combination of Structural Time Series analysis and Temporal Abstractions for the interpretation of data coming from home monitoring of diabetic patients. Blood Glucose data are analyzed by a novel Bayesian technique for time series analysis. The results obtained are post-processed using Temporal Abstractions in order to extract knowledge that can be exploited "at the point of use" from physicians. The proposed data analysis procedure can be viewed as a Knowledge Discovery in Data Base process that is applied to time-varying data. The work here described is part of a Web-based telemedicine system for the management of Insulin Dependent Diabetes Mellitus patients, called T-IDDM. PMID:9929202

  12. Qualitative and quantitative analysis of volatile constituents from latrines.

    PubMed

    Lin, Jianming; Aoll, Jackline; Niclass, Yvan; Velazco, Maria Inés; Wünsche, Laurent; Pika, Jana; Starkenmann, Christian

    2013-07-16

    More than 2.5 billion people defecate in the open. The increased commitment of private and public organizations to improving this situation is driving the research and development of new technologies for toilets and latrines. Although key technical aspects are considered by researchers when designing new technologies for developing countries, the basic aspect of offending malodors from human waste is often neglected. With the objective of contributing to technical solutions that are acceptable to global consumers, we investigated the chemical composition of latrine malodors sampled in Africa and India. Field latrines in four countries were evaluated olfactively and the odors qualitatively and quantitatively characterized with three analytical techniques. Sulfur compounds including H2S, methyl mercaptan, and dimethyl-mono-(di;tri) sulfide are important in sewage-like odors of pit latrines under anaerobic conditions. Under aerobic conditions, in Nairobi for example, paracresol and indole reached concentrations of 89 and 65 μg/g, respectively, which, along with short chain fatty acids such as butyric acid (13 mg/g) explained the strong rancid, manure and farm yard odor. This work represents the first qualitative and quantitative study of volatile compounds sampled from seven pit latrines in a variety of geographic, technical, and economic contexts in addition to three single stools from India and a pit latrine model system. PMID:23829328

  13. Quantitative analysis of radiation-induced changes in sperm morphology.

    PubMed

    Young, I T; Gledhill, B L; Lake, S; Wyrobek, A J

    1982-09-01

    When developing spermatogenic cells are exposed to radiation, chemical carcinogens or mutagens, the transformation in the morphology of the mature sperm can be used to determine the severity of the exposure. In this study five groups of mice with three mice per group received testicular doses of X irradiation at dosage levels ranging from 0 rad to 120 rad. A random sample of 100 mature sperm per mouse was analyzed five weeks later for the quantitative morphologic transformation as a function of dosage level. The cells were stained with gallocyanin chrome alum (GCA) so that only the DNA in the sperm head was visible. The ACUity quantitative microscopy system at Lawrence Livermore National Laboratory was used to scan the sperm at a sampling density of 16 points per linear micrometer and with 256 brightness levels per point. The contour of each cell was extracted using conventional thresholding techniques on the high-contrast images. For each contour a variety of shape features was then computed to characterize the morphology of that cell. Using the control group and the distribution of their shape features to establish the variability of a normal sperm population, the 95% limits on normal morphology were established. Using only four shape features, a doubling dose of approximately 39 rad was determined. That is, at 39 rad exposure the percentage of abnormal cells was twice that occurring in the control population. This compared to a doubling dose of approximately 70 rad obtained from a concurrent visual procedure. PMID:6184000

  14. Quantitative phenotypic analysis of multistress response in Zygosaccharomyces rouxii complex.

    PubMed

    Solieri, Lisa; Dakal, Tikam C; Bicciato, Silvio

    2014-06-01

    Zygosaccharomyces rouxii complex comprises three yeasts clusters sourced from sugar- and salt-rich environments: haploid Zygosaccharomyces rouxii, diploid Zygosaccharomyces sapae and allodiploid/aneuploid strains of uncertain taxonomic affiliations. These yeasts have been characterized with respect to gene copy number variation, karyotype variability and change in ploidy, but functional diversity in stress responses has not been explored yet. Here, we quantitatively analysed the stress response variation in seven strains of the Z. rouxii complex by modelling growth variables via model and model-free fitting methods. Based on the spline fit as most reliable modelling method, we resolved different interstrain responses to 15 environmental perturbations. Compared with Z. rouxii CBS 732(T) and Z. sapae strains ABT301(T) and ABT601, allodiploid strain ATCC 42981 and aneuploid strains CBS 4837 and CBS 4838 displayed higher multistress resistance and better performance in glycerol respiration even in the presence of copper. μ-based logarithmic phenotypic index highlighted that ABT601 is a slow-growing strain insensitive to stress, whereas ABT301(T) grows fast on rich medium and is sensitive to suboptimal conditions. Overall, the differences in stress response could imply different adaptation mechanisms to sugar- and salt-rich niches. The obtained phenotypic profiling contributes to provide quantitative insights for elucidating the adaptive mechanisms to stress in halo- and osmo-tolerant Zygosaccharomyces yeasts. PMID:24533625

  15. Quantitative analysis of laminin 5 gene expression in human keratinocytes.

    PubMed

    Akutsu, Nobuko; Amano, Satoshi; Nishiyama, Toshio

    2005-05-01

    To examine the expression of laminin 5 genes (LAMA3, LAMB3, and LAMC2) encoding the three polypeptide chains alpha3, beta3, and gamma2, respectively, in human keratinocytes, we developed novel quantitative polymerase chain reaction (PCR) methods utilizing Thermus aquaticus DNA polymerase, specific primers, and fluorescein-labeled probes with the ABI PRISM 7700 sequence detector system. Gene expression levels of LAMA3, LAMB3, and LAMC2 and glyceraldehyde-3-phosphate dehydrogenase were quantitated reproducibly and sensitively in the range from 1 x 10(2) to 1 x 10(8) gene copies. Basal gene expression level of LAMB3 was about one-tenth of that of LAMA3 or LAMC2 in human keratinocytes, although there was no clear difference among immunoprecipitated protein levels of alpha3, beta3, and gamma2 synthesized in radio-labeled keratinocytes. Human serum augmented gene expressions of LAMA3, LAMB3, and LAMC2 in human keratinocytes to almost the same extent, and this was associated with an increase of the laminin 5 protein content measured by a specific sandwich enzyme-linked immunosorbent assay. These results demonstrate that the absolute mRNA levels generated from the laminin 5 genes do not determine the translated protein levels of the laminin 5 chains in keratinocytes, and indicate that the expression of the laminin 5 genes may be controlled by common regulation mechanisms. PMID:15854126

  16. Quantitative Analysis of the Enhanced Permeation and Retention (EPR) Effect

    PubMed Central

    Ulmschneider, Martin B.; Searson, Peter C.

    2015-01-01

    Tumor vasculature is characterized by a variety of abnormalities including irregular architecture, poor lymphatic drainage, and the upregulation of factors that increase the paracellular permeability. The increased permeability is important in mediating the uptake of an intravenously administered drug in a solid tumor and is known as the enhanced permeation and retention (EPR) effect. Studies in animal models have demonstrated a cut-off size of 500 nm - 1 µm for molecules or nanoparticles to extravasate into a tumor, however, surprisingly little is known about the kinetics of the EPR effect. Here we present a pharmacokinetic model to quantitatively assess the influence of the EPR effect on the uptake of a drug into a solid tumor. We use pharmacokinetic data for Doxil and doxorubicin from human clinical trials to illustrate how the EPR effect influences tumor uptake. This model provides a quantitative framework to guide preclinical trials of new chemotherapies and ultimately to develop design rules that can increase targeting efficiency and decrease unwanted side effects in normal tissue. PMID:25938565

  17. Quantitative analysis of Babesia ovis infection in sheep and ticks.

    PubMed

    Erster, Oran; Roth, Asael; Wollkomirsky, Ricardo; Leibovich, Benjamin; Savitzky, Igor; Zamir, Shmuel; Molad, Thea; Shkap, Varda

    2016-05-15

    A quantitative PCR, based on the gene encoding Babesia ovis Surface Protein D (BoSPD) was developed and applied to investigate the presence of Babesia ovis (B. ovis) in its principal vector, the tick Rhipicephalus bursa (R. bursa), and in the ovine host. Quantification of B. ovis in experimentally-infected lambs showed a sharp increase in parasitemia 10-11days in blood-inoculated and adult tick-infested lambs, and 24days in a larvae-infested lamb. A gradual decrease of parasitemia was observed in the following months, with parasites detectable 6-12 months post-infection. Examination of the parasite load in adult R. bursa during the post-molting period using the quantitative PCR assay revealed a low parasite load during days 2-7 post-molting, followed by a sharp increase, until day 11, which corresponded to the completion of the pre-feeding period. The assay was then used to detect B. ovis in naturally-infected sheep and ticks. Examination of samples from 8 sheep and 2 goats from infected flocks detected B. ovis in both goats and in 7 out of the 8 sheep. Additionally, B. ovis was detected in 9 tick pools (5 ticks in each pool) and two individual ticks removed from sheep in infected flocks. PMID:27084469

  18. Quantitative analysis of thermal spray deposits using stereology

    SciTech Connect

    Leigh, S.H.; Sampath, S.; Herman, H.; Berndt, C.C.; Montavon, G.; Coddet, C.

    1995-12-31

    Stereology deals with protocols for describing a 3-D space, when only 2-D sections through solid bodies are available. This paper describes a stereological characterization of the microstructure of a thermal spray deposit. The aim of this work is to present results on the stereological characterization of a thermal spray deposit, using two approaches known as DeHoff`s and Cruz-Orive`s protocols. The individual splats are assumed to have an oblate spheroidal shape. The splat size distribution and elongation ratio distribution of splats are calculated using quantitative information from 2-D plane sections. The stereological methods are implemented to investigate the microstructure of a water stabilized plasma spray-formed Al{sub 2}O{sub 3}-13wt.%TiO{sub 2}. Results are obtained with both protocols. The splat sizes range from 0 to 60 {micro}m and shape factors from 0.4 to 1.0. The splats within the deposit seem to be much smaller and thicker (i.e., lower spreading) than those of the first layer deposited onto the substrate. The approach described in this work provides helpful quantitative information on the 3-D microstructure of thermal spray deposit.

  19. Central mechanisms of temporal analysis in the knollenorgan pathway of mormyrid electric fish

    PubMed

    Xu-Friedman; Hopkins

    1999-05-01

    Mormyrid electric fish communicate using pulse-type electric organ discharges (EODs). The fine temporal structure of the waveforms of EODs varies widely throughout the 200 or more species of mormyrids. These signals carry information about the species, the sex and even the individual identity of the signaller. Behavioral experiments have shown that some species of fish are capable of using this information. Of the four known types of electroreceptors in mormyrid fish, the knollenorgan electroreceptor is the one most likely to be involved in the detection of conspecific EOD signals. Here, we review some recent advances in understanding how the central knollenorgan pathway might be analyzing the temporal structure of the EOD waveform. Fine temporal analysis appears to take place in the nucleus exterolateralis pars anterior (ELa), where tightly phase-locked inputs from the hindbrain drive a direct, excitatory input through a long axonal delay line and also drive an indirect, inhibitory input with negligible delay through the ELa large cell. These two inputs converge on ELa small cells, where they are hypothesized to interact in a 'delay-line/blanking' model. This initial temporal analysis is further refined in the nucleus exterolateralis pars posterior, where units tuned to ranges of pulse durations have been identified physiologically. PMID:10210671

  20. Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain

    PubMed Central

    Chou, Shen-Ju; Wang, Chindi; Sintupisut, Nardnisa; Niou, Zhen-Xian; Lin, Chih-Hsu; Li, Ker-Chau; Yeang, Chen-Hsiang

    2016-01-01

    Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development. PMID:26786896

  1. Spatio-Temporal Drought Analysis on Example of the Central European Gridded Dataset

    NASA Astrophysics Data System (ADS)

    Stepanek, P.; Trnka, M.; Zahradníček, P.; Semerádová, D.; Hlavinka, P.

    2014-12-01

    Drought may have severe impacts on many human activities. Understanding its spatio-temporal variations is thus very important in many research fields. On example of the Central Europe dataset we analyzed and compared some products based on drought analyses, which may help to answer important questions for impact studies: 1) evaluation of the added value coming from inclusion of spatial aspect (not only temporal one) in the drought analysis; 2) comparison of drought indices calculated from various number of available input meteorological elements (backwards into history less and less meteorological elements are available); 3) linking together meteorological drought with agriculture one. Basis for the study was production of gridded dataset of basic meteorological elements (daily minimum and maximum temperature, precipitation, sunshine duration, relative humidity and wind speed). From the station location time series in the period 1961-2013, gridded dataset was created applying geostatistical methods using both spatial and temporal aspects of the data (spacetime package under R). From such gridded dataset, SPEI (standardized precipitation evaporation index) was calculated using various approaches: Thornthwaite (potential evapotranspiration), Hargreaves and Penman-Monteith (reference evapotranspiration). The outputs were gridded datasets of the SPEIs that were then analyzed for the Central Europe both from temporal (based on station data) and spatial aspects. In order to estimate how this meteorological drought analysis may contribute to drought impact analysis (in our case we chose agriculture), we compared the results with the analysis coming from the agrometeorological drought monitoring system (based on SoilClim - dynamical model of soil water content) which is now used for drought monitoring and analysis in the Central Europe. Such comparison is important either for drought analysis in the past (when soil observations are not available) or also for future climate

  2. Annotating spatio-temporal datasets for meaningful analysis in the Web

    NASA Astrophysics Data System (ADS)

    Stasch, Christoph; Pebesma, Edzer; Scheider, Simon

    2014-05-01

    More and more environmental datasets that vary in space and time are available in the Web. This comes along with an advantage of using the data for other purposes than originally foreseen, but also with the danger that users may apply inappropriate analysis procedures due to lack of important assumptions made during the data collection process. In order to guide towards a meaningful (statistical) analysis of spatio-temporal datasets available in the Web, we have developed a Higher-Order-Logic formalism that captures some relevant assumptions in our previous work [1]. It allows to proof on meaningful spatial prediction and aggregation in a semi-automated fashion. In this poster presentation, we will present a concept for annotating spatio-temporal datasets available in the Web with concepts defined in our formalism. Therefore, we have defined a subset of the formalism as a Web Ontology Language (OWL) pattern. It allows capturing the distinction between the different spatio-temporal variable types, i.e. point patterns, fields, lattices and trajectories, that in turn determine whether a particular dataset can be interpolated or aggregated in a meaningful way using a certain procedure. The actual annotations that link spatio-temporal datasets with the concepts in the ontology pattern are provided as Linked Data. In order to allow data producers to add the annotations to their datasets, we have implemented a Web portal that uses a triple store at the backend to store the annotations and to make them available in the Linked Data cloud. Furthermore, we have implemented functions in the statistical environment R to retrieve the RDF annotations and, based on these annotations, to support a stronger typing of spatio-temporal datatypes guiding towards a meaningful analysis in R. [1] Stasch, C., Scheider, S., Pebesma, E., Kuhn, W. (2014): "Meaningful spatial prediction and aggregation", Environmental Modelling & Software, 51, 149-165.

  3. Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase growth during electrondonor depletion

    SciTech Connect

    Clark, M.E.; He, Q.; He, Z.; Huang, K.H.; Alm, E.J.; Wan, X.-F.; Hazen, T.C.; Arkin, A.P.; Wall, J.D.; Zhou, J.-Z.; Fields, M.W.

    2006-08-01

    Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe{sup 2+} acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute

  4. Quantitative Estimates of Temporal Mixing across a 4th-order Depositional Sequence: Variation in Time-averaging along the Holocene Marine Succession of the Po Plain, Italy

    NASA Astrophysics Data System (ADS)

    Scarponi, D.; Kaufman, D.; Bright, J.; Kowalewski, M.

    2009-04-01

    Single fossiliferous beds contain biotic remnants that commonly vary in age over a time span of hundreds to thousands of years. Multiple recent studies suggest that such temporal mixing is a widespread phenomenon in marine depositional systems. This research focuses on quantitative estimates of temporal mixing obtained by direct dating of individual corbulid bivalve shells (Lentidium mediterraneum and Corbula gibba) from Po plain marine units of the Holocene 4th-order depositional sequence, including Transgressive Systems Tract [TST] and Highstand Systems Tract [HST]. These units displays a distinctive succession of facies consisting of brackish to marginal marine retrogradational deposits, (early TST), overlain by fully marine fine to coarse gray sands (late TST), and capped with progradational deltaic clays and sands (HST). More than 300 corbulid specimens, representing 19 shell-rich horizons evenly distributed along the depositional sequence and sampled from 9 cores, have been dated by means of aspartic acid racemization calibrated using 23 AMS-radiocarbon dates (14 dates for Lentidium mediterraneum and 9 dates for Corbula gibba, respectively). The results indicate that the scale of time-averaging is comparable when similar depositional environments from the same systems tract are compared across cores. However, time averaging is notably different when similar depositional environments from TST and HST segments of the sequence are compared. Specifically, late HST horizons (n=8) display relatively low levels of time-averaging: the mean within-horizon range of shell ages is 537 years and standard deviation averages 165 years. In contrast, late TST horizons (n=7) are dramatically more time-averaged: mean range of 5104 years and mean standard deviations of 1420 years. Thus, late TST horizons experience a 1 order of magnitude higher time-averaging than environmentally comparable late HST horizons. In conclusion the HST and TST systems tracts of the Po Plain display

  5. Detection of dominant modelled nitrate processes with a high temporally resolved parameter sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Haas, Marcelo; Guse, Björn; Pfannerstill, Matthias; Fohrer, Nicola

    2015-04-01

    The river systems in the catchment are impacted by nutrient inputs from different sources of the landscape. The input of nitrate from agricultural areas into the river systems is related to numerous processes which occur simultaneously and influence each other permanently. These complex nitrate processes are represented in eco-hydrological models. To obtain reliable future predictions of nitrate concentrations in rivers, the nitrogen cycle needs to be reproduced accurately in these models. For complex research questions dealing with nitrate impacts, it is thus essential to better understand the nitrate process dynamics in models and to reduce the uncertainties in water quality predictions. This study aims to improve the understanding of nitrate process dynamics by using a temporal parameter sensitivity analysis, which is applied on an eco-hydrological model. With this method, the dominant model parameters are detected for each day. Thus, by deriving temporal variations in dominant model parameters, the nitrate process dynamic is investigated for phases with different conditions for nitrate transport and transformations. The results show that the sensitivity of different nitrate parameters varies temporally. These temporal dynamics in dominant parameters are explained by temporal variations in nitrate transport and plant uptake processes. An extended view on the dynamics of the temporal parameter sensitivity is obtained by analysing different modelled runoff components and nitrate pathways. Thereby, the interpretation of seasonal variations in dominant nitrate pathways is assisted and a better understanding of the role of nitrate in the environment is achieved. We conclude that this method improves the reliability of modelled nitrate processes. In this way, a better basis for recent and future scenarios of nitrate loads management is provided.

  6. Bridging the gaps for global sustainable development: a quantitative analysis.

    PubMed

    Udo, Victor E; Jansson, Peter Mark

    2009-09-01

    Global human progress occurs in a complex web of interactions between society, technology and the environment as driven by governance and infrastructure management capacity among nations. In our globalizing world, this complex web of interactions over the last 200 years has resulted in the chronic widening of economic and political gaps between the haves and the have-nots with consequential global cultural and ecosystem challenges. At the bottom of these challenges is the issue of resource limitations on our finite planet with increasing population. The problem is further compounded by pleasure-driven and poverty-driven ecological depletion and pollution by the haves and the have-nots respectively. These challenges are explored in this paper as global sustainable development (SD) quantitatively; in order to assess the gaps that need to be bridged. Although there has been significant rhetoric on SD with very many qualitative definitions offered, very few quantitative definitions of SD exist. The few that do exist tend to measure SD in terms of social, energy, economic and environmental dimensions. In our research, we used several human survival, development, and progress variables to create an aggregate SD parameter that describes the capacity of nations in three dimensions: social sustainability, environmental sustainability and technological sustainability. Using our proposed quantitative definition of SD and data from relatively reputable secondary sources, 132 nations were ranked and compared. Our comparisons indicate a global hierarchy of needs among nations similar to Maslow's at the individual level. As in Maslow's hierarchy of needs, nations that are struggling to survive are less concerned with environmental sustainability than advanced and stable nations. Nations such as the United States, Canada, Finland, Norway and others have higher SD capacity, and thus, are higher on their hierarchy of needs than nations such as Nigeria, Vietnam, Mexico and other

  7. SPATIAL AND TEMPORAL ANALYSIS OF NON-URBAN OZONE CONCENTRATIONS OVER THE EASTERN UNITED STATES USING ROTATED PRINCIPAL COMPONENT ANALYSIS

    EPA Science Inventory

    The spatial and temporal variability of 03 concentrations over the eastern United States during the period of 1985 through 1990 was examined through the use of a multivariate statistical technique called Principal Component Analysis. he original data set, which contained 77 corre...

  8. [Quantitative analysis of alloy steel based on laser induced breakdown spectroscopy with partial least squares method].

    PubMed

    Cong, Zhi-Bo; Sun, Lan-Xiang; Xin, Yong; Li, Yang; Qi, Li-Feng; Yang, Zhi-Jia

    2014-02-01

    In the present paper both the partial least squares (PLS) method and the calibration curve (CC) method are used to quantitatively analyze the laser induced breakdown spectroscopy data obtained from the standard alloy steel samples. Both the major and trace elements were quantitatively analyzed. By comparing the results of two different calibration methods some useful results were obtained: for major elements, the PLS method is better than the CC method in quantitative analysis; more importantly, for the trace elements, the CC method can not give the quantitative results due to the extremely weak characteristic spectral lines, but the PLS method still has a good ability of quantitative analysis. And the regression coefficient of PLS method is compared with the original spectral data with background interference to explain the advantage of the PLS method in the LIBS quantitative analysis. Results proved that the PLS method used in laser induced breakdown spectroscopy is suitable for quantitative analysis of trace elements such as C in the metallurgical industry. PMID:24822436

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  10. Quantitative analysis of CT scans of ceramic candle filters

    SciTech Connect

    Ferer, M.V.; Smith, D.H.

    1996-12-31

    Candle filters are being developed to remove coal ash and other fine particles (<15{mu}m) from hot (ca. 1000 K) gas streams. In the present work, a color scanner was used to digitize hard-copy CT X-ray images of cylindrical SiC filters, and linear regressions converted the scanned (color) data to a filter density for each pixel. These data, with the aid of the density of SiC, gave a filter porosity for each pixel. Radial averages, density-density correlation functions, and other statistical analyses were performed on the density data. The CT images also detected the presence and depth of cracks that developed during usage of the filters. The quantitative data promise to be a very useful addition to the color images.

  11. Fast multidimensional ensemble empirical mode decomposition for the analysis of big spatio-temporal datasets.

    PubMed

    Wu, Zhaohua; Feng, Jiaxin; Qiao, Fangli; Tan, Zhe-Min

    2016-04-13

    In this big data era, it is more urgent than ever to solve two major issues: (i) fast data transmission methods that can facilitate access to data from non-local sources and (ii) fast and efficient data analysis methods that can reveal the key information from the available data for particular purposes. Although approaches in different fields to address these two questions may differ significantly, the common part must involve data compression techniques and a fast algorithm. This paper introduces the recently developed adaptive and spatio-temporally local analysis method, namely the fast multidimensional ensemble empirical mode decomposition (MEEMD), for the analysis of a large spatio-temporal dataset. The original MEEMD uses ensemble empirical mode decomposition to decompose time series at each spatial grid and then pieces together the temporal-spatial evolution of climate variability and change on naturally separated timescales, which is computationally expensive. By taking advantage of the high efficiency of the expression using principal component analysis/empirical orthogonal function analysis for spatio-temporally coherent data, we design a lossy compression method for climate data to facilitate its non-local transmission. We also explain the basic principles behind the fast MEEMD through decomposing principal components instead of original grid-wise time series to speed up computation of MEEMD. Using a typical climate dataset as an example, we demonstrate that our newly designed methods can (i) compress data with a compression rate of one to two orders; and (ii) speed-up the MEEMD algorithm by one to two orders. PMID:26953173

  12. Spatial and Temporal Dust Source Variability in Northern China Identified Using Advanced Remote Sensing Analysis

    NASA Technical Reports Server (NTRS)

    Taramelli, A.; Pasqui, M.; Barbour, J.; Kirschbaum, D.; Bottai, L.; Busillo, C.; Calastrini, F.; Guarnieri, F.; Small, C.

    2013-01-01

    The aim of this research is to provide a detailed characterization of spatial patterns and temporal trends in the regional and local dust source areas within the desert of the Alashan Prefecture (Inner Mongolia, China). This problem was approached through multi-scale remote sensing analysis of vegetation changes. The primary requirements for this regional analysis are high spatial and spectral resolution data, accurate spectral calibration and good temporal resolution with a suitable temporal baseline. Landsat analysis and field validation along with the low spatial resolution classifications from MODIS and AVHRR are combined to provide a reliable characterization of the different potential dust-producing sources. The representation of intra-annual and inter-annual Normalized Difference Vegetation Index (NDVI) trend to assess land cover discrimination for mapping potential dust source using MODIS and AVHRR at larger scale is enhanced by Landsat Spectral Mixing Analysis (SMA). The combined methodology is to determine the extent to which Landsat can distinguish important soils types in order to better understand how soil reflectance behaves at seasonal and inter-annual timescales. As a final result mapping soil surface properties using SMA is representative of responses of different land and soil cover previously identified by NDVI trend. The results could be used in dust emission models even if they are not reflecting aggregate formation, soil stability or particle coatings showing to be critical for accurately represent dust source over different regional and local emitting areas.

  13. Spatio-temporal analysis of the relationship between WNV dissemination and environmental variables in Indianapolis, USA

    PubMed Central

    Liu, Hua; Weng, Qihao; Gaines, David

    2008-01-01

    Background This study developed a multi-temporal analysis on the relationship between West Nile Virus (WNV) dissemination and environmental variables by using an integrated approach of remote sensing, GIS, and statistical techniques. WNV mosquito cases in seven months (April-October) of the six years (2002–2007) were collected in Indianapolis, USA. Epidemic curves were plotted to identify the temporal outbreaks of WNV. Spatial-temporal analysis and k-mean cluster analysis were further applied to determine the high-risk areas. Finally, the relationship between environmental variables and WNV outbreaks were examined by using Discriminant Analysis. Results The results show that the WNV epidemic curve reached its peak in August for all years in the study area except in 2007, where the peak was reached in July. WNV dissemination started from the central longitudinal corridor of the city and spread out to the east and west. Different years and seasons had different high-risk areas, but the southwest and southeast corners show the highest risk for WNV infection due to their high percentages of agriculture and water sources. Conclusion Major environmental factors contributing to the outbreak of WNV in Indianapolis were the percentages of agriculture and water, total length of streams, and total size of wetlands. This study provides important information for urban public health prevention and management. It also contributes to the optimization of mosquito control and arrangement of future sampling efforts. PMID:19094221

  14. Quantitative Analysis of Cancer Metastasis using an Avian Embryo Model

    PubMed Central

    Palmer, Trenis D.; Lewis, John; Zijlstra, Andries

    2011-01-01

    During metastasis cancer cells disseminate from the primary tumor, invade into surrounding tissues, and spread to distant organs. Metastasis is a complex process that can involve many tissue types, span variable time periods, and often occur deep within organs, making it difficult to investigate and quantify. In addition, the efficacy of the metastatic process is influenced by multiple steps in the metastatic cascade making it difficult to evaluate the contribution of a single aspect of tumor cell behavior. As a consequence, metastasis assays are frequently performed in experimental animals to provide a necessarily realistic context in which to study metastasis. Unfortunately, these models are further complicated by their complex physiology. The chick embryo is a unique in vivo model that overcomes many limitations to studying metastasis, due to the accessibility of the chorioallantoic membrane (CAM), a well-vascularized extra-embryonic tissue located underneath the eggshell that is receptive to the xenografting of tumor cells (figure 1). Moreover, since the chick embryo is naturally immunodeficient, the CAM readily supports the engraftment of both normal and tumor tissues. Most importantly, the avian CAM successfully supports most cancer cell characteristics including growth, invasion, angiogenesis, and remodeling of the microenvironment. This makes the model exceptionally useful for the investigation of the pathways that lead to cancer metastasis and to predict the response of metastatic cancer to new potential therapeutics. The detection of disseminated cells by species-specific Alu PCR makes it possible to quantitatively assess metastasis in organs that are colonized by as few as 25 cells. Using the Human Epidermoid Carcinoma cell line (HEp3) we use this model to analyze spontaneous metastasis of cancer cells to distant organs, including the chick liver and lung. Furthermore, using the Alu-PCR protocol we demonstrate the sensitivity and reproducibility of the

  15. Quantitative error analysis for computer assisted navigation: a feasibility study

    PubMed Central

    Güler, Ö.; Perwög, M.; Kral, F.; Schwarm, F.; Bárdosi, Z. R.; Göbel, G.; Freysinger, W.

    2013-01-01

    Purpose The benefit of computer-assisted navigation depends on the registration process, at which patient features are correlated to some preoperative imagery. The operator-induced uncertainty in localizing patient features – the User Localization Error (ULE) - is unknown and most likely dominating the application accuracy. This initial feasibility study aims at providing first data for ULE with a research navigation system. Methods Active optical navigation was done in CT-images of a plastic skull, an anatomic specimen (both with implanted fiducials) and a volunteer with anatomical landmarks exclusively. Each object was registered ten times with 3, 5, 7, and 9 registration points. Measurements were taken at 10 (anatomic specimen and volunteer) and 11 targets (plastic skull). The active NDI Polaris system was used under ideal working conditions (tracking accuracy 0.23 mm root mean square, RMS; probe tip calibration was 0.18 mm RMS. Variances of tracking along the principal directions were measured as 0.18 mm2, 0.32 mm2, and 0.42 mm2. ULE was calculated from predicted application accuracy with isotropic and anisotropic models and from experimental variances, respectively. Results The ULE was determined from the variances as 0.45 mm (plastic skull), 0.60 mm (anatomic specimen), and 4.96 mm (volunteer). The predicted application accuracy did not yield consistent values for the ULE. Conclusions Quantitative data of application accuracy could be tested against prediction models with iso- and anisotropic noise models and revealed some discrepancies. This could potentially be due to the facts that navigation and one prediction model wrongly assume isotropic noise (tracking is anisotropic), while the anisotropic noise prediction model assumes an anisotropic registration strategy (registration is isotropic in typical navigation systems). The ULE data are presumably the first quantitative values for the precision of localizing anatomical landmarks and implanted fiducials

  16. Tree species mapping in tropical forests using multi-temporal imaging spectroscopy: Wavelength adaptive spectral mixture analysis

    NASA Astrophysics Data System (ADS)

    Somers, B.; Asner, G. P.

    2014-09-01

    The use of imaging spectroscopy for florisic mapping of forests is complicated by the spectral similarity among co-existing species. Here we evaluated an alternative spectral unmixing strategy combining a time series of EO-1 Hyperion images and an automated feature selection in Multiple Endmember Spectral Mixture Analysis (MESMA). The temporal analysis provided a way to incorporate species phenology while feature selection indicated the best phenological time and best spectral feature set to optimize the separability between tree species. Instead of using the same set of spectral bands throughout the image which is the standard approach in MESMA, our modified Wavelength Adaptive Spectral Mixture Analysis (WASMA) approach allowed the spectral subsets to vary on a per pixel basis. As such we were able to optimize the spectral separability between the tree species present in each pixel. The potential of the new approach for floristic mapping of tree species in Hawaiian rainforests was quantitatively assessed using both simulated and actual hyperspectral image time-series. With a Cohen's Kappa coefficient of 0.65, WASMA provided a more accurate tree species map compared to conventional MESMA (Kappa = 0.54; p-value < 0.05. The flexible or adaptive use of band sets in WASMA provides an interesting avenue to address spectral similarities in complex vegetation canopies.

  17. Spatio-Temporal Distribution Characteristics and Trajectory Similarity Analysis of Tuberculosis in Beijing, China.

    PubMed

    Li, Lan; Xi, Yuliang; Ren, Fu

    2016-03-01

    Tuberculosis (TB) is an infectious disease with one of the highest reported incidences in China. The detection of the spatio-temporal distribution characteristics of TB is indicative of its prevention and control conditions. Trajectory similarity analysis detects variations and loopholes in prevention and provides urban public health officials and related decision makers more information for the allocation of public health resources and the formulation of prioritized health-related policies. This study analysed the spatio-temporal distribution characteristics of TB from 2009 to 2014 by utilizing spatial statistics, spatial autocorrelation analysis, and space-time scan statistics. Spatial statistics measured the TB incidence rate (TB patients per 100,000 residents) at the district level to determine its spatio-temporal distribution and to identify characteristics of change. Spatial autocorrelation analysis was used to detect global and local spatial autocorrelations across the study area. Purely spatial, purely temporal and space-time scan statistics were used to identify purely spatial, purely temporal and spatio-temporal clusters of TB at the district level. The other objective of this study was to compare the trajectory similarities between the incidence rates of TB and new smear-positive (NSP) TB patients in the resident population (NSPRP)/new smear-positive TB patients in the TB patient population (NSPTBP)/retreated smear-positive (RSP) TB patients in the resident population (RSPRP)/retreated smear-positive TB patients in the TB patient population (RSPTBP) to detect variations and loopholes in TB prevention and control among the districts in Beijing. The incidence rates in Beijing exhibited a gradual decrease from 2009 to 2014. Although global spatial autocorrelation was not detected overall across all of the districts of Beijing, individual districts did show evidence of local spatial autocorrelation: Chaoyang and Daxing were Low-Low districts over the six

  18. Spatio-Temporal Distribution Characteristics and Trajectory Similarity Analysis of Tuberculosis in Beijing, China

    PubMed Central

    Li, Lan; Xi, Yuliang; Ren, Fu

    2016-01-01

    Tuberculosis (TB) is an infectious disease with one of the highest reported incidences in China. The detection of the spatio-temporal distribution characteristics of TB is indicative of its prevention and control conditions. Trajectory similarity analysis detects variations and loopholes in prevention and provides urban public health officials and related decision makers more information for the allocation of public health resources and the formulation of prioritized health-related policies. This study analysed the spatio-temporal distribution characteristics of TB from 2009 to 2014 by utilizing spatial statistics, spatial autocorrelation analysis, and space-time scan statistics. Spatial statistics measured the TB incidence rate (TB patients per 100,000 residents) at the district level to determine its spatio-temporal distribution and to identify characteristics of change. Spatial autocorrelation analysis was used to detect global and local spatial autocorrelations across the study area. Purely spatial, purely temporal and space-time scan statistics were used to identify purely spatial, purely temporal and spatio-temporal clusters of TB at the district level. The other objective of this study was to compare the trajectory similarities between the incidence rates of TB and new smear-positive (NSP) TB patients in the resident population (NSPRP)/new smear-positive TB patients in the TB patient population (NSPTBP)/retreated smear-positive (RSP) TB patients in the resident population (RSPRP)/retreated smear-positive TB patients in the TB patient population (RSPTBP) to detect variations and loopholes in TB prevention and control among the districts in Beijing. The incidence rates in Beijing exhibited a gradual decrease from 2009 to 2014. Although global spatial autocorrelation was not detected overall across all of the districts of Beijing, individual districts did show evidence of local spatial autocorrelation: Chaoyang and Daxing were Low-Low districts over the six

  19. Temporal discounting: basic research and the analysis of socially important behavior.

    PubMed Central

    Critchfield, T S; Kollins, S H

    2001-01-01

    Recent basic research on human temporal discounting is reviewed to illustrate procedures, summarize key findings, and draw parallels with both nonhuman animal research and conceptual writings on self-control. Lessons derived from this research are then applied to the challenge of analyzing socially important behaviors such as drug abuse, eating and exercise, and impulsiveness associated with attention deficit hyperactivity disorder. Attending to the broader temporal context in which behavior occurs may aid in the analysis of socially important behavior. Applying this perspective to the study of behavior in natural environments also highlights the importance of combining methodological flexibility with conceptual rigor to promote the extension of applied behavior analysis to a broader array of socially important behaviors. PMID:11317983

  20. The cortical analysis of speech-specific temporal structure revealed by responses to sound quilts.

    PubMed

    Overath, Tobias; McDermott, Josh H; Zarate, Jean Mary; Poeppel, David

    2015-06-01

    Speech contains temporal structure that the brain must analyze to enable linguistic processing. To investigate the neural basis of this analysis, we used sound quilts, stimuli constructed by shuffling segments of a natural sound, approximately preserving its properties on short timescales while disrupting them on longer scales. We generated quilts from foreign speech to eliminate language cues and manipulated the extent of natural acoustic structure by varying the segment length. Using functional magnetic resonance imaging, we identified bilateral regions of the superior temporal sulcus (STS) whose responses varied with segment length. This effect was absent in primary auditory cortex and did not occur for quilts made from other natural sounds or acoustically matched synthetic sounds, suggesting tuning to speech-specific spectrotemporal structure. When examined parametrically, the STS response increased with segment length up to ∼500 ms. Our results identify a locus of speech analysis in human auditory cortex that is distinct from lexical, semantic or syntactic processes. PMID:25984889

  1. The cortical analysis of speech-specific temporal structure revealed by responses to sound quilts

    PubMed Central

    Overath, Tobias; McDermott, Josh H; Zarate, Jean Mary; Poeppel, David

    2016-01-01

    Speech contains temporal structure that the brain must analyze to enable linguistic processing. To investigate the neural basis of this analysis, we used sound quilts, stimuli constructed by shuffling segments of a natural sound, approximately preserving its properties on short timescales while disrupting them on longer scales. We generated quilts from foreign speech to eliminate language cues and manipulated the extent of natural acoustic structure by varying the segment length. Using functional magnetic resonance imaging, we identified bilateral regions of the superior temporal sulcus (STS) whose responses varied with segment length. This effect was absent in primary auditory cortex and did not occur for quilts made from other natural sounds or acoustically matched synthetic sounds, suggesting tuning to speech-specific spectrotemporal structure. When examined parametrically, the STS response increased with segment length up to ~500 ms. Our results identify a locus of speech analysis in human auditory cortex that is distinct from lexical, semantic or syntactic processes. PMID:25984889

  2. Response Neighborhoods in Online Learning Networks: A Quantitative Analysis

    ERIC Educational Resources Information Center

    Aviv, Reuven; Erlich, Zippy; Ravid, Gilad

    2005-01-01

    Theoretical foundation of Response mechanisms in networks of online learners are revealed by Statistical Analysis of p* Markov Models for the Networks. Our comparative analysis of two networks shows that the minimal-effort hunt-for-social-capital mechanism controls a major behavior of both networks: negative tendency to respond. Differences in…

  3. [Research progress of quantitative analysis for respiratory sinus arrhythmia].

    PubMed

    Sun, Congcong; Zhang, Zhengbo; Wang, Buqing; Liu, Hongyun; Ang, Qing; Wang, Weidong

    2011-12-01

    Respiratory sinus arrhythmia (RSA) is known as fluctuations of heart rate associated with breathing. It has been increasingly used as a noninvasive index of cardiac vagal tone in psychophysiological research recently. Its analysis is often influenced or distorted by respiratory parameters, posture and action, etc. This paper reviews five methods of quantification, including the root mean square of successive differences (RMSSD), peak valley RSA (pvRSA), cosinor fitting, spectral analysis, and joint timing-frequency analysis (JTFA). Paced breathing, analysis of covariance, residua method and msRSA per liter tidal volume are adjustment strategies of measurement and analysis of RSA in this article as well. At last, some prospects of solutions of the problems of RSA research are given. PMID:22295719

  4. Technical note: Sampling and processing of mesocosm sediment trap material for quantitative biogeochemical analysis

    NASA Astrophysics Data System (ADS)

    Boxhammer, Tim; Bach, Lennart T.; Czerny, Jan; Riebesell, Ulf

    2016-05-01

    Sediment traps are the most common tool to investigate vertical particle flux in the marine realm. However, the spatial and temporal decoupling between particle formation in the surface ocean and particle collection in sediment traps at depth often handicaps reconciliation of production and sedimentation even within the euphotic zone. Pelagic mesocosms are restricted to the surface ocean, but have the advantage of being closed systems and are therefore ideally suited to studying how processes in natural plankton communities influence particle formation and settling in the ocean's surface. We therefore developed a protocol for efficient sample recovery and processing of quantitatively collected pelagic mesocosm sediment trap samples for biogeochemical analysis. Sedimented material was recovered by pumping it under gentle vacuum through a silicon tube to the sea surface. The particulate matter of these samples was subsequently separated from bulk seawater by passive settling, centrifugation or flocculation with ferric chloride, and we discuss the advantages and efficiencies of each approach. After concentration, samples were freeze-dried and ground with an easy to adapt procedure using standard lab equipment. Grain size of the finely ground samples ranged from fine to coarse silt (2-63 µm), which guarantees homogeneity for representative subsampling, a widespread problem in sediment trap research. Subsamples of the ground material were perfectly suitable for a variety of biogeochemical measurements, and even at very low particle fluxes we were able to get a detailed insight into various parameters characterizing the sinking particles. The methods and recommendations described here are a key improvement for sediment trap applications in mesocosms, as they facilitate the processing of large amounts of samples and allow for high-quality biogeochemical flux data.

  5. China's water resources vulnerability: A spatio-temporal analysis during 2003-2013

    NASA Astrophysics Data System (ADS)

    Cai, J.; Varis, O.; Yin, H.

    2015-12-01

    The present highly serious situation of China's water environment and aquatic ecosystems has occurred in the context of its stunning socioeconomic development over the past several decades. Therefore, an analysis with a high spatio-temporal resolution of the vulnerability assessment of water resources (VAWR) in China is burningly needed. However, to our knowledge, the temporal analysis of VAWR has been not yet addressed. Consequently, we performed, for the first time, a comprehensive spatio-temporal analysis of China's water resources vulnerability (WRV), using a composite index approach with an array of aspects highlighting key challenges that China's water resources system is nowadays facing. During our study period of 2003-2013, the political weight of China's integrated water resources management has been increasing continuously. Hence, it is essential and significant, based on the historical socioeconomic changes influenced by water-environment policy making and implementation, to reveal China's WRV for pinpointing key challenges to the healthy functionality of its water resources system. The water resources system in North and Central Coast appeared more vulnerable than that in Western China. China's water use efficiency has grown substantially over the study period, and so is water supply and sanitation coverage. In contrast, water pollution has been worsening remarkably in most parts of China, and so have water scarcity and shortage in the most stressed parts of the country. This spatio-temporal analysis implies that the key challenges to China's water resources system not only root in the geographical mismatch between socioeconomic development (e.g. water demand) and water resources endowments (e.g. water resources availability), but also stem from the intertwinement between socioeconomic development and national strategic policy making.

  6. A Quantitative Analysis of Rift Processes in the Northern North Sea and Central Greece.

    NASA Astrophysics Data System (ADS)

    Bryon, J. G.; White, N. J.

    2003-12-01

    Actively extending sedimentary basins provide a snapshot of the way in which basins evolve. Our observations from such regions are temporally limited: we have little understanding of the long-term processes involved but an excellent understanding of the short-term motions (100-102 years). The converse is true of tectonically dead basins where the deformation has ceased and only the end product can be observed. Studies of active basin formation in central Greece have provided a quantitative understanding of the kinematics of extensional tectonics. The use of GPS, SAR interferometry and geomorphological analysis has constrained the rate of extension and fault kinematics and geometries. Central Greece has often been cited as a present-day analogue for formation of the now inactive East Shetland Basin (ESB) in the northern North Sea. A large 3D seismic dataset has been compiled giving complete coverage of the ESB, a region comparable in size to central Greece ( ˜10,000 km2). A quantitative comparison between Greece and the ESB will close the gap in knowledge between short-term and long-term motions. Whilst the two regions have many features in common, such as tilted fault blocks, fault segments of comparable length and similar fault geometries, there are also important differences. For example, one difference between Greece and the northern North Sea is the rate of extension. The North Sea had a peak strain rate that was an order of magnitude slower than the rate at which Greece is currently extending across the gulfs of Corinth and Evia. Another difference is that the distance between large active faults in Greece appears to be significantly longer than in the ESB. A specific example of this difference in scale is the Tern-Eider ridge, which is a horst block in the ESB that appears superficially similar to the island of Evia in Greece. However, the rigid island of Evia is significantly wider than the Tern-Eider ridge. A link between this inter-fault distance and

  7. Flash Floods: A Spatial and Temporal Analysis A Case Study of the Flash Floods in Southwestern Missouri

    NASA Astrophysics Data System (ADS)

    Pollak, D. A.

    2009-12-01

    Floods are the leading cause of weather-related fatalities in the United States and the second most common cause of weather-related death worldwide. Of all floods, flash floods are found to be the most deadly with an average global mortality rate of 3.62%. This study performed a spatial and temporal analysis of flash flood risk using Geographic Information Systems (GIS) to analyze an event that occurred in southwestern Missouri in March 2008. The goals of the study were to identify different impacts of the disaster as indicated by flood reports; examine the social and natural factors that account for the spatial and temporal distribution and severity of the impacts; and to compare the results with a previous study of a flash flood event in France. In the Missouri case, the analysis confirmed that small catchments react faster than large catchments and to smaller amounts of rainfall. Seventy-seven percent of incidents (water rescues, fatalities, flooded homes, and flooded roads) occurred in catchments smaller than 200 km2. The study also showed that a majority of the severe impacts (water rescues, fatalities, and flooded homes) occurred after the rainfall had tapered off, perhaps indicating that people erroneously perceive the danger has passed once the rain has stopped. When looking at water rescues and fatalities, the results of this study found that fewer incidents occurred in medium size catchments (50-450 km2) than in either large (>450 km2) or small catchments (<50 km2). This is similar to the French study which found that no fatalities occurred in medium-sized catchments. Using GIS to examine flash flood risk, will take strides forward comparing human vulnerability with size of catchment. This project integrated qualitative and quantitative data using GIS. Displays the time series before, during, and after the flood report/accident which occurred in catchment 5.

  8. Temporal Analysis of the Magnaporthe Oryzae Proteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation*

    PubMed Central

    Franck, William L.; Gokce, Emine; Oh, Yeonyee; Muddiman, David C.; Dean, Ralph A.

    2013-01-01

    Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and

  9. Spatial-Temporal Epidemiology of Tuberculosis in Mainland China: An Analysis Based on Bayesian Theory

    PubMed Central

    Cao, Kai; Yang, Kun; Wang, Chao; Guo, Jin; Tao, Lixin; Liu, Qingrong; Gehendra, Mahara; Zhang, Yingjie; Guo, Xiuhua

    2016-01-01

    Objective: To explore the spatial-temporal interaction effect within a Bayesian framework and to probe the ecological influential factors for tuberculosis. Methods: Six different statistical models containing parameters of time, space, spatial-temporal interaction and their combination were constructed based on a Bayesian framework. The optimum model was selected according to the deviance information criterion (DIC) value. Coefficients of climate variables were then estimated using the best fitting model. Results: The model containing spatial-temporal interaction parameter was the best fitting one, with the smallest DIC value (−4,508,660). Ecological analysis results showed the relative risks (RRs) of average temperature, rainfall, wind speed, humidity, and air pressure were 1.00324 (95% CI, 1.00150–1.00550), 1.01010 (95% CI, 1.01007–1.01013), 0.83518 (95% CI, 0.93732–0.96138), 0.97496 (95% CI, 0.97181–1.01386), and 1.01007 (95% CI, 1.01003–1.01011), respectively. Conclusions: The spatial-temporal interaction was statistically meaningful and the prevalence of tuberculosis was influenced by the time and space interaction effect. Average temperature, rainfall, wind speed, and air pressure influenced tuberculosis. Average humidity had no influence on tuberculosis. PMID:27164117

  10. Whole-Genome Analysis of Temporal Gene Expression during Foregut Development

    PubMed Central

    2004-01-01

    We have investigated the cis-regulatory network that mediates temporal gene expression during organogenesis. Previous studies demonstrated that the organ selector gene pha-4/FoxA is critical to establish the onset of transcription of Caenorhabditis elegans foregut (pharynx) genes. Here, we discover additional cis-regulatory elements that function in combination with PHA-4. We use a computational approach to identify candidate cis-regulatory sites for genes activated either early or late during pharyngeal development. Analysis of natural or synthetic promoters reveals that six of these sites function in vivo. The newly discovered temporal elements, together with predicted PHA-4 sites, account for the onset of expression of roughly half of the pharyngeal genes examined. Moreover, combinations of temporal elements and PHA-4 sites can be used in genome-wide searches to predict pharyngeal genes, with more than 85% accuracy for their onset of expression. These findings suggest a regulatory code for temporal gene expression during foregut development and provide a means to predict gene expression patterns based solely on genomic sequence. PMID:15492775

  11. Fourier-transform method of data compression and temporal fringe pattern analysis

    SciTech Connect

    Tuck Wah Ng; Kar Tien Ang

    2005-11-20

    Temporal fringe pattern analysis is invaluable in studies of transient phenomena but necessitates large data storage for two essential sets of data, i.e., fringe pattern intensity and deformation phase. We describe a compression scheme based on the Fourier-transform method for temporal fringe data storage that permits retrieval of both the intensity and the deformation phase. When the scheme was used with simulated temporal wavefront interferometry intensity fringe patterns, a high compression ratio of 10.77 was achieved, with a significant useful data ratio of 0.859. The average root-mean-square error in phase value restored was a low 0.0015 rad. With simulated temporal speckle interferometry intensity fringe patterns, the important paremeters varied with the modulation cutoff value applied. For a zero modulation cutoff value, the ratio of data points and the compression ratio values obtained were roughly the same as in wavelength interferometry, albeit the average root-mean-square error in the phase value restored was far higher. By increasing the modulation cutoff value we attained significant reduction and increase in the ratio of data points and the compression ratio, respectively, whereas the average root-mean-square error in the restored phase values was reduced only slightly.

  12. Quantitative analysis of numerical solvers for oscillatory biomolecular system models

    PubMed Central

    Quo, Chang F; Wang, May D

    2008-01-01

    Background This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, the ODEs can be stiff and ill-conditioned, resulting in non-unique, non-existing, or non-reproducible modeling solutions. Previous studies have not examined in depth how to best select numerical solvers for biomolecular system models, which makes it difficult to experimentally validate the modeling results. To address this problem, we have chosen one of the well-known stiff initial value problems with limit cycle behavior as a test-bed system model. Solving this model, we have illustrated that different answers may result from different numerical solvers. We use MATLAB numerical solvers because they are optimized and widely used by the modeling community. We have also conducted a systematic study of numerical solver performances by using qualitative and quantitative measures such as convergence, accuracy, and computational cost (i.e. in terms of function evaluation, partial derivative, LU decomposition, and "take-off" points). The results show that the modeling solutions can be drastically different using different numerical solvers. Thus, it is important to intelligently select numerical solvers when solving biomolecular system models. Results The classic Belousov-Zhabotinskii (BZ) reaction is described by the Oregonator model and is used as a case study. We report two guidelines in selecting optimal numerical solver(s) for stiff, complex oscillatory systems: (i) for problems with unknown parameters, ode45 is the optimal choice regardless of the relative error tolerance; (ii) for known stiff problems, both ode113 and ode15s are good choices under strict relative tolerance conditions. Conclusions For any given biomolecular model, by building a library of numerical solvers with quantitative performance assessment metric, we show that it is possible

  13. ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

    PubMed

    Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. PMID:21705250

  14. ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

    NASA Astrophysics Data System (ADS)

    Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

  15. A quantitative analysis of rock cliff erosion environments

    NASA Astrophysics Data System (ADS)

    Lim, M.; Rosser, N.; Petley, D. N.; Norman, E. C.; Barlow, J.

    2009-12-01

    The spatial patterns and temporal sequencing of failures from coastal rock cliffs are complex and typically generate weak correlations with environmental variables such as tidal inundation, wave energy, wind and rain. Consequently, understanding of rock cliff behaviour, its response to predicted changes in environmental forcing and, more specifically, the interaction between marine and climatic factors in influencing failure processes has remained limited. This work presents the results from the first attempt to characterise and quantify the conditions on coastal cliffs that lead to accelerated rates of material detachment. The rate of change in an 80 m high section of coastal rock cliffs has been surveyed annually with high-resolution terrestrial laser scanning (TLS). The rockfall data have been analysed according to a simplified source geology that exhibit distinct magnitude-frequency distributions relating to the dominance of particular failure types. An integrated network of sensors and instrumentation designed to reflect the lithological control on failure has been installed to examine both the distinction between prevailing conditions and those affecting the local cliff environment and the physical response of different rock types to micro-climatic processes. The monitoring system records near-surface rock strain, temperature, moisture and micro-seismic displacement in addition to air temperature, humidity, radiation, precipitation, water-level and three-dimensional wind characteristics. A characteristic environmental signal, unique to the cliff face material, has been identified that differs substantially from that experienced by the surrounding area; suggesting that established methods of meteorological and tidal data collection are insufficient and inappropriate to represent erosive processes. The interaction between thermo- and hydro-dynamics of the cliff environment and the physical response of the rock highlights the composite environmental effects

  16. Mapping tonotopic organization in human temporal cortex: representational similarity analysis in EMEG source space.

    PubMed

    Su, Li; Zulfiqar, Isma; Jamshed, Fawad; Fonteneau, Elisabeth; Marslen-Wilson, William

    2014-01-01

    A wide variety of evidence, from neurophysiology, neuroanatomy, and imaging studies in humans and animals, suggests that human auditory cortex is in part tonotopically organized. Here we present a new means of resolving this spatial organization using a combination of non-invasive observables (EEG, MEG, and MRI), model-based estimates of spectrotemporal patterns of neural activation, and multivariate pattern analysis. The method exploits both the fine-grained temporal patterning of auditory cortical responses and the millisecond scale temporal resolution of EEG and MEG. Participants listened to 400 English words while MEG and scalp EEG were measured simultaneously. We estimated the location of cortical sources using the MRI anatomically constrained minimum norm estimate (MNE) procedure. We then combined a form of multivariate pattern analysis (representational similarity analysis) with a spatiotemporal searchlight approach to successfully decode information about patterns of neuronal frequency preference and selectivity in bilateral superior temporal cortex. Observed frequency preferences in and around Heschl's gyrus matched current proposals for the organization of tonotopic gradients in primary acoustic cortex, while the distribution of narrow frequency selectivity similarly matched results from the fMRI literature. The spatial maps generated by this novel combination of techniques seem comparable to those that have emerged from fMRI or ECOG studies, and a considerable advance over earlier MEG results. PMID:25429257

  17. A geomatic methodology for spatio-temporal analysis of climatologic variables and water related diseases

    NASA Astrophysics Data System (ADS)

    Quentin, E.; Gómez Albores, M. A.; Díaz Delgado, C.

    2009-04-01

    The main objective of this research is to propose, by the way of geomatic developments, an integrated tool to analyze and model the spatio-temporal pattern of human diseases related to environmental conditions, in particular the ones that are linked to water resources. The geomatic developments follows four generic steps : requirement analysis, conceptual modeling, geomatic modeling and implementation (in Idrisi GIS software). A first development consists of the preprocessing of water, population and health data in order to facilitate the conversion and validation of tabular data into the required structure for spatio-temporal analysis. Three parallel developments follow : water balance, demographic state and evolution, epidemiological measures (morbidity and mortality rates, diseases burden). The new geomatic modules in their actual state have been tested on various regions of Mexico Republic (Lerma watershed, Chiapas state) focusing on diarrhea and vector borne diseases (dengue and malaria) and considering records over the last decade : a yearly as well as seasonal spreading trend can be observed in correlation with precipitation and temperature data. In an ecohealth perspective, the geomatic approach results particularly appropriate since one of its purposes is the integration of the various spatial themes implied in the study problem, environmental as anthropogenic. By the use of powerful spatial analysis functions, it permits the detection of spatial trends which, combined to the temporal evolution, can be of particularly use for example in climate change context, if sufficiently valid historical data can be obtain.

  18. Laser speckle imaging of rat retinal blood flow with hybrid temporal and spatial analysis method

    NASA Astrophysics Data System (ADS)

    Cheng, Haiying; Yan, Yumei; Duong, Timothy Q.

    2009-02-01

    Noninvasive monitoring of blood flow in retinal circulation will reveal the progression and treatment of ocular disorders, such as diabetic retinopathy, age-related macular degeneration and glaucoma. A non-invasive and direct BF measurement technique with high spatial-temporal resolution is needed for retinal imaging. Laser speckle imaging (LSI) is such a method. Currently, there are two analysis methods for LSI: spatial statistics LSI (SS-LSI) and temporal statistical LSI (TS-LSI). Comparing these two analysis methods, SS-LSI has higher signal to noise ratio (SNR) and TSLSI is less susceptible to artifacts from stationary speckle. We proposed a hybrid temporal and spatial analysis method (HTS-LSI) to measure the retinal blood flow. Gas challenge experiment was performed and images were analyzed by HTS-LSI. Results showed that HTS-LSI can not only remove the stationary speckle but also increase the SNR. Under 100% O2, retinal BF decreased by 20-30%. This was consistent with the results observed with laser Doppler technique. As retinal blood flow is a critical physiological parameter and its perturbation has been implicated in the early stages of many retinal diseases, HTS-LSI will be an efficient method in early detection of retina diseases.

  19. Joint modality fusion and temporal context exploitation for semantic video analysis

    NASA Astrophysics Data System (ADS)

    Papadopoulos, Georgios Th; Mezaris, Vasileios; Kompatsiaris, Ioannis; Strintzis, Michael G.

    2011-12-01

    In this paper, a multi-modal context-aware approach to semantic video analysis is presented. Overall, the examined video sequence is initially segmented into shots and for every resulting shot appropriate color, motion and audio features are extracted. Then, Hidden Markov Models (HMMs) are employed for performing an initial association of each shot with the semantic classes that are of interest separately for each modality. Subsequently, a graphical modeling-based approach is proposed for jointly performing modality fusion and temporal context exploitation. Novelties of this work include the combined use of contextual information and multi-modal fusion, and the development of a new representation for providing motion distribution information to HMMs. Specifically, an integrated Bayesian Network is introduced for simultaneously performing information fusion of the individual modality analysis results and exploitation of temporal context, contrary to the usual practice of performing each task separately. Contextual information is in the form of temporal relations among the supported classes. Additionally, a new computationally efficient method for providing motion energy distribution-related information to HMMs, which supports the incorporation of motion characteristics from previous frames to the currently examined one, is presented. The final outcome of this overall video analysis framework is the association of a semantic class with every shot. Experimental results as well as comparative evaluation from the application of the proposed approach to four datasets belonging to the domains of tennis, news and volleyball broadcast video are presented.

  20. Quantitative assessment of human motion using video motion analysis

    NASA Technical Reports Server (NTRS)

    Probe, John D.

    1990-01-01

    In the study of the dynamics and kinematics of the human body, a wide variety of technologies was developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development coupled with recent advances in video technology have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System to develop data on shirt-sleeved and space-suited human performance in order to plan efficient on orbit intravehicular and extravehicular activities. The system is described.

  1. Space-to-Ground Communication for Columbus: A Quantitative Analysis

    PubMed Central

    Uhlig, Thomas; Mannel, Thurid; Fortunato, Antonio; Illmer, Norbert

    2015-01-01

    The astronauts on board the International Space Station (ISS) are only the most visible part of a much larger team engaged around the clock in the performance of science and technical activities in space. The bulk of such team is scattered around the globe in five major Mission Control Centers (MCCs), as well as in a number of smaller payload operations centres. Communication between the crew in space and the flight controllers at those locations is an essential element and one of the key drivers to efficient space operations. Such communication can be carried out in different forms, depending on available technical assets and the selected operational approach for the activity at hand. This paper focuses on operational voice communication and provides a quantitative overview of the balance achieved in the Columbus program between collaborative space/ground operations and autonomous on-board activity execution. An interpretation of the current situation is provided, together with a description of potential future approaches for deep space exploration missions. PMID:26290898

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

    PubMed

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

    2015-01-01

    We report on quantitative comparison between the electric dipole energy and the Rashba band splitting in model systems of Bi and Sb triangular monolayers under a perpendicular electric field. We used both first-principles and tight binding calculations on p-orbitals with spin-orbit coupling. First-principles calculation shows Rashba band splitting in both systems. It also shows asymmetric charge distributions in the Rashba split bands which are induced by the orbital angular momentum. We calculated the electric dipole energies from coupling of the asymmetric charge distribution and external electric field, and compared it to the Rashba splitting. Remarkably, the total split energy is found to come mostly from the difference in the electric dipole energy for both Bi and Sb systems. A perturbative approach for long wave length limit starting from tight binding calculation also supports that the Rashba band splitting originates mostly from the electric dipole energy difference in the strong atomic spin-orbit coupling regime. PMID:26323493

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

    PubMed Central

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

    2015-01-01

    We report on quantitative comparison between the electric dipole energy and the Rashba band splitting in model systems of Bi and Sb triangular monolayers under a perpendicular electric field. We used both first-principles and tight binding calculations on p-orbitals with spin-orbit coupling. First-principles calculation shows Rashba band splitting in both systems. It also shows asymmetric charge distributions in the Rashba split bands which are induced by the orbital angular momentum. We calculated the electric dipole energies from coupling of the asymmetric charge distribution and external electric field, and compared it to the Rashba splitting. Remarkably, the total split energy is found to come mostly from the difference in the electric dipole energy for both Bi and Sb systems. A perturbative approach for long wave length limit starting from tight binding calculation also supports that the Rashba band splitting originates mostly from the electric dipole energy difference in the strong atomic spin-orbit coupling regime. PMID:26323493

  4. Quantitative analysis of electroluminescence images from polymer solar cells

    NASA Astrophysics Data System (ADS)

    Seeland, Marco; Rösch, Roland; Hoppe, Harald

    2012-01-01

    We introduce the micro-diode-model (MDM) based on a discrete network of interconnected diodes, which allows for quantitative description of lateral electroluminescence emission images obtained from organic bulk heterojunction solar cells. Besides the distributed solar cell description, the equivalent circuit, respectively, network model considers interface and bulk resistances as well as the sheet resistance of the semitransparent electrode. The application of this model allows direct calculation of the lateral current and voltage distribution within the solar cell and thus accounts well for effects known as current crowding. In addition, network parameters such as internal resistances and the sheet-resistance of the higher resistive electrode can be determined. Furthermore, upon introduction of current sources the micro-diode-model also is able to describe and predict current-voltage characteristics for solar cell devices under illumination. The local nature of this description yields important conclusions concerning the geometry dependent performance and the validity of classical models and equivalent circuits describing thin film solar cells.

  5. Quantitative analysis of ultrasound images for computer-aided diagnosis.

    PubMed

    Wu, Jie Ying; Tuomi, Adam; Beland, Michael D; Konrad, Joseph; Glidden, David; Grand, David; Merck, Derek

    2016-01-01

    We propose an adaptable framework for analyzing ultrasound (US) images quantitatively to provide computer-aided diagnosis using machine learning. Our preliminary clinical targets are hepatic steatosis, adenomyosis, and craniosynostosis. For steatosis and adenomyosis, we collected US studies from 288 and 88 patients, respectively, as well as their biopsy or magnetic resonanceconfirmed diagnosis. Radiologists identified a region of interest (ROI) on each image. We filtered the US images for various texture responses and use the pixel intensity distribution within each ROI as feature parameterizations. Our craniosynostosis dataset consisted of 22 CT-confirmed cases and 22 age-matched controls. One physician manually measured the vectors from the center of the skull to the outer cortex at every 10 deg for each image and we used the principal directions as shape features for parameterization. These parameters and the known diagnosis were used to train classifiers. Testing with cross-validation, we obtained 72.74% accuracy and 0.71 area under receiver operating characteristics curve for steatosis ([Formula: see text]), 77.27% and 0.77 for adenomyosis ([Formula: see text]), and 88.63% and 0.89 for craniosynostosis ([Formula: see text]). Our framework is able to detect a variety of diseases with high accuracy. We hope to include it as a routinely available support system in the clinic. PMID:26835502

  6. Quantitative proteomic analysis of the Salmonella-lettuce interaction

    PubMed Central

    Zhang, Yuping; Nandakumar, Renu; Bartelt-Hunt, Shannon L; Snow, Daniel D; Hodges, Laurie; Li, Xu

    2014-01-01

    Human pathogens can internalize food crops through root and surface uptake and persist inside crop plants. The goal of the study was to elucidate the global modulation of bacteria and plant protein expression after Salmonella internalizes lettuce. A quantitative proteomic approach was used to analyse the protein expression of Salmonella enterica serovar Infantis and lettuce cultivar Green Salad Bowl 24 h after infiltrating S. Infantis into lettuce leaves. Among the 50 differentially expressed proteins identified by comparing internalized S. Infantis against S. Infantis grown in Luria Broth, proteins involved in glycolysis were down-regulated, while one protein involved in ascorbate uptake was up-regulated. Stress response proteins, especially antioxidant proteins, were up-regulated. The modulation in protein expression suggested that internalized S. Infantis might utilize ascorbate as a carbon source and require multiple stress response proteins to cope with stresses encountered in plants. On the other hand, among the 20 differentially expressed lettuce proteins, proteins involved in defense response to bacteria were up-regulated. Moreover, the secreted effector PipB2 of S. Infantis and R proteins of lettuce were induced after bacterial internalization into lettuce leaves, indicating human pathogen S. Infantis triggered the defense mechanisms of lettuce, which normally responds to plant pathogens. PMID:24512637

  7. Quantitative analysis of pheromone-binding protein specificity

    PubMed Central

    Katti, S.; Lokhande, N.; González, D.; Cassill, A.; Renthal, R.

    2012-01-01

    Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins (OBPs), using β-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila OBP that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in E. coli was assessed by measuring N-phenyl-1-naphthylamine (NPN) binding and Förster resonance energy transfer between LUSH tryptophan 123 (W123) and NPN. Binding of cVA was measured from quenching of W123 fluorescence as a function of cVA concentration. The equilibrium constant for transfer of cVA between β-cyclodextrin and LUSH was determined from a linked equilibria model. This constant, multiplied by the β-cyclodextrin-cVA dissociation constant, gives the LUSH-cVA dissociation constant: ~100 nM. It was also found that other ligands quench W123 fluorescence. The LUSH-ligand dissociation constants were determined to be ~200 nM for the silk moth pheromone bombykol and ~90 nM for methyl oleate. The results indicate that the ligand-binding cavity of LUSH can accommodate a variety ligands with strong binding interactions. Implications of this for the pheromone receptor model proposed by Laughlin et al. (Cell 133: 1255–65, 2008) are discussed. PMID:23121132

  8. Quantitative Dopant/Impurity Analysis for ICF Targets

    NASA Astrophysics Data System (ADS)

    Huang, Haibo; Nikroo, Abbas; Stephens, Richard; Eddinger, Samual; Xu, Hongwei; Chen, K. C.; Moreno, Kari

    2008-11-01

    We developed a number of new or improved metrology techniques to measure the spatial distributions of multiple elements in ICF ablator capsules to tight NIF specifications (0.5±0.1 at% Cu, 0.25±0.10 at% Ar, 0.4±0.4 at% O). The elements are either the graded dopants for shock timing, such as Cu in Be, or process-induced impurities, such as Ar and O. Their low concentration, high spatial variation and simultaneous presence make the measurement very difficult. We solved this metrology challenge by combining several techniques: Cu and Ar profiles can be nondestructively measured by operating Contact Radiography (CR) in a differential mode. The result, as well as the O profile, can be checked destructively by a quantitative Energy Dispersive Spectroscopy (EDS) method. Non-spatially resolved methods, such as absorption edge spectroscopy (and to a lesser accuracy, x-ray fluorescence) can calibrate the Ar and Cu measurement in EDS and CR. In addition, oxygen pick-up during mandrel removal can be validated by before-and-after CR and by density change. Use of all these methods gives multiple checks on the reported profiles.

  9. Analysis of alpha-synuclein-associated proteins by quantitative proteomics.

    PubMed

    Zhou, Yong; Gu, Guangyu; Goodlett, David R; Zhang, Terry; Pan, Catherine; Montine, Thomas J; Montine, Kathleen S; Aebersold, Ruedi H; Zhang, Jing

    2004-09-10

    To identify the proteins associated with soluble alpha-synuclein (AS) that might promote AS aggregation, a key event leading to neurodegeneration, we quantitatively compared protein profiles of AS-associated protein complexes in MES cells exposed to rotenone, a pesticide that produces parkinsonism in animals and induces Lewy body (LB)-like inclusions in the remaining dopaminergic neurons, and to vehicle. We identified more than 250 proteins associated with Nonidet P-40 soluble AS, and demonstrated that at least 51 of these proteins displayed significant differences in their relative abundance in AS complexes under conditions where rotenone was cytotoxic and induced formation of cytoplasmic inclusions immunoreactive to anti-AS. Overexpressing one of these proteins, heat shock protein (hsp) 70, not only protected cells from rotenone-mediated cytotoxicity but also decreased soluble AS aggregation. Furthermore, the protection afforded by hsp70 transfection appeared to be related to suppression of rotenone-induced oxidative stress as well as mitochondrial and proteasomal dysfunction. PMID:15234983

  10. Quantitative analysis of virus and plasmid trafficking in cells

    NASA Astrophysics Data System (ADS)

    Lagache, Thibault; Dauty, Emmanuel; Holcman, David

    2009-01-01

    Intracellular transport of DNA carriers is a fundamental step of gene delivery. By combining both theoretical and numerical approaches we study here single and several viruses and DNA particles trafficking in the cell cytoplasm to a small nuclear pore. We present a physical model to account for certain aspects of cellular organization, starting with the observation that a viral trajectory consists of epochs of pure diffusion and epochs of active transport along microtubules. We define a general degradation rate to describe the limitations of the delivery of plasmid or viral particles to a nuclear pore imposed by various types of direct and indirect hydrolysis activity inside the cytoplasm. By replacing the switching dynamics by a single steady state stochastic description, we obtain estimates for the probability and the mean time for the first one of many particles to go from the cell membrane to a small nuclear pore. Computational simulations confirm that our model can be used to analyze and interpret viral trajectories and estimate quantitatively the success of nuclear delivery.

  11. Analysis of copy number variation using quantitative interspecies competitive PCR.

    PubMed

    Williams, Nigel M; Williams, Hywel; Majounie, Elisa; Norton, Nadine; Glaser, Beate; Morris, Huw R; Owen, Michael J; O'Donovan, Michael C

    2008-10-01

    Over recent years small submicroscopic DNA copy-number variants (CNVs) have been highlighted as an important source of variation in the human genome, human phenotypic diversity and disease susceptibility. Consequently, there is a pressing need for the development of methods that allow the efficient, accurate and cheap measurement of genomic copy number polymorphisms in clinical cohorts. We have developed a simple competitive PCR based method to determine DNA copy number which uses the entire genome of a single chimpanzee as a competitor thus eliminating the requirement for competitive sequences to be synthesized for each assay. This results in the requirement for only a single reference sample for all assays and dramatically increases the potential for large numbers of loci to be analysed in multiplex. In this study we establish proof of concept by accurately detecting previously characterized mutations at the PARK2 locus and then demonstrating the potential of quantitative interspecies competitive PCR (qicPCR) to accurately genotype CNVs in association studies by analysing chromosome 22q11 deletions in a sample of previously characterized patients and normal controls. PMID:18697816

  12. Quantitative proteomic analysis of the Salmonella-lettuce interaction.

    PubMed

    Zhang, Yuping; Nandakumar, Renu; Bartelt-Hunt, Shannon L; Snow, Daniel D; Hodges, Laurie; Li, Xu

    2014-11-01

    Human pathogens can internalize food crops through root and surface uptake and persist inside crop plants. The goal of the study was to elucidate the global modulation of bacteria and plant protein expression after Salmonella internalizes lettuce. A quantitative proteomic approach was used to analyse the protein expression of Salmonella enterica serovar Infantis and lettuce cultivar Green Salad Bowl 24 h after infiltrating S. Infantis into lettuce leaves. Among the 50 differentially expressed proteins identified by comparing internalized S. Infantis against S. Infantis grown in Luria Broth, proteins involved in glycolysis were down-regulated, while one protein involved in ascorbate uptake was up-regulated. Stress response proteins, especially antioxidant proteins, were up-regulated. The modulation in protein expression suggested that internalized S. Infantis might utilize ascorbate as a carbon source and require multiple stress response proteins to cope with stresses encountered in plants. On the other hand, among the 20 differentially expressed lettuce proteins, proteins involved in defense response to bacteria were up-regulated. Moreover, the secreted effector PipB2 of S. Infantis and R proteins of lettuce were induced after bacterial internalization into lettuce leaves, indicating human pathogen S. Infantis triggered the defense mechanisms of lettuce, which normally responds to plant pathogens. PMID:24512637

  13. Quantitative Analysis of CME Deflections in the Corona

    NASA Astrophysics Data System (ADS)

    Gui, Bin; Shen, Chenglong; Wang, Yuming; Ye, Pinzhong; Liu, Jiajia; Wang, Shui; Zhao, Xuepu

    2011-07-01

    In this paper, ten CME events viewed by the STEREO twin spacecraft are analyzed to study the deflections of CMEs during their propagation in the corona. Based on the three-dimensional information of the CMEs derived by the graduated cylindrical shell (GCS) model (Thernisien, Howard, and Vourlidas in Astrophys. J. 652, 1305, 2006), it is found that the propagation directions of eight CMEs had changed. By applying the theoretical method proposed by Shen et al. ( Solar Phys. 269, 389, 2011) to all the CMEs, we found that the deflections are consistent, in strength and direction, with the gradient of the magnetic energy density. There is a positive correlation between the deflection rate and the strength of the magnetic energy density gradient and a weak anti-correlation between the deflection rate and the CME speed. Our results suggest that the deflections of CMEs are mainly controlled by the background magnetic field and can be quantitatively described by the magnetic energy density gradient (MEDG) model.

  14. Analysis of quantitative trait loci for behavioral laterality in mice.

    PubMed Central

    Roubertoux, Pierre L; Le Roy, Isabelle; Tordjman, Sylvie; Cherfou, Améziane; Migliore-Samour, Danièle

    2003-01-01

    Laterality is believed to have genetic components, as has been deduced from family studies in humans and responses to artificial selection in mice, but these genetic components are unknown and the underlying physiological mechanisms are still a subject of dispute. We measured direction of laterality (preferential use of left or right paws) and degree of laterality (absolute difference between the use of left and right paws) in C57BL/6ByJ (B) and NZB/BlNJ (N) mice and in their F(1) and F(2) intercrosses. Measurements were taken of both forepaws and hind paws. Quantitative trait loci (QTL) did not emerge for direction but did for degree of laterality. One QTL for forepaw (LOD score = 5.6) and the second QTL for hind paw (LOD score = 7.2) were both located on chromosome 4 and their peaks were within the same confidence interval. A QTL for plasma luteinizing hormone concentration was also found in the confidence interval of these two QTL. These results suggest that the physiological mechanisms underlying degree of laterality react to gonadal steroids. PMID:12663540

  15. Quantitative Proteome Analysis of Leishmania donovani under Spermidine Starvation

    PubMed Central

    Singh, Shalini; Dubey, Vikash Kumar

    2016-01-01

    We have earlier reported antileishmanial activity of hypericin by spermidine starvation. In the current report, we have used label free proteome quantitation approach to identify differentially modulated proteins after hypericin treatment. A total of 141 proteins were found to be differentially regulated with ANOVA P value less than 0.05 in hypericin treated Leishmania promastigotes. Differentially modulated proteins have been broadly classified under nine major categories. Increase in ribosomal protein S7 protein suggests the repression of translation. Inhibition of proteins related to ubiquitin proteasome system, RNA binding protein and translation initiation factor also suggests altered translation. We have also observed increased expression of Hsp 90, Hsp 83–1 and stress inducible protein 1. Significant decreased level of cyclophilin was observed. These stress related protein could be cellular response of the parasite towards hypericin induced cellular stress. Also, defective metabolism, biosynthesis and replication of nucleic acids, flagellar movement and signalling of the parasite were observed as indicated by altered expression of proteins involved in these pathways. The data was analyzed rigorously to get further insight into hypericin induced parasitic death. PMID:27123864

  16. Space-to-Ground Communication for Columbus: A Quantitative Analysis.

    PubMed

    Uhlig, Thomas; Mannel, Thurid; Fortunato, Antonio; Illmer, Norbert

    2015-01-01

    The astronauts on board the International Space Station (ISS) are only the most visible part of a much larger team engaged around the clock in the performance of science and technical activities in space. The bulk of such team is scattered around the globe in five major Mission Control Centers (MCCs), as well as in a number of smaller payload operations centres. Communication between the crew in space and the flight controllers at those locations is an essential element and one of the key drivers to efficient space operations. Such communication can be carried out in different forms, depending on available technical assets and the selected operational approach for the activity at hand. This paper focuses on operational voice communication and provides a quantitative overview of the balance achieved in the Columbus program between collaborative space/ground operations and autonomous on-board activity execution. An interpretation of the current situation is provided, together with a description of potential future approaches for deep space exploration missions. PMID:26290898

  17. Quantitative analysis of synaptic release at the photoreceptor synapse.

    PubMed

    Duncan, Gabriel; Rabl, Katalin; Gemp, Ian; Heidelberger, Ruth; Thoreson, Wallace B

    2010-05-19

    Exocytosis from the rod photoreceptor is stimulated by submicromolar Ca(2+) and exhibits an unusually shallow dependence on presynaptic Ca(2+). To provide a quantitative description of the photoreceptor Ca(2+) sensor for exocytosis, we tested a family of conventional and allosteric computational models describing the final Ca(2+)-binding steps leading to exocytosis. Simulations were fit to two measures of release, evoked by flash-photolysis of caged Ca(2+): exocytotic capacitance changes from individual rods and postsynaptic currents of second-order neurons. The best simulations supported the occupancy of only two Ca(2+) binding sites on the rod Ca(2+) sensor rather than the typical four or five. For most models, the on-rates for Ca(2+) binding and maximal fusion rate were comparable to those of other neurons. However, the off-rates for Ca(2+) unbinding were unexpectedly slow. In addition to contributing to the high-affinity of the photoreceptor Ca(2+) sensor, slow Ca(2+) unbinding may support the fusion of vesicles located at a distance from Ca(2+) channels. In addition, partial sensor occupancy due to slow unbinding may contribute to the linearization of the first synapse in vision. PMID:20483317

  18. Quantitative Analysis of Synaptic Release at the Photoreceptor Synapse

    PubMed Central

    Duncan, Gabriel; Rabl, Katalin; Gemp, Ian; Heidelberger, Ruth; Thoreson, Wallace B.

    2010-01-01

    Abstract Exocytosis from the rod photoreceptor is stimulated by submicromolar Ca2+ and exhibits an unusually shallow dependence on presynaptic Ca2+. To provide a quantitative description of the photoreceptor Ca2+ sensor for exocytosis, we tested a family of conventional and allosteric computational models describing the final Ca2+-binding steps leading to exocytosis. Simulations were fit to two measures of release, evoked by flash-photolysis of caged Ca2+: exocytotic capacitance changes from individual rods and postsynaptic currents of second-order neurons. The best simulations supported the occupancy of only two Ca2+ binding sites on the rod Ca2+ sensor rather than the typical four or five. For most models, the on-rates for Ca2+ binding and maximal fusion rate were comparable to those of other neurons. However, the off-rates for Ca2+ unbinding were unexpectedly slow. In addition to contributing to the high-affinity of the photoreceptor Ca2+ sensor, slow Ca2+ unbinding may support the fusion of vesicles located at a distance from Ca2+ channels. In addition, partial sensor occupancy due to slow unbinding may contribute to the linearization of the first synapse in vision. PMID:20483317

  19. Quantitative analysis of task selection for brain-computer interfaces

    NASA Astrophysics Data System (ADS)

    Llera, Alberto; Gómez, Vicenç; Kappen, Hilbert J.

    2014-10-01

    Objective. To assess quantitatively the impact of task selection in the performance of brain-computer interfaces (BCI). Approach. We consider the task-pairs derived from multi-class BCI imagery movement tasks in three different datasets. We analyze for the first time the benefits of task selection on a large-scale basis (109 users) and evaluate the possibility of transferring task-pair information across days for a given subject. Main results. Selecting the subject-dependent optimal task-pair among three different imagery movement tasks results in approximately 20% potential increase in the number of users that can be expected to control a binary BCI. The improvement is observed with respect to the best task-pair fixed across subjects. The best task-pair selected for each subject individually during a first day of recordings is generally a good task-pair in subsequent days. In general, task learning from the user side has a positive influence in the generalization of the optimal task-pair, but special attention should be given to inexperienced subjects. Significance. These results add significant evidence to existing literature that advocates task selection as a necessary step towards usable BCIs. This contribution motivates further research focused on deriving adaptive methods for task selection on larger sets of mental tasks in practical online scenarios.

  20. Radiomorphometric quantitative analysis of vasculature utilizing micro-computed tomography and vessel perfusion in the murine mandible.

    PubMed

    Jing, Xi Lin; Farberg, Aaron S; Monson, Laura A; Donneys, Alexis; Tchanque-Fossuo, Catherine N; Buchman, Steven R

    2012-12-01

    Purpose Biomechanical, densitometric, and histological analyses have been the mainstay for reproducible outcome measures for investigation of new bone formation and osseous healing. Here we report the addition of radiomorphometric vascular analysis as a quantitative measure of vascularity in the murine mandible. To our knowledge this is the first description of using micro-computed tomography (micro-CT) to evaluate the temporal and spatial pattern of angiogenesis in the craniofacial skeleton. Methods The vessel perfusion technique was performed on 10 Sprague-Dawley rats using Microfil (MV-122, Flow Tech; Carver, MA). After decalcification, hemimandibles were imaged using high-resolution micro-CT. Six separate radiomorphometric vascular metrics were calculated. Results Radiomorphometric values were analyzed using three different thresholds on micro-CT. Experimentally, 1000 Hounsfield units was found to be the optimal threshold for analysis to capture the maximal vascular content of the bone. Data from seven hemimandibles were analyzed. Minimal statistical variance in each of the quantitative measures of vascularity resulted in reproducible metrics for each of the radiomorphometric parameters. Conclusions We have demonstrated that micro-CT vascular imaging provides a robust methodology for evaluation of vascular networks in the craniofacial skeleton. This technique provides 3D quantitative data analysis that differs significantly from laser Doppler and microsphere methods, which simply measure flow. This technique is advantageous over labor-intensive 2D conventional analyses using histology and X-ray microangiography. Our data establish the appropriate thresholding for optimal vascular analyses and provide baseline measurements that can be used to analyze the role of angiogenesis in bone regeneration and repair in the craniofacial skeleton. PMID:24294405

  1. [Quantitative spectrum analysis of characteristic gases of spontaneous combustion coal].

    PubMed

    Liang, Yun-Tao; Tang, Xiao-Jun; Luo, Hai-Zhu; Sun, Yong

    2011-09-01

    Aimed at the characteristics of spontaneous combustion gas such as a variety of gases, lou limit of detection, and critical requirement of safety, Fourier transform infrared (FTIR) spectral analysis is presented to analyze characteristic gases of spontaneous combustion In this paper, analysis method is introduced at first by combing characteristics of absorption spectra of analyte and analysis requirement. Parameter setting method, sample preparation, feature variable abstract and analysis model building are taken into consideration. The methods of sample preparation, feature abstraction and analysis model are introduced in detail. And then, eleven kinds of gases were tested with Tensor 27 spectrometer. CH4, C2H6, C3H8, iC4H10, nC4H10, C2 H4, C3 H6, C3 H2, SF6, CO and CO2 were included. The optical path length was 10 cm while the spectra resolution was set as 1 cm(-1). The testing results show that the detection limit of all analytes is less than 2 x 10(-6). All the detection limits fit the measurement requirement of spontaneous combustion gas, which means that FTIR may be an ideal instrument and the analysis method used in this paper is competent for spontaneous combustion gas measurement on line. PMID:22097853

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

    PubMed Central

    Hur, Kwang-Ho; Mueller, Joachim D.

    2015-01-01

    The brightness measured by fluorescence fluctuation spectroscopy specifies the average stoichiometry of a labeled protein in a sample. Here we extended brightness analysis, which has been mainly applied in eukaryotic cells, to prokaryotic cells with E. coli serving as a model system. The small size of the E. coli cell introduces unique challenges for applying brightness analysis that are addressed in this work. Photobleaching leads to a depletion of fluorophores and a reduction of the brightness of protein complexes. In addition, the E. coli cell and the point spread function of the instrument only partially overlap, which influences intensity fluctuations. To address these challenges we developed MSQ analysis, which is based on the mean Q-value of segmented photon count data, and combined it with the analysis of axial scans through the E. coli cell. The MSQ method recovers brightness, concentration, and diffusion time of soluble proteins in E. coli. We applied MSQ to measure the brightness of EGFP in E. coli and compared it to solution measurements. We further used MSQ analysis to determine the oligomeric state of nuclear transport factor 2 labeled with EGFP expressed in E. coli cells. The results obtained demonstrate the feasibility of quantifying the stoichiometry of proteins by brightness analysis in a prokaryotic cell. PMID:26099032

  3. Fractal analysis and graph theory applied to the spatial and temporal variability of soil water content

    NASA Astrophysics Data System (ADS)

    Vieira, Sidney R.; Vidal Vázquez, Eva; Miranda, José G. V.; Paz Ferreiro, Jorge; Topp, George C.

    2010-05-01

    Spatial and temporal variability of soil moisture content has been frequently evaluated using statistical and geostatistical methods for several issues. For example, the statistical study of the temporal persistence or temporal stability in spatial patterns of soil moisture content has found interest to improve soil water monitoring strategies and to correct the average soil water content for missing data. Fractal analysis and graph theory are additional tools that can provide information and further insight to assess and to model indirect or hidden interactions in soil moisture content. In fractal analysis the fractal dimension (D) is an indicator of the pattern and extent of spatial and/or temporal variability. Large D values indicate the importance of short-range variation, while small D values reflect the importance of long-range variation when spatial and temporal data sets are analyzed. Moreover, for spatial and temporal variability, D can range from 1 to 2 for a profile and from 2 to 3 for a two dimensional network. Moreover, as the fractal dimension value increases the degree of roughness also increases. Graph theory tools take into account network structure by modelling pair wise relations between objects, which allow considering explicitly spatial-temporal connectivity of a given data set. The objective of this study was to use fractal analysis and graph theory to characterize the pattern of spatial and temporal variability of soil moisture content. The experimental field was located at Ottawa, Canada. Volumetric water content was monitored using Time Domain Reflectometry (TDR) during 34 dates at 164 locations per date. The depth of the TDR probes was 20 cm. The first and last measurements were 21 month apart and no data were taken in winter when the soil was covered by snow. The fractal dimension, D, was estimated from the slope of the regression line of log semivariogram versus distance for each of studied data sets. Using graph theory various

  4. [Quantitative Analysis of Immuno-fluorescence of Nuclear Factor-κB Activation].

    PubMed

    Xiu, Min; He, Feng; Lou, Yuanlei; Xu, Lu; Xiong Jieqi; Wang, Ping; Liu, Sisun; Guo, Fei

    2015-06-01

    Immuno-fluorescence technique can qualitatively determine certain nuclear translocation, of which NF-κB/ p65 implicates the activation of NF-κB signal pathways. Immuno-fluorescence analysis software with independent property rights is able to quantitatively analyze dynamic location of NF-κB/p65 by computing relative fluorescence units in nuclei and cytoplasm. We verified the quantitative analysis by Western Blot. When we applied the software to analysis of nuclear translocation in lipopolysaccharide (LPS) induced (0. 5 h, 1 h, 2 h, 4 h) primary human umbilical vein endothelial cells (HUVECs) , we found that nuclear translocation peak showed up at 2h as with calculated Western blot verification results, indicating that the inventive immuno-fluorescence analysis software can be applied to the quantitative analysis of immuno-fluorescence. PMID:26485997

  5. Quantitative assessment of human motion using video motion analysis

    NASA Technical Reports Server (NTRS)

    Probe, John D.

    1993-01-01

    In the study of the dynamics and kinematics of the human body a wide variety of technologies has been developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development, coupled with recent advances in video technology, have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System (APAS) to develop data on shirtsleeved and space-suited human performance in order to plan efficient on-orbit intravehicular and extravehicular activities. APAS is a fully integrated system of hardware and software for biomechanics and the analysis of human performance and generalized motion measurement. Major components of the complete system include the video system, the AT compatible computer, and the proprietary software.

  6. Multi-temporal MRI carpal bone volumes analysis by principal axes registration

    NASA Astrophysics Data System (ADS)

    Ferretti, Roberta; Dellepiane, Silvana

    2016-03-01

    In this paper, a principal axes registration technique is presented, with the relevant application to segmented volumes. The purpose of the proposed registration is to compare multi-temporal volumes of carpal bones from Magnetic Resonance Imaging (MRI) acquisitions. Starting from the study of the second-order moment matrix, the eigenvectors are calculated to allow the rotation of volumes with respect to reference axes. Then the volumes are spatially translated to become perfectly overlapped. A quantitative evaluation of the results obtained is carried out by computing classical indices from the confusion matrix, which depict similarity measures between the volumes of the same organ as extracted from MRI acquisitions executed at different moments. Within the medical field, the way a registration can be used to compare multi-temporal images is of great interest, since it provides the physician with a tool which allows a visual monitoring of a disease evolution. The segmentation method used herein is based on the graph theory and is a robust, unsupervised and parameters independent method. Patients affected by rheumatic diseases have been considered.

  7. Quantitative Analysis of 3′-Hydroxynorcotinine in Human Urine

    PubMed Central

    Upadhyaya, Pramod

    2015-01-01

    Introduction: Based on previous metabolism studies carried out in patas monkeys, we hypothesized that urinary 3′-hydroxynorcotinine could be a specific biomarker for uptake and metabolism of the carcinogen N′-nitrosonornicotine in people who use tobacco products. Methods: We developed a method for quantitation of 3′-hydroxynorcotinine in human urine. [Pyrrolidinone-13C4]3′-hydroxynorcotinine was added to urine as an internal standard, the samples were treated with β-glucuronidase, partially purified by solid supported liquid extraction and quantified by liquid chromatography–electrospray ionization–tandem mass spectrometry. Results: The method was accurate (average accuracy = 102%) and precise (coefficient of variation = 5.6%) in the range of measurement. 3′-Hydroxynorcotinine was detected in 48 urine samples from smokers (mean 393±287 pmol/ml urine) and 12 samples from individuals who had stopped smoking and were using the nicotine patch (mean 658±491 pmol/ml urine), but not in any of 10 samples from nonsmokers. Conclusions: Since the amounts of 3′-hydroxynorcotinine found in smokers’ urine were approximately 50 times greater than the anticipated daily dose of N′-nitrosonornicotine, we concluded that it is a metabolite of nicotine or one of its metabolites, comprising perhaps 1% of nicotine intake in smokers. Therefore, it would not be suitable as a specific biomarker for uptake and metabolism of N′-nitrosonornicotine. Since 3′-hydroxynorcotinine has never been previously reported as a constituent of human urine, further studies are required to determine its source and mode of formation. PMID:25324430

  8. Quantitative analysis of nailfold capillary morphology in patients with fibromyalgia

    PubMed Central

    Choi, Dug-Hyun

    2015-01-01

    Background/Aims Nailfold capillaroscopy (NFC) has been used to examine morphological and functional microcirculation changes in connective tissue diseases. It has been demonstrated that NFC patterns reflect abnormal microvascular dynamics, which may play a role in fibromyalgia (FM) syndrome. The aim of this study was to determine NFC patterns in FM, and their association with clinical features of FM. Methods A total of 67 patients with FM, and 30 age- and sex-matched healthy controls, were included. Nailfold capillary patterns were quantitatively analyzed using computerized NFC. The parameters of interest were as follows: number of capillaries within the central 3 mm, deletion score, apical limb width, capillary width, and capillary dimension. Capillary dimension was determined by calculating the number of capillaries using the Adobe Photoshop version 7.0. Results FM patients had a lower number of capillaries and higher deletion scores on NFC compared to healthy controls (17.3 ± 1.7 vs. 21.8 ± 2.9, p < 0.05; 2.2 ± 0.9 vs. 0.7 ± 0.6, p < 0.05, respectively). Both apical limb width (µm) and capillary width (µm) were significantly decreased in FM patients (1.1 ± 0.2 vs. 3.7 ± 0.6; 5.4 ± 0.5 vs. 7.5 ± 1.4, respectively), indicating that FM patients have abnormally decreased digital capillary diameter and density. Interestingly, there was no difference in capillary dimension between the two groups, suggesting that the length or tortuosity of capillaries in FM patients is increased to compensate for diminished microcirculation. Conclusions FM patients had altered capillary density and diameter in the digits. Diminished microcirculation on NFC may alter capillary density and increase tortuosity. PMID:26161020

  9. Quantitative analysis of wrist electrodermal activity during sleep.

    PubMed

    Sano, Akane; Picard, Rosalind W; Stickgold, Robert

    2014-12-01

    We present the first quantitative characterization of electrodermal activity (EDA) patterns on the wrists of healthy adults during sleep using dry electrodes. We compare the new results on the wrist to the prior findings on palmar or finger EDA by characterizing data measured from 80 nights of sleep consisting of 9 nights of wrist and palm EDA from 9 healthy adults sleeping at home, 56 nights of wrist and palm EDA from one healthy adult sleeping at home, and 15 nights of wrist EDA from 15 healthy adults in a sleep laboratory, with the latter compared to concurrent polysomnography. While high frequency patterns of EDA called "storms" were identified by eye in the 1960s, we systematically compare thresholds for automatically detecting EDA peaks and establish criteria for EDA storms. We found that more than 80% of the EDA peaks occurred in non-REM sleep, specifically during slow-wave sleep (SWS) and non-REM stage 2 sleep (NREM2). Also, EDA amplitude is higher in SWS than in other sleep stages. Longer EDA storms were more likely to occur in the first two quarters of sleep and during SWS and NREM2. We also found from the home studies (65 nights) that EDA levels were higher and the skin conductance peaks were larger and more frequent when measured on the wrist than when measured on the palm. These EDA high frequency peaks and high amplitude were sometimes associated with higher skin temperature, but more work is needed looking at neurological and other EDA elicitors in order to elucidate their complete behavior. PMID:25286449

  10. Spatio-Temporal Gap Analysis of OBIS-SEAMAP Project Data: Assessment and Way Forward

    PubMed Central

    Kot, Connie Y.; Fujioka, Ei; Hazen, Lucie J.; Best, Benjamin D.; Read, Andrew J.; Halpin, Patrick N.

    2010-01-01

    The OBIS-SEAMAP project has acquired and served high-quality marine mammal, seabird, and sea turtle data to the public since its inception in 2002. As data accumulated, spatial and temporal biases resulted and a comprehensive gap analysis was needed in order to assess coverage to direct data acquisition for the OBIS-SEAMAP project and for taxa researchers should true gaps in knowledge exist. All datasets published on OBIS-SEAMAP up to February 2009 were summarized spatially and temporally. Seabirds comprised the greatest number of records, compared to the other two taxa, and most records were from shipboard surveys, compared to the other three platforms. Many of the point observations and polyline tracklines were located in northern and central Atlantic and the northeastern and central-eastern Pacific. The Southern Hemisphere generally had the lowest representation of data, with the least number of records in the southern Atlantic and western Pacific regions. Temporally, records of observations for all taxa were the lowest in fall although the number of animals sighted was lowest in the winter. Oceanographic coverage of observations varied by platform for each taxa, which showed that using two or more platforms represented habitat ranges better than using only one alone. Accessible and published datasets not already incorporated do exist within spatial and temporal gaps identified. Other related open-source data portals also contain data that fill gaps, emphasizing the importance of dedicated data exchange. Temporal and spatial gaps were mostly a result of data acquisition effort, development of regional partnerships and collaborations, and ease of field data collection. Future directions should include fostering partnerships with researchers in the Southern Hemisphere while targeting datasets containing species with limited representation. These results can facilitate prioritizing datasets needed to be represented and for planning research for true gaps in space

  11. EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis.

    PubMed

    Pulido-Tamayo, Sergio; Duitama, Jorge; Marchal, Kathleen

    2016-07-01

    Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/. PMID:27105844

  12. Development of spatial-temporal ventilation heterogeneity and probability analysis tools for hyperpolarized 3He magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Choy, S.; Ahmed, H.; Wheatley, A.; McCormack, D. G.; Parraga, G.

    2010-03-01

    We developed image analysis tools to evaluate spatial and temporal 3He magnetic resonance imaging (MRI) ventilation in asthma and cystic fibrosis. We also developed temporal ventilation probability maps to provide a way to describe and quantify ventilation heterogeneity over time, as a way to test respiratory exacerbations or treatment predictions and to provide a discrete probability measurement of 3He ventilation defect persistence.

  13. Physically-based quantitative analysis of soil erosion induced by heavy rainfall on steep slopes

    NASA Astrophysics Data System (ADS)

    Della Sala, Maria; Cuomo, Sabatino; Novità, Antonio

    2014-05-01

    Heavy rainstorms cause either shallow landslides or soil superficial erosion in steep hillslopes covered by coarse unsaturated soils (Cascini et al., 2013), even over large areas (Cuomo and Della Sala, 2013a). The triggering stage of both phenomena is related to ground infiltration, runoff and overland flow (Cuomo and Della Sala, 2013), which are key processes to be investigated. In addition, the mobilization of solid particles deserves a proper physical-based modeling whether a quantitative estimation of solid particles discharge at the outlet of mountain basin is required. In this work, the approaches for soil superficial erosion analysis are firstly reviewed; then, a relevant case study of two medium-sized mountain basins, affected by flow-like phenomena with huge consequences (Cascini et al., 2009) is presented, which motivates a parametric numerical analysis with a physically-based model carried out for a wide class of soil properties and rainfall scenarios (Cuomo et al., 2013b). The achieved results outline that the peak discharge of water and solid particles driven by overland flow depends on rainfall intensity while volumetric solid concentration within the washout is related to the morphometric features of the whole mountain basin. Furthermore, soil suction is outlined as a key factor for the spatial-temporal evolution of infiltration and runoff in the basin, also affecting the discharge of water and solid particles at the outlet of the basin. Based on these insights, selected cases are analyzed aimed to provide a wide class of possible slope erosion scenarios. It is shown that, provided the same amount of cumulated rainfall, the sequence of high and low intensity rainfall events strongly affects the time-discharge at the outlet of the basin without significant variations of the maximum volumetric solid concentration. References Cascini, L., Cuomo, S., Ferlisi, S., Sorbino, G. (2009). Detection of mechanisms for destructive landslides in Campania region

  14. Quantitative analysis and purity evaluation of medroxyprogesterone acetate by HPLC.

    PubMed

    Cavina, G; Valvo, L; Alimenti, R

    1985-01-01

    A reversed-phase high-performance liquid chromatographic method was developed for the assay of medroxyprogesterone acetate and for the detection and determination of related steroids present as impurities in the drug. The method was compared with the normal-phase technique of the USP XX and was also applied to the analysis of tablets and injectable suspensions. PMID:16867645

  15. Quantitative modeling and analysis in environmental studies. Technical report

    SciTech Connect

    Gaver, D.P.

    1994-10-01

    This paper reviews some of the many mathematical modeling and statistical data analysis problems that arise in environmental studies. It makes no claim to be comprehensive nor truly up-to-date. It will appear as a chapter in a book on ecotoxicology to be published by CRC Press, probably in 1995. Workshops leading to the book creation were sponsored by The Conte Foundation.

  16. Procedures for Quantitative Analysis of Change Facilitator Interventions.

    ERIC Educational Resources Information Center

    Hord, Shirley M.; Hall, Gene E.

    The procedures and coding schema that have been developed by the Research on the Improvement Process (RIP) Program for analyzing the frequency of interventions and for examining their internal characteristics are described. In two in-depth ethnographic studies of implementation efforts, interventions were the focus of data collection and analysis.…

  17. Regression Commonality Analysis: A Technique for Quantitative Theory Building

    ERIC Educational Resources Information Center

    Nimon, Kim; Reio, Thomas G., Jr.

    2011-01-01

    When it comes to multiple linear regression analysis (MLR), it is common for social and behavioral science researchers to rely predominately on beta weights when evaluating how predictors contribute to a regression model. Presenting an underutilized statistical technique, this article describes how organizational researchers can use commonality…

  18. Concentration Analysis: A Quantitative Assessment of Student States.

    ERIC Educational Resources Information Center

    Bao, Lei; Redish, Edward F.

    2001-01-01

    Explains that multiple-choice tests such as the Force Concept Inventory (FCI) provide useful instruments to probe the distribution of student difficulties on a large scale. Introduces a new method, concentration analysis, to measure how students' responses on multiple-choice questions are distributed. (Contains 18 references.) (Author/YDS)

  19. Concentration Analysis: A Quantitative Assessment of Student States.

    ERIC Educational Resources Information Center

    Bao, Lei; Redish, Edward F.

    Multiple-choice tests such as the Force Concept Inventory (FCI) provide useful instruments to probe the distribution of student difficulties on a large scale. However, traditional analysis often relies solely on scores (number of students giving the correct answer). This ignores what can be significant and important information: the distribution…

  20. Reflectance spectroscopy: quantitative analysis techniques for remote sensing applications.

    USGS Publications Warehouse

    Clark, R.N.; Roush, T.L.

    1984-01-01

    Several methods for the analysis of remotely sensed reflectance data are compared, including empirical methods and scattering theories, both of which are important for solving remote sensing problems. The concept of the photon mean path length and the implications for use in modeling reflectance spectra are presented.-from Authors

  1. Using principal component analysis to monitor spatial and temporal changes in water quality.

    PubMed

    Bengraïne, Karim; Marhaba, Taha F

    2003-06-27

    Chemical, biological and physical data monitored at 12 locations along the Passaic River, New Jersey, during the year 1998 are analyzed. Principal component analysis (PCA) was used: (i) to extract the factors associated with the hydrochemistry variability; (ii) to obtain the spatial and temporal changes in the water quality. Solute content, temperature, nutrients and organics were the main patterns extracted. The spatial analysis isolated two stations showing a possible point or non-point source of pollution. This study shows the importance of environmental monitoring associated with simple but powerful statistics to better understand a complex water system. PMID:12835021

  2. Development of an apnea detection algorithm based on temporal analysis of thoracic respiratory effort signal

    NASA Astrophysics Data System (ADS)

    Dell’Aquila, C. R.; Cañadas, G. E.; Correa, L. S.; Laciar, E.

    2016-04-01

    This work describes the design of an algorithm for detecting apnea episodes, based on analysis of thorax respiratory effort signal. Inspiration and expiration time, and range amplitude of respiratory cycle were evaluated. For range analysis the standard deviation statistical tool was used over respiratory signal temporal windows. The validity of its performance was carried out in 8 records of Apnea-ECG database that has annotations of apnea episodes. The results are: sensitivity (Se) 73%, specificity (Sp) 83%. These values can be improving eliminating artifact of signal records.

  3. Quantitative histology analysis of the ovarian tumour microenvironment.

    PubMed

    Lan, Chunyan; Heindl, Andreas; Huang, Xin; Xi, Shaoyan; Banerjee, Susana; Liu, Jihong; Yuan, Yinyin

    2015-01-01

    Concerted efforts in genomic studies examining RNA transcription and DNA methylation patterns have revealed profound insights in prognostic ovarian cancer subtypes. On the other hand, abundant histology slides have been generated to date, yet their uses remain very limited and largely qualitative. Our goal is to develop automated histology analysis as an alternative subtyping technology for ovarian cancer that is cost-efficient and does not rely on DNA quality. We developed an automated system for scoring primary tumour sections of 91 late-stage ovarian cancer to identify single cells. We demonstrated high accuracy of our system based on expert pathologists' scores (cancer = 97.1%, stromal = 89.1%) as well as compared to immunohistochemistry scoring (correlation = 0.87). The percentage of stromal cells in all cells is significantly associated with poor overall survival after controlling for clinical parameters including debulking status and age (multivariate analysis p = 0.0021, HR = 2.54, CI = 1.40-4.60) and progression-free survival (multivariate analysis p = 0.022, HR = 1.75, CI = 1.09-2.82). We demonstrate how automated image analysis enables objective quantification of microenvironmental composition of ovarian tumours. Our analysis reveals a strong effect of the tumour microenvironment on ovarian cancer progression and highlights the potential of therapeutic interventions that target the stromal compartment or cancer-stroma signalling in the stroma-high, late-stage ovarian cancer subset. PMID:26573438

  4. Clinical value of quantitative analysis of ST slope during exercise.

    PubMed Central

    Ascoop, C A; Distelbrink, C A; De Lang, P A

    1977-01-01

    The diagnostic performance of automatic analysis of the exercise electrocardiogram in detecting ischaemic heart disease was studied in 147 patients with angiographically documented coronary disease. The results were compared with the results of visual analysis of the same recordings. Using a bicycle ergometer we tried to reach at least 90 per cent of the predicted maximal heart rate of the patient. Two bipolar thoracic leads (CM5, CC5) were used. In the visual analysis the criterion of the so-called ischaemic ST segment was applied. For the automatic analysis the population was divided into a learning group (N=87) and a testing group (N=60). In the learning group first critical values were computed for different ST measurements that provided optimal separation between patients with (CAG POS.) and without (CAG. NEG.) significant coronary stenoses as revealed by coronary arteriography. These critical values were kept unchanged when applied to the testing group. With respect to the visual method an increase of the sensitivity by 0-45 and 0-36 was obtained by the automatic analysis in the learning and testing group, respectively. The best separation between CAG. POS. and CAG. NEG. group was reached using a criterion consisting of a linear combination of the slope of the initial part of the ST segment and the ST depression; the sensitivity being 0-70 and 0-60, respectively, in the learning and testing group. Using a criterion based on the area between the baseline and the ST segment (the SX integral) these values were 0-42 and 0-49, respectively. All specificities were kept to at least 0-90. PMID:319813

  5. Quantitative analysis of acrylamide labeled serum proteins by LC-MS/MS.

    PubMed

    Faca, Vitor; Coram, Marc; Phanstiel, Doug; Glukhova, Veronika; Zhang, Qing; Fitzgibbon, Matthew; McIntosh, Martin; Hanash, Samir

    2006-08-01

    Isotopic labeling of cysteine residues with acrylamide was previously utilized for relative quantitation of proteins by MALDI-TOF. Here, we explored and compared the application of deuterated and (13)C isotopes of acrylamide for quantitative proteomic analysis using LC-MS/MS and high-resolution FTICR mass spectrometry. The method was applied to human serum samples that were immunodepleted of abundant proteins. Our results show reliable quantitation of proteins across an abundance range that spans 5 orders of magnitude based on ion intensities and known protein concentration in plasma. The use of (13)C isotope of acrylamide had a slightly greater advantage relative to deuterated acrylamide, because of shifts in elution of deuterated acrylamide relative to its corresponding nondeuterated compound by reversed-phase chromatography. Overall, the use of acrylamide for differentially labeling intact proteins in complex mixtures, in combination with LC-MS/MS provides a robust method for quantitative analysis of complex proteomes. PMID:16889424

  6. Analysis and modelling of spatio-temporal properties of daily rainfall over the Danube basin

    NASA Astrophysics Data System (ADS)

    Serinaldi, F.; Kilsby, C. G.

    2012-04-01

    Central and Eastern Europe are prone to severe floods due to heavy rainfall that cause societal and economic damages, ranging from agriculture to water resources, from the insurance/reinsurance sector to the energy industry. To improve the flood risk analysis, a better characterisation and modelling of the rainfall patterns over this area, which involves the Danube river watershed, is strategically important. In this study, we analyse the spatio-temporal properties of a large data set of daily rainfall time series from 15 countries in the Central Eastern Europe through different lagged and non-lagged indices of associations that quantify both the overall dependence and extreme dependence of pairwise observations. We also show that these measures are linked to each other and can be written in a unique and coherent notation within the copula framework. Moreover, the lagged version of these measures allows exploring some important spatio-temporal properties of the rainfall fields. The exploratory analysis is complemented by the preliminary results of a spatio-temporal rainfall simulation performed via a compound model based upon the Generalized Additive Models for Location, Scale and Shape (GAMLSS) and meta-elliptical multivariate distributions.

  7. Spatio-temporal analysis of Rayleigh-B{acute e}nard convection

    SciTech Connect

    Lainscsek, C.S.; Schuerrer, F.

    1996-06-01

    The analysis of Rayleigh-B{acute e}nard convection in a thin layer of an incompressible fluid caused by heating from below, is based on the Navier-Stokes equations. In planar geometry the Navier-Stokes equations in Bousinesq-approximation reduce to two nonlinear coupled partial differential equations for the velocity flux function {xi} and the temperature deviation {theta}. These equations are analyzed in form of spatial Fourier modes with time-dependent amplitudes. Only modes corresponding to free-free boundary conditions were selected. In this way, a set of ten coupled nonlinear ordinary differential equations for the mode amplitudes was obtained. These equations were solved numerically for different Rayleigh numbers. The temporal information in the ten dimensional phase space of the mode amplitudes is analyzed with respect to the dimension of the attractor. In addition, a time series of flow patterns in real space is constructed. For this spatio-temporal patterns the empirical orthonormal functions are determined and used to find the temporal evolution from the projection onto the basic vectors. Finally the result of different types of analysis were compared. This should lead to a better understanding how to analyze real systems in terms of observational data, e.g., thermal convection on the surface of the sun. {copyright} {ital 1996 American Institute of Physics.}

  8. Tropical cyclone intensity estimation using temporal and image analysis of satellite data

    NASA Astrophysics Data System (ADS)

    Fetanat, G.; Homaifar, A.; Knapp, K.

    2012-12-01

    Tropical cyclones (TCs) are becoming an increasing threat to life and property. Developing an automated technique to estimate TC intensity and to overcome the existing errors in estimation is still a challenge. The Dvorak technique (DT) is the state-of-the-art method that has been used over three decades for estimating the intensity of a tropical cyclone. The DT subjectively estimates TC intensity based on visible and infrared satellite images. In spite of wide usage of the DT for TC analysis, it has some limitations. The most important one is that the DT does not use the valuable historical data mainly because of the challenges on computing and human resources. This research is inspired by the availability of historical TC satellite data. We hypothesize that discovering unknown regularities and abnormalities that may exist in the large group of past observations could help human experts interpret TC intensity changes from various points of view. Our goal is to provide a data mining tool that increases the ability of human experts to analyze huge amount of historical data for TC intensity estimation. The proposed intensity estimation algorithm has two parts: temporal constraints and image analysis. Temporal information provides a priori estimates of storm intensity (in terms of wind speed) prior to using any satellite image analysis. Hurricane Satellite data (HURSAT-B1) includes best-track intensity are used as a training data. A case study using North Atlantic Hurricane Satellite data from 1988-2009 is considered. The temporal analysis uses the age of the cyclone, 6, 12 and 24 hours prior intensities as predictors of the expected intensity. The 10 closest analogs (determined by a K-nearest-neighbor algorithm) are averaged to estimate the intensity. The distribution of intensity estimation errors of the proposed technique shows that 50% of the estimates have a mean absolute error less than 4.4 knots, 75% are 6.3 knots and 90% are within 8 knots. Several validation

  9. Quantitative analysis of cell-free DNA in ovarian cancer

    PubMed Central

    SHAO, XUEFENG; He, YAN; JI, MIN; CHEN, XIAOFANG; QI, JING; SHI, WEI; HAO, TIANBO; JU, SHAOQING

    2015-01-01

    The aim of the present study was to investigate the association between cell-free DNA (cf-DNA) levels and clinicopathological characteristics of patients with ovarian cancer using a branched DNA (bDNA) technique, and to determine the value of quantitative cf-DNA detection in assisting with the diagnosis of ovarian cancer. Serum specimens were collected from 36 patients with ovarian cancer on days 1, 3 and 7 following surgery, and additional serum samples were also collected from 22 benign ovarian tumor cases, and 19 healthy, non-cancerous ovaries. bDNA techniques were used to detect serum cf-DNA concentrations. All data were analyzed using SPSS version 18.0. The cf-DNA levels were significantly increased in the ovarian cancer group compared with those of the benign ovarian tumor group and healthy ovarian group (P<0.01). Furthermore, cf-DNA levels were significantly increased in stage III and IV ovarian cancer compared with those of stages I and II (P<0.01). In addition, cf-DNA levels were significantly increased on the first day post-surgery (P<0.01), and subsequently demonstrated a gradual decrease. In the ovarian cancer group, the area under the receiver operating characteristic curve of cf-DNA and the sensitivity were 0.917 and 88.9%, respectively, which was higher than those of cancer antigen 125 (0.724, 75%) and human epididymis protein 4 (0.743, 80.6%). There was a correlation between the levels of serum cf-DNA and the occurrence and development of ovarian cancer in the patients evaluated. bDNA techniques possessed higher sensitivity and specificity than other methods for the detection of serum cf-DNA in patients exhibiting ovarian cancer, and bDNA techniques are more useful for detecting cf-DNA than other factors. Thus, the present study demonstrated the potential value for the use of bDNA as an adjuvant diagnostic method for ovarian cancer. PMID:26788153

  10. Mass Spectrometric Analysis of Spatio-Temporal Dynamics of Crustacean Neuropeptides

    PubMed Central

    OuYang, Chuanzi; Liang, Zhidan; Li, Lingjun

    2014-01-01

    Neuropeptides represent one of the largest classes of signaling molecules used by nervous systems to regulate a wide range of physiological processes. Over the past several years, mass spectrometry (MS)-based strategies have revolutionized the discovery of neuropeptides in numerous model organisms, especially in decapod crustaceans. Here, we focus our discussion on recent advances in the use of MS-based techniques to map neuropeptides in spatial domain and monitoring their dynamic changes in temporal domain. These MS-enabled investigations provide valuable information about the distribution, secretion and potential function of neuropeptides with high molecular specificity and sensitivity. In situ MS imaging and in vivo microdialysis are highlighted as key technologies for probing spatio-temporal dynamics of neuropeptides in the crustacean nervous system. This review summarizes the latest advancement in MS-based methodologies for neuropeptide analysis including typical workflow and sample preparation strategies as well as major neuropeptide families discovered in decapod crustaceans. PMID:25448012

  11. Spatio-temporal registration in multiplane MRI acquisitions for 3D colon motiliy analysis

    NASA Astrophysics Data System (ADS)

    Kutter, Oliver; Kirchhoff, Sonja; Berkovich, Marina; Reiser, Maximilian; Navab, Nassir

    2008-03-01

    In this paper we present a novel method for analyzing and visualizing dynamic peristaltic motion of the colon in 3D from two series of differently oriented 2D MRI images. To this end, we have defined an MRI examination protocol, and introduced methods for spatio-temporal alignment of the two MRI image series into a common reference. This represents the main contribution of this paper, which enables the 3D analysis of peristaltic motion. The objective is to provide a detailed insight into this complex motion, aiding in the diagnosis and characterization of colon motion disorders. We have applied the proposed spatio-temporal method on Cine MRI data sets of healthy volunteers. The results have been inspected and validated by an expert radiologist. Segmentation and cylindrical approximation of the colon results in a 4D visualization of the peristaltic motion.

  12. Probabilistic reliability analysis, quantitative safety goals, and nuclear licensing in the United Kingdom.

    PubMed

    Cannell, W

    1987-09-01

    Although unpublicized, the use of quantitative safety goals and probabilistic reliability analysis for licensing nuclear reactors has become a reality in the United Kingdom. This conclusion results from an examination of the process leading to the licensing of the Sizewell B PWR in England. The licensing process for this reactor has substantial implications for nuclear safety standards in Britain, and is examined in the context of the growing trend towards quantitative safety goals in the United States. PMID:3685540

  13. Integrated quantitative fractal polarimetric analysis of monolayer lung cancer cells

    NASA Astrophysics Data System (ADS)

    Shrestha, Suman; Zhang, Lin; Quang, Tri; Farrahi, Tannaz; Narayan, Chaya; Deshpande, Aditi; Na, Ying; Blinzler, Adam; Ma, Junyu; Liu, Bo; Giakos, George C.

    2014-05-01

    Digital diagnostic pathology has become one of the most valuable and convenient advancements in technology over the past years. It allows us to acquire, store and analyze pathological information from the images of histological and immunohistochemical glass slides which are scanned to create digital slides. In this study, efficient fractal, wavelet-based polarimetric techniques for histological analysis of monolayer lung cancer cells will be introduced and different monolayer cancer lines will be studied. The outcome of this study indicates that application of fractal, wavelet polarimetric principles towards the analysis of squamous carcinoma and adenocarcinoma cancer cell lines may be proved extremely useful in discriminating among healthy and lung cancer cells as well as differentiating among different lung cancer cells.

  14. Quantitative Immunofluorescence Analysis of Nucleolus-Associated Chromatin.

    PubMed

    Dillinger, Stefan; Németh, Attila

    2016-01-01

    The nuclear distribution of eu- and heterochromatin is nonrandom, heterogeneous, and dynamic, which is mirrored by specific spatiotemporal arrangements of histone posttranslational modifications (PTMs). Here we describe a semiautomated method for the analysis of histone PTM localization patterns within the mammalian nucleus using confocal laser scanning microscope images of fixed, immunofluorescence stained cells as data source. The ImageJ-based process includes the segmentation of the nucleus, furthermore measurements of total fluorescence intensities, the heterogeneity of the staining, and the frequency of the brightest pixels in the region of interest (ROI). In the presented image analysis pipeline, the perinucleolar chromatin is selected as primary ROI, and the nuclear periphery as secondary ROI. PMID:27576710

  15. Fast multidimensional ensemble empirical mode decomposition for the analysis of big spatio-temporal datasets

    PubMed Central

    Wu, Zhaohua; Feng, Jiaxin; Qiao, Fangli; Tan, Zhe-Min

    2016-01-01

    In this big data era, it is more urgent than ever to solve two major issues: (i) fast data transmission methods that can facilitate access to data from non-local sources and (ii) fast and efficient data analysis methods that can reveal the key information from the available data for particular purposes. Although approaches in different fields to address these two questions may differ significantly, the common part must involve data compression techniques and a fast algorithm. This paper introduces the recently developed adaptive and spatio-temporally local analysis method, namely the fast multidimensional ensemble empirical mode decomposition (MEEMD), for the analysis of a large spatio-temporal dataset. The original MEEMD uses ensemble empirical mode decomposition to decompose time series at each spatial grid and then pieces together the temporal–spatial evolution of climate variability and change on naturally separated timescales, which is computationally expensive. By taking advantage of the high efficiency of the expression using principal component analysis/empirical orthogonal function analysis for spatio-temporally coherent data, we design a lossy compression method for climate data to facilitate its non-local transmission. We also explain the basic principles behind the fast MEEMD through decomposing principal components instead of original grid-wise time series to speed up computation of MEEMD. Using a typical climate dataset as an example, we demonstrate that our newly designed methods can (i) compress data with a compression rate of one to two orders; and (ii) speed-up the MEEMD algorithm by one to two orders. PMID:26953173

  16. Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

    PubMed Central

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L.; Ljubimova, Julia Y.; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  17. Watershed Planning within a Quantitative Scenario Analysis Framework.

    PubMed

    Merriam, Eric R; Petty, J Todd; Strager, Michael P

    2016-01-01

    There is a critical need for tools and methodologies capable of managing aquatic systems within heavily impacted watersheds. Current efforts often fall short as a result of an inability to quantify and predict complex cumulative effects of current and future land use scenarios at relevant spatial scales. The goal of this manuscript is to provide methods for conducting a targeted watershed assessment that enables resource managers to produce landscape-based cumulative effects models for use within a scenario analysis management framework. Sites are first selected for inclusion within the watershed assessment by identifying sites that fall along independent gradients and combinations of known stressors. Field and laboratory techniques are then used to obtain data on the physical, chemical, and biological effects of multiple land use activities. Multiple linear regression analysis is then used to produce landscape-based cumulative effects models for predicting aquatic conditions. Lastly, methods for incorporating cumulative effects models within a scenario analysis framework for guiding management and regulatory decisions (e.g., permitting and mitigation) within actively developing watersheds are discussed and demonstrated for 2 sub-watersheds within the mountaintop mining region of central Appalachia. The watershed assessment and management approach provided herein enables resource managers to facilitate economic and development activity while protecting aquatic resources and producing opportunity for net ecological benefits through targeted remediation. PMID:27501287

  18. Phase analysis in duplex stainless steel: comparison of EBSD and quantitative metallography methods

    NASA Astrophysics Data System (ADS)

    Michalska, J.; Chmiela, B.

    2014-03-01

    The purpose of the research was to work out the qualitative and quantitative analysis of phases in DSS in as-received state and after thermal aging. For quantitative purposes, SEM observations, EDS analyses and electron backscattered diffraction (EBSD) methods were employed. Qualitative analysis of phases was performed by two methods: EBSD and classical quantitative metallography. A juxtaposition of different etchants for the revealing of microstructure and brief review of sample preparation methods for EBSD studies were presented. Different ways of sample preparation were tested and based on these results a detailed methodology of DSS phase analysis was developed including: surface finishing, selective etching methods and image acquisition. The advantages and disadvantages of applied methods were pointed out and compared the accuracy of the analysis phase performed by both methods.

  19. Digitally Enhanced Thin-Layer Chromatography: An Inexpensive, New Technique for Qualitative and Quantitative Analysis

    ERIC Educational Resources Information Center

    Hess, Amber Victoria Irish

    2007-01-01

    A study conducted shows that if digital photography is combined with regular thin-layer chromatography (TLC), it could perform highly improved qualitative analysis as well as make accurate quantitative analysis possible for a much lower cost than commercial equipment. The findings suggest that digitally enhanced TLC (DE-TLC) is low-cost and easy…

  20. Kinetic Analysis of Amylase Using Quantitative Benedict's and Iodine Starch Reagents

    ERIC Educational Resources Information Center

    Cochran, Beverly; Lunday, Deborah; Miskevich, Frank

    2008-01-01

    Quantitative analysis of carbohydrates is a fundamental analytical tool used in many aspects of biology and chemistry. We have adapted a technique developed by Mathews et al. using an inexpensive scanner and open-source image analysis software to quantify amylase activity using both the breakdown of starch and the appearance of glucose. Breakdown…

  1. Integrating Data Analysis (IDA): Working with Sociology Departments to Address the Quantitative Literacy Gap

    ERIC Educational Resources Information Center

    Howery, Carla B.; Rodriguez, Havidan

    2006-01-01

    The NSF-funded Integrating Data Analysis (IDA) Project undertaken by the American Sociological Association (ASA) and the Social Science Data Analysis Network sought to close the quantitative literacy gap for sociology majors. Working with twelve departments, the project built on lessons learned from ASA's Minority Opportunities through School…

  2. A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals

    ERIC Educational Resources Information Center

    Takusi, Gabriel Samuto

    2010-01-01

    This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA…

  3. A Quantitative Content Analysis of Mercer University MEd, EdS, and Doctoral Theses

    ERIC Educational Resources Information Center

    Randolph, Justus J.; Gaiek, Lura S.; White, Torian A.; Slappey, Lisa A.; Chastain, Andrea; Harris, Rose Prejean

    2010-01-01

    Quantitative content analysis of a body of research not only helps budding researchers understand the culture, language, and expectations of scholarship, it helps identify deficiencies and inform policy and practice. Because of these benefits, an analysis of a census of 980 Mercer University MEd, EdS, and doctoral theses was conducted. Each thesis…

  4. Some remarks on the quantitative analysis of behavior

    PubMed Central

    Marr, M. Jackson

    1989-01-01

    This paper discusses similarities between the mathematization of operant behavior and the early history of the most mathematical of sciences—physics. Galileo explored the properties of motion without dealing with the causes of motion, focusing on changes in motion. Newton's dynamics were concerned with the action of forces as causes of change. Skinner's rationale for using rate to describe behavior derived from an interest in changes in rate. Reinforcement has played the role of force in the dynamics of behavior. Behavioral momentum and maximization have received mathematical formulations in behavior analysis. Yet to be worked out are the relations between molar and molecular formulations of behavioral theory. PMID:22478028

  5. Identifying severity of electroporation through quantitative image analysis

    NASA Astrophysics Data System (ADS)

    Morshed, Bashir I.; Shams, Maitham; Mussivand, Tofy

    2011-04-01

    Electroporation is the formation of reversible hydrophilic pores in the cell membrane under electric fields. Severity of electroporation is challenging to measure and quantify. An image analysis method is developed, and the initial results with a fabricated microfluidic device are reported. The microfluidic device contains integrated microchannels and coplanar interdigitated electrodes allowing low-voltage operation and low-power consumption. Noninvasive human buccal cell samples were specifically stained, and electroporation was induced. Captured image sequences were analyzed for pixel color ranges to quantify the severity of electroporation. The method can detect even a minor occurrence of electroporation and can perform comparative studies.

  6. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton.

    PubMed

    Pauli, Duke; Andrade-Sanchez, Pedro; Carmo-Silva, A Elizabete; Gazave, Elodie; French, Andrew N; Heun, John; Hunsaker, Douglas J; Lipka, Alexander E; Setter, Tim L; Strand, Robert J; Thorp, Kelly R; Wang, Sam; White, Jeffrey W; Gore, Michael A

    2016-01-01

    The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010-2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars. PMID:26818078

  7. Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton

    PubMed Central

    Pauli, Duke; Andrade-Sanchez, Pedro; Carmo-Silva, A. Elizabete; Gazave, Elodie; French, Andrew N.; Heun, John; Hunsaker, Douglas J.; Lipka, Alexander E.; Setter, Tim L.; Strand, Robert J.; Thorp, Kelly R.; Wang, Sam; White, Jeffrey W.; Gore, Michael A.

    2016-01-01

    The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010–2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars. PMID:26818078

  8. Quantitative proteomic analysis of cold-responsive proteins in rice.

    PubMed

    Neilson, Karlie A; Mariani, Michael; Haynes, Paul A

    2011-05-01

    Rice is susceptible to cold stress and with a future of climatic instability we will be unable to produce enough rice to satisfy increasing demand. A thorough understanding of the molecular responses to thermal stress is imperative for engineering cultivars, which have greater resistance to low temperature stress. In this study we investigated the proteomic response of rice seedlings to 48, 72 and 96 h of cold stress at 12-14°C. The use of both label-free and iTRAQ approaches in the analysis of global protein expression enabled us to assess the complementarity of the two techniques for use in plant proteomics. The approaches yielded a similar biological response to cold stress despite a disparity in proteins identified. The label-free approach identified 236 cold-responsive proteins compared to 85 in iTRAQ results, with only 24 proteins in common. Functional analysis revealed differential expression of proteins involved in transport, photosynthesis, generation of precursor metabolites and energy; and, more specifically, histones and vitamin B biosynthetic proteins were observed to be affected by cold stress. PMID:21433000

  9. Quantitative Computed Tomography and Image Analysis for Advanced Muscle Assessment

    PubMed Central

    Edmunds, Kyle Joseph; Gíslason, Magnus K.; Arnadottir, Iris D.; Marcante, Andrea; Piccione, Francesco; Gargiulo, Paolo

    2016-01-01

    Medical imaging is of particular interest in the field of translational myology, as extant literature describes the utilization of a wide variety of techniques to non-invasively recapitulate and quantity various internal and external tissue morphologies. In the clinical context, medical imaging remains a vital tool for diagnostics and investigative assessment. This review outlines the results from several investigations on the use of computed tomography (CT) and image analysis techniques to assess muscle conditions and degenerative process due to aging or pathological conditions. Herein, we detail the acquisition of spiral CT images and the use of advanced image analysis tools to characterize muscles in 2D and 3D. Results from these studies recapitulate changes in tissue composition within muscles, as visualized by the association of tissue types to specified Hounsfield Unit (HU) values for fat, loose connective tissue or atrophic muscle, and normal muscle, including fascia and tendon. We show how results from these analyses can be presented as both average HU values and compositions with respect to total muscle volumes, demonstrating the reliability of these tools to monitor, assess and characterize muscle degeneration. PMID:27478562

  10. Quantitative assessment of human body shape using Fourier analysis

    NASA Astrophysics Data System (ADS)

    Friess, Martin; Rohlf, F. J.; Hsiao, Hongwei

    2004-04-01

    Fall protection harnesses are commonly used to reduce the number and severity of injuries. Increasing the efficiency of harness design requires the size and shape variation of the user population to be assessed as detailed and as accurately as possible. In light of the unsatisfactory performance of traditional anthropometry with respect to such assessments, we propose the use of 3D laser surface scans of whole bodies and the statistical analysis of elliptic Fourier coefficients. Ninety-eight male and female adults were scanned. Key features of each torso were extracted as a 3D curve along front, back and the thighs. A 3D extension of Elliptic Fourier analysis4 was used to quantify their shape through multivariate statistics. Shape change as a function of size (allometry) was predicted by regressing the coefficients onto stature, weight and hip circumference. Upper and lower limits of torso shape variation were determined and can be used to redefine the design of the harness that will fit most individual body shapes. Observed allometric changes are used for adjustments to the harness shape in each size. Finally, the estimated outline data were used as templates for a free-form deformation of the complete torso surface using NURBS models (non-uniform rational B-splines).

  11. iTRAQ-Based Quantitative Proteomic Analysis of Nasopharyngeal Carcinoma.

    PubMed

    Cai, Xin-Zhang; Zeng, Wei-Qun; Xiang, Yi; Liu, Yi; Zhang, Hong-Min; Li, Hong; She, Sha; Yang, Min; Xia, Kun; Peng, Shi-Fang

    2015-07-01

    Nasopharyngeal carcinoma (NPC) is a common disease in the southern provinces of China with a poor prognosis. To better understand the pathogenesis of NPC and identify proteins involved in NPC carcinogenesis, we applied iTRAQ coupled with two-dimensional LC-MS/MS to compare the proteome profiles of NPC tissues and the adjacent non-tumor tissues. We identified 54 proteins with differential expression in NPC and the adjacent non-tumor tissues. The differentially expressed proteins were further determined by RT-PCR and Western blot analysis. In addition, the up-regulation of HSPB1, NPM1 and NCL were determined by immunohistochemistry using tissue microarray. Functionally, we found that siRNA mediated knockdown of NPM1 inhibited the migration and invasion of human NPC CNE1 cell line. In summary, this is the first study on proteome analysis of NPC tissues using an iTRAQ method, and we identified many new differentially expressed proteins which are potential targets for the diagnosis and therapy of NPC. PMID:25648846

  12. Mapping land cover gradients through analysis of hyper-temporal NDVI imagery

    NASA Astrophysics Data System (ADS)

    Ali, Amjad; de Bie, C. A. J. M.; Skidmore, A. K.; Scarrott, R. G.; Hamad, Amina; Venus, V.; Lymberakis, Petros

    2013-08-01

    The green cover of the earth exhibits various spatial gradients that represent gradual changes in space of vegetation density and/or in species composition. To date, land cover mapping methods differentiate at best, mapping units with different cover densities and/or species compositions, but typically fail to express such differences as gradients. Present interpretation techniques still make insufficient use of freely available spatial-temporal Earth Observation (EO) data that allow detection of existing land cover gradients. This study explores the use of hyper-temporal NDVI imagery to detect and delineate land cover gradients analyzing the temporal behavior of NDVI values. MODIS-Terra MVC-images (250 m, 16-day) of Crete, Greece, from February 2000 to July 2009 are used. The analysis approach uses an ISODATA unsupervised classification in combination with a Hierarchical Clustering Analysis (HCA). Clustering of class-specific temporal NDVI profiles through HCA resulted in the identification of gradients in landcover vegetation growth patterns. The detected gradients were arranged in a relational diagram, and mapped. Three groups of NDVI-classes were evaluated by correlating their class-specific annual average NDVI values with the field data (tree, shrub, grass, bare soil, stone, litter fraction covers). Multiple regression analysis showed that within each NDVI group, the fraction cover data were linearly related with the NDVI data, while NDVI groups were significantly different with respect to tree cover (adj. R2 = 0.96), shrub cover (adj. R2 = 0.83), grass cover (adj. R2 = 0.71), bare soil (adj. R2 = 0.88), stone cover (adj. R2 = 0.83) and litter cover (adj. R2 = 0.69) fractions. Similarly, the mean Sorenson dissimilarity values were found high and significant at confidence interval of 95% in all pairs of three NDVI groups. The study demonstrates that hyper-temporal NDVI imagery can successfully detect and map land cover gradients. The results may improve land

  13. [Quantitative analysis of seven phenolic acids in eight Yinqiao Jiedu serial preparations by quantitative analysis of multi-components with single-marker].

    PubMed

    Wang, Jun-jun; Zhang, Li; Guo, Qing; Kou, Jun-ping; Yu, Bo-yang; Gu, Dan-hua

    2015-04-01

    The study aims to develop a unified method to determine seven phenolic acids (neochlorogenic acid, chlorogenic acid, 4-caffeoylquinic acid, caffeic acid, isochlorogenic acid B, isochlorogenic acid A and isochlorogenic acid C) contained in honeysuckle flower that is the monarch drug of all the eight Yinqiao Jiedu serial preparations using quantitative analysis of multi-components by single-marker (QAMS). Firstly, chlorogenic acid was used as a reference to get the average relative correction factors (RCFs) of the other phenolic acids in ratios to the reference; columns and instruments from different companies were used to validate the durability of the achieved RCFs in different levels of standard solutions; and honeysuckle flower extract was used as the reference substance to fix the positions of chromatographic peaks. Secondly, the contents of seven phenolic acids in eight different Yinqiao Jiedu serial preparations samples were calculated based on the RCFs durability. Finally, the quantitative results were compared between QAMS and the external standard (ES) method. The results have showed that the durability of the achieved RCFs is good (RSD during 0.80% - 2.56%), and there are no differences between the quantitative results of QAMS and ES (the relative average deviation < 0.93%). So it can be successfully used to the quantitative control of honeysuckle flower principally prescribed in Yinqiao Jiedu serial preparations. PMID:26223132

  14. Quantitative Analysis of Spectral Impacts on Silicon Photodiode Radiometers: Preprint

    SciTech Connect

    Myers, D. R.

    2011-04-01

    Inexpensive broadband pyranometers with silicon photodiode detectors have a non-uniform spectral response over the spectral range of 300-1100 nm. The response region includes only about 70% to 75% of the total energy in the terrestrial solar spectral distribution from 300 nm to 4000 nm. The solar spectrum constantly changes with solar position and atmospheric conditions. Relative spectral distributions of diffuse hemispherical irradiance sky radiation and total global hemispherical irradiance are drastically different. This analysis convolves a typical photodiode response with SMARTS 2.9.5 spectral model spectra for different sites and atmospheric conditions. Differences in solar component spectra lead to differences on the order of 2% in global hemispherical and 5% or more in diffuse hemispherical irradiances from silicon radiometers. The result is that errors of more than 7% can occur in the computation of direct normal irradiance from global hemispherical irradiance and diffuse hemispherical irradiance using these radiometers.

  15. Quantitative radiographic analysis of fiber reinforced polymer composites.

    PubMed

    Baidya,