A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

PubMed

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

Preserved pontine glucose metabolism in Alzheimer disease: A reference region for functional brain image (PET) analysis

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

Minoshima, Satoshi; Frey, K.A.; Foster, N.L.

1995-07-01

Our goal was to examine regional preservation of energy metabolism in Alzheimer disease (AD) and to evaluate effects of PET data normalization to reference regions. Regional metabolic rates in the pons, thalamus, putamen, sensorimotor cortex, visual cortex, and cerebellum (reference regions) were determined stereotaxically and examined in 37 patients with probable AD and 22 normal controls based on quantitative {sup 18}FDG-PET measurements. Following normalization of metabolic rates of the parietotemporal association cortex and whole brain to each reference region, distinctions of the two groups were assessed. The pons showed the best preservation of glucose metabolism in AD. Other reference regionsmore » showed relatively preserved metabolism compared with the parietotemporal association cortex and whole brain, but had significant metabolic reduction. Data normalization to the pons not only enhanced statistical significance of metabolic reduction in the parietotemporal association cortex, but also preserved the presence of global cerebral metabolic reduction indicated in analysis of the quantitative data. Energy metabolism in the pons in probable AD is well preserved. The pons is a reliable reference for data normalization and will enhance diagnostic accuracy and efficiency of quantitative and nonquantitative functional brain imaging. 39 refs., 2 figs., 3 tabs.« less

Hyperspectral and differential CARS microscopy for quantitative chemical imaging in human adipocytes

PubMed Central

Di Napoli, Claudia; Pope, Iestyn; Masia, Francesco; Watson, Peter; Langbein, Wolfgang; Borri, Paola

2014-01-01

In this work, we demonstrate the applicability of coherent anti-Stokes Raman scattering (CARS) micro-spectroscopy for quantitative chemical imaging of saturated and unsaturated lipids in human stem-cell derived adipocytes. We compare dual-frequency/differential CARS (D-CARS), which enables rapid imaging and simple data analysis, with broadband hyperspectral CARS microscopy analyzed using an unsupervised phase-retrieval and factorization method recently developed by us for quantitative chemical image analysis. Measurements were taken in the vibrational fingerprint region (1200–2000/cm) and in the CH stretch region (2600–3300/cm) using a home-built CARS set-up which enables hyperspectral imaging with 10/cm resolution via spectral focussing from a single broadband 5 fs Ti:Sa laser source. Through a ratiometric analysis, both D-CARS and phase-retrieved hyperspectral CARS determine the concentration of unsaturated lipids with comparable accuracy in the fingerprint region, while in the CH stretch region D-CARS provides only a qualitative contrast owing to its non-linear behavior. When analyzing hyperspectral CARS images using the blind factorization into susceptibilities and concentrations of chemical components recently demonstrated by us, we are able to determine vol:vol concentrations of different lipid components and spatially resolve inhomogeneities in lipid composition with superior accuracy compared to state-of-the art ratiometric methods. PMID:24877002

Use of near infrared correlation spectroscopy for quantitation of surface iron, absorbed water and stored electronic energy in a suite of Mars soil analog materials

NASA Technical Reports Server (NTRS)

Coyne, Lelia M.; Banin, Amos; Carle, Glenn; Orenberg, James; Scattergood, Thomas

1989-01-01

A number of questions concerning the surface mineralogy and the history of water on Mars remain unresolved using the Viking analyses and Earth-based telescopic data. Identification and quantitation of iron-bearing clays on Mars would elucidate these outstanding issues. Near infrared correlation analysis, a method typically applied to qualitative and quantitative analysis of individual constituents of multicomponent mixtures, is adapted here to selection of distinctive features of a small, highly homologous series of Fe/Ca-exchanged montmorillonites and several kalinites. Independently determined measures of surface iron, relative humidity and stored electronic energy were used as constituent data for linear regression of the constituent vs. reflectance data throughout the spectral region 0.68 to 2.5 micrometers. High correlations were found in appropriate regions for all three constituents, though that with stored energy is still considered tenuous. Quantitation was improved using 1st and 2nd derivative spectra. High resolution data over a broad spectral range would be required to quantitatively identify iron-bearing clays by remotely sensed reflectance.

Defining an Analytic Framework to Evaluate Quantitative MRI Markers of Traumatic Axonal Injury: Preliminary Results in a Mouse Closed Head Injury Model

PubMed Central

Sadeghi, N.; Namjoshi, D.; Irfanoglu, M. O.; Wellington, C.; Diaz-Arrastia, R.

2017-01-01

Diffuse axonal injury (DAI) is a hallmark of traumatic brain injury (TBI) pathology. Recently, the Closed Head Injury Model of Engineered Rotational Acceleration (CHIMERA) was developed to generate an experimental model of DAI in a mouse. The characterization of DAI using diffusion tensor magnetic resonance imaging (MRI; diffusion tensor imaging, DTI) may provide a useful set of outcome measures for preclinical and clinical studies. The objective of this study was to identify the complex neurobiological underpinnings of DTI features following DAI using a comprehensive and quantitative evaluation of DTI and histopathology in the CHIMERA mouse model. A consistent neuroanatomical pattern of pathology in specific white matter tracts was identified across ex vivo DTI maps and photomicrographs of histology. These observations were confirmed by voxelwise and regional analysis of DTI maps, demonstrating reduced fractional anisotropy (FA) in distinct regions such as the optic tract. Similar regions were identified by quantitative histology and exhibited axonal damage as well as robust gliosis. Additional analysis using a machine-learning algorithm was performed to identify regions and metrics important for injury classification in a manner free from potential user bias. This analysis found that diffusion metrics were able to identify injured brains almost with the same degree of accuracy as the histology metrics. Good agreement between regions detected as abnormal by histology and MRI was also found. The findings of this work elucidate the complexity of cellular changes that give rise to imaging abnormalities and provide a comprehensive and quantitative evaluation of the relative importance of DTI and histological measures to detect brain injury. PMID:28966972

LANDSCAPE STRUCTURE AND ESTUARINE CONDITION IN THE MID-ATLANTIC REGION OF THE UNITED STATES: I. DEVELOPING QUANTITATIVE RELATIONSHIPS

EPA Science Inventory

In a previously published study, quantitative relationships were developed between landscape metrics and sediment contamination for 25 small estuarine systems within Chesapeake Bay. Nonparametric statistical analysis (rank transformation) was used to develop an empirical relation...

Receiver-operating-characteristic analysis of an automated program for analyzing striatal uptake of 123I-ioflupane SPECT images: calibration using visual reads.

PubMed

Kuo, Phillip Hsin; Avery, Ryan; Krupinski, Elizabeth; Lei, Hong; Bauer, Adam; Sherman, Scott; McMillan, Natalie; Seibyl, John; Zubal, George

2013-03-01

A fully automated objective striatal analysis (OSA) program that quantitates dopamine transporter uptake in subjects with suspected Parkinson's disease was applied to images from clinical (123)I-ioflupane studies. The striatal binding ratios or alternatively the specific binding ratio (SBR) of the lowest putamen uptake was computed, and receiver-operating-characteristic (ROC) analysis was applied to 94 subjects to determine the best discriminator using this quantitative method. Ninety-four (123)I-ioflupane SPECT scans were analyzed from patients referred to our clinical imaging department and were reconstructed using the manufacturer-supplied reconstruction and filtering parameters for the radiotracer. Three trained readers conducted independent visual interpretations and reported each case as either normal or showing dopaminergic deficit (abnormal). The same images were analyzed using the OSA software, which locates the striatal and occipital structures and places regions of interest on the caudate and putamen. Additionally, the OSA places a region of interest on the occipital region that is used to calculate the background-subtracted SBR. The lower SBR of the 2 putamen regions was taken as the quantitative report. The 33 normal (bilateral comma-shaped striata) and 61 abnormal (unilateral or bilateral dopaminergic deficit) studies were analyzed to generate ROC curves. Twenty-nine of the scans were interpreted as normal and 59 as abnormal by all 3 readers. For 12 scans, the 3 readers did not unanimously agree in their interpretations (discordant). The ROC analysis, which used the visual-majority-consensus interpretation from the readers as the gold standard, yielded an area under the curve of 0.958 when using 1.08 as the threshold SBR for the lowest putamen. The sensitivity and specificity of the automated quantitative analysis were 95% and 89%, respectively. The OSA program delivers SBR quantitative values that have a high sensitivity and specificity, compared with visual interpretations by trained nuclear medicine readers. Such a program could be a helpful aid for readers not yet experienced with (123)I-ioflupane SPECT images and if further adapted and validated may be useful to assess disease progression during pharmaceutical testing of therapies.

Practical applications of the bioinformatics toolbox for narrowing quantitative trait loci.

PubMed

Burgess-Herbert, Sarah L; Cox, Allison; Tsaih, Shirng-Wern; Paigen, Beverly

2008-12-01

Dissecting the genes involved in complex traits can be confounded by multiple factors, including extensive epistatic interactions among genes, the involvement of epigenetic regulators, and the variable expressivity of traits. Although quantitative trait locus (QTL) analysis has been a powerful tool for localizing the chromosomal regions underlying complex traits, systematically identifying the causal genes remains challenging. Here, through its application to plasma levels of high-density lipoprotein cholesterol (HDL) in mice, we demonstrate a strategy for narrowing QTL that utilizes comparative genomics and bioinformatics techniques. We show how QTL detected in multiple crosses are subjected to both combined cross analysis and haplotype block analysis; how QTL from one species are mapped to the concordant regions in another species; and how genomewide scans associating haplotype groups with their phenotypes can be used to prioritize the narrowed regions. Then we illustrate how these individual methods for narrowing QTL can be systematically integrated for mouse chromosomes 12 and 15, resulting in a significantly reduced number of candidate genes, often from hundreds to <10. Finally, we give an example of how additional bioinformatics resources can be combined with experiments to determine the most likely quantitative trait genes.

Rapid analysis of glucose, fructose, sucrose, and maltose in honeys from different geographic regions using fourier transform infrared spectroscopy and multivariate analysis.

PubMed

Wang, Jun; Kliks, Michael M; Jun, Soojin; Jackson, Mel; Li, Qing X

2010-03-01

Quantitative analysis of glucose, fructose, sucrose, and maltose in different geographic origin honey samples in the world using the Fourier transform infrared (FTIR) spectroscopy and chemometrics such as partial least squares (PLS) and principal component regression was studied. The calibration series consisted of 45 standard mixtures, which were made up of glucose, fructose, sucrose, and maltose. There were distinct peak variations of all sugar mixtures in the spectral "fingerprint" region between 1500 and 800 cm(-1). The calibration model was successfully validated using 7 synthetic blend sets of sugars. The PLS 2nd-derivative model showed the highest degree of prediction accuracy with a highest R(2) value of 0.999. Along with the canonical variate analysis, the calibration model further validated by high-performance liquid chromatography measurements for commercial honey samples demonstrates that FTIR can qualitatively and quantitatively determine the presence of glucose, fructose, sucrose, and maltose in multiple regional honey samples.

Quantitative analysis of glycated albumin in serum based on ATR-FTIR spectrum combined with SiPLS and SVM.

PubMed

Li, Yuanpeng; Li, Fucui; Yang, Xinhao; Guo, Liu; Huang, Furong; Chen, Zhenqiang; Chen, Xingdan; Zheng, Shifu

2018-08-05

A rapid quantitative analysis model for determining the glycated albumin (GA) content based on Attenuated total reflectance (ATR)-Fourier transform infrared spectroscopy (FTIR) combining with linear SiPLS and nonlinear SVM has been developed. Firstly, the real GA content in human serum was determined by GA enzymatic method, meanwhile, the ATR-FTIR spectra of serum samples from the population of health examination were obtained. The spectral data of the whole spectra mid-infrared region (4000-600 cm -1 ) and GA's characteristic region (1800-800 cm -1 ) were used as the research object of quantitative analysis. Secondly, several preprocessing steps including first derivative, second derivative, variable standardization and spectral normalization, were performed. Lastly, quantitative analysis regression models were established by using SiPLS and SVM respectively. The SiPLS modeling results are as follows: root mean square error of cross validation (RMSECV T ) = 0.523 g/L, calibration coefficient (R C ) = 0.937, Root Mean Square Error of Prediction (RMSEP T ) = 0.787 g/L, and prediction coefficient (R P ) = 0.938. The SVM modeling results are as follows: RMSECV T  = 0.0048 g/L, R C  = 0.998, RMSEP T  = 0.442 g/L, and R p  = 0.916. The results indicated that the model performance was improved significantly after preprocessing and optimization of characteristic regions. While modeling performance of nonlinear SVM was considerably better than that of linear SiPLS. Hence, the quantitative analysis model for GA in human serum based on ATR-FTIR combined with SiPLS and SVM is effective. And it does not need sample preprocessing while being characterized by simple operations and high time efficiency, providing a rapid and accurate method for GA content determination. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

PubMed Central

2012-01-01

Background Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings. Results We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments. Conclusions We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport. PMID:23148417

Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2

PubMed Central

Takahashi, Yuji; Shomura, Ayahiko; Sasaki, Takuji; Yano, Masahiro

2001-01-01

Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica variety Nipponbare and the indica variety Kasalath. To isolate a gene at Hd6, we used a large segregating population for the high-resolution and fine-scale mapping of Hd6 and constructed genomic clone contigs around the Hd6 region. Linkage analysis with P1-derived artificial chromosome clone-derived DNA markers delimited Hd6 to a 26.4-kb genomic region. We identified a gene encoding the α subunit of protein kinase CK2 (CK2α) in this region. The Nipponbare allele of CK2α contains a premature stop codon, and the resulting truncated product is undoubtedly nonfunctional. Genetic complementation analysis revealed that the Kasalath allele of CK2α increases days-to-heading. Map-based cloning with advanced backcross progeny enabled us to identify a gene underlying a quantitative trait locus even though it exhibited a relatively small effect on the phenotype. PMID:11416158

Dominant region: a basic feature for group motion analysis and its application to teamwork evaluation in soccer games

NASA Astrophysics Data System (ADS)

Taki, Tsuyoshi; Hasegawa, Jun-ichi

1998-12-01

This paper proposes a basic feature for quantitative measurement and evaluation of group behavior of persons. This feature called 'dominant region' is a kind of sphere of influence for each person in the group. The dominant region is defined as a region in where the person can arrive earlier than any other persons and can be formulated as Voronoi region modified by replacing the distance function with a time function. This time function is calculated based on a computational model of moving ability of the person. As an application of the dominant region, we present a motion analysis system of soccer games. The purpose of this system is to evaluate the teamwork quantitatively based on movement of all the players in the game. From experiments using motion pictures of actual games, it is suggested that the proposed feature is useful for measurement and evaluation of group behavior in team sports. This basic feature may be applied to other team ball games, such as American football, basketball, handball and water polo.

Peptide code-on-a-microplate for protease activity analysis via MALDI-TOF mass spectrometric quantitation.

PubMed

Hu, Junjie; Liu, Fei; Ju, Huangxian

2015-04-21

A peptide-encoded microplate was proposed for MALDI-TOF mass spectrometric (MS) analysis of protease activity. The peptide codes were designed to contain a coding region and the substrate of protease for enzymatic cleavage, respectively, and an internal standard method was proposed for the MS quantitation of the cleavage products of these peptide codes. Upon the cleavage reaction in the presence of target proteases, the coding regions were released from the microplate, which were directly quantitated by using corresponding peptides with one-amino acid difference as the internal standards. The coding region could be used as the unique "Protease ID" for the identification of corresponding protease, and the amount of the cleavage product was used for protease activity analysis. Using trypsin and chymotrypsin as the model proteases to verify the multiplex protease assay, the designed "Trypsin ID" and "Chymotrypsin ID" occurred at m/z 761.6 and 711.6. The logarithm value of the intensity ratio of "Protease ID" to internal standard was proportional to trypsin and chymotrypsin concentration in a range from 5.0 to 500 and 10 to 500 nM, respectively. The detection limits for trypsin and chymotrypsin were 2.3 and 5.2 nM, respectively. The peptide-encoded microplate showed good selectivity. This proposed method provided a powerful tool for convenient identification and activity analysis of multiplex proteases.

Quantitative classification of a historic northern Wisconsin (U.S.A.) landscape: mapping forests at regional scales

Treesearch

Lisa A. Schulte; David J. Mladenoff; Erik V. Nordheim

2002-01-01

We developed a quantitative and replicable classification system to improve understanding of historical composition and structure within northern Wisconsin's forests. The classification system was based on statistical cluster analysis and two forest metrics, relative dominance (% basal area) and relative importance (mean of relative dominance and relative density...

Idiopathic normal pressure hydrocephalus, quantitative EEG findings, and the cerebrospinal fluid tap test: a pilot study.

PubMed

Seo, Jong-Geun; Kang, Kyunghun; Jung, Ji-Young; Park, Sung-Pa; Lee, Maan-Gee; Lee, Ho-Won

2014-12-01

In this pilot study, we analyzed relationships between quantitative EEG measurements and clinical parameters in idiopathic normal pressure hydrocephalus patients, along with differences in these quantitative EEG markers between cerebrospinal fluid tap test responders and nonresponders. Twenty-six idiopathic normal pressure hydrocephalus patients (9 cerebrospinal fluid tap test responders and 17 cerebrospinal fluid tap test nonresponders) constituted the final group for analysis. The resting EEG was recorded and relative powers were computed for seven frequency bands. Cerebrospinal fluid tap test nonresponders, when compared with responders, showed a statistically significant increase in alpha2 band power at the right frontal and centrotemporal regions. Higher delta2 band powers in the frontal, central, parietal, and occipital regions and lower alpha1 band powers in the right temporal region significantly correlated with poorer cognitive performance. Higher theta1 band powers in the left parietal and occipital regions significantly correlated with gait dysfunction. And higher delta1 band powers in the right frontal regions significantly correlated with urinary disturbance. Our findings may encourage further research using quantitative EEG in patients with ventriculomegaly as a potential electrophysiological marker for predicting cerebrospinal fluid tap test responders. This study additionally suggests that the delta, theta, and alpha bands are statistically correlated with the severity of symptoms in idiopathic normal pressure hydrocephalus patients.

Posterior hypoperfusion in Parkinson's disease with and without dementia measured with arterial spin labeling MRI.

PubMed

Kamagata, Koji; Motoi, Yumiko; Hori, Masaaki; Suzuki, Michimasa; Nakanishi, Atsushi; Shimoji, Keigo; Kyougoku, Shinsuke; Kuwatsuru, Ryohei; Sasai, Keisuke; Abe, Osamu; Mizuno, Yoshikuni; Aoki, Shigeki; Hattori, Nobutaka

2011-04-01

To determine whether quantitative arterial spin labeling (ASL) can be used to evaluate regional cerebral blood flow in Parkinson's disease with dementia (PDD) and without dementia (PD). Thirty-five PD patients, 11 PDD patients, and 35 normal controls were scanned by using a quantitative ASL method with a 3 Tesla MRI unit. Regional cerebral blood flow was compared in the posterior cortex using region-of-interest analysis. PD and PDD patients showed lower regional cerebral blood flow in the posterior cortex than normal controls (P = 0.002 and P = 0.001, respectively, analysis of variance with a Bonferroni post hoc test). This is the first study to detect hypoperfusion in the posterior cortex in PD and PDD patients using ASL perfusion MRI. Because ASL perfusion MRI is completely noninvasive and can, therefore, safely be used for repeated assessments, this method can be used to monitor treatment effects or disease progression in PD. Copyright © 2011 Wiley-Liss, Inc.

Fine-Mapping and Selective Sweep Analysis of QTL for Cold Tolerance in Drosophila melanogaster

PubMed Central

Wilches, Ricardo; Voigt, Susanne; Duchen, Pablo; Laurent, Stefan; Stephan, Wolfgang

2014-01-01

There is a growing interest in investigating the relationship between genes with signatures of natural selection and genes identified in QTL mapping studies using combined population and quantitative genetics approaches. We dissected an X-linked interval of 6.2 Mb, which contains two QTL underlying variation in chill coma recovery time (CCRT) in Drosophila melanogaster from temperate (European) and tropical (African) regions. This resulted in two relatively small regions of 131 kb and 124 kb. The latter one co-localizes with a very strong selective sweep in the European population. We examined the genes within and near the sweep region individually using gene expression analysis and P-element insertion lines. Of the genes overlapping with the sweep, none appears to be related to CCRT. However, we have identified a new candidate gene of CCRT, brinker, which is located just outside the sweep region and is inducible by cold stress. We discuss these results in light of recent population genetics theories on quantitative traits. PMID:24970882

Contribution of Insula in Parkinson’s Disease: A Quantitative Meta-Analysis Study

PubMed Central

Criaud, Marion; Christopher, Leigh; Boulinguez, Philippe; Ballanger, Benedicte; Lang, Anthony E.; Cho, Sang S.; Houle, Sylvain; Strafella, Antonio P.

2016-01-01

The insula region is known to be an integrating hub interacting with multiple brain networks involved in cognitive, affective, sensory, and autonomic processes. There is growing evidence suggesting that this region may have an important role in Parkinson’s disease (PD). Thus, to investigate the functional organization of the insular cortex and its potential role in parkinsonian features, we used a coordinate-based quantitative meta-analysis approach, the activation likelihood estimation. A total of 132 insular foci were selected from 96 published experiments comprising the five functional categories: cognition, affective/behavioral symptoms, bodily awareness/autonomic function, sensorimotor function, and nonspecific resting functional changes associated with the disease. We found a significant convergence of activation maxima related to PD in different insular regions including anterior and posterior regions bilaterally. This study provides evidence of an important functional distribution of different domains within the insular cortex in PD, particularly in relation to nonmotor aspects, with an influence of medication effect. PMID:26800238

Contribution of insula in Parkinson's disease: A quantitative meta-analysis study.

PubMed

Criaud, Marion; Christopher, Leigh; Boulinguez, Philippe; Ballanger, Benedicte; Lang, Anthony E; Cho, Sang S; Houle, Sylvain; Strafella, Antonio P

2016-04-01

The insula region is known to be an integrating hub interacting with multiple brain networks involved in cognitive, affective, sensory, and autonomic processes. There is growing evidence suggesting that this region may have an important role in Parkinson's disease (PD). Thus, to investigate the functional organization of the insular cortex and its potential role in parkinsonian features, we used a coordinate-based quantitative meta-analysis approach, the activation likelihood estimation. A total of 132 insular foci were selected from 96 published experiments comprising the five functional categories: cognition, affective/behavioral symptoms, bodily awareness/autonomic function, sensorimotor function, and nonspecific resting functional changes associated with the disease. We found a significant convergence of activation maxima related to PD in different insular regions including anterior and posterior regions bilaterally. This study provides evidence of an important functional distribution of different domains within the insular cortex in PD, particularly in relation to nonmotor aspects, with an influence of medication effect. © 2016 Wiley Periodicals, Inc.

Topography of brain glucose hypometabolism and epileptic network in glucose transporter 1 deficiency.

PubMed

Akman, Cigdem Inan; Provenzano, Frank; Wang, Dong; Engelstad, Kristin; Hinton, Veronica; Yu, Julia; Tikofsky, Ronald; Ichese, Masonari; De Vivo, Darryl C

2015-02-01

(18)F fluorodeoxyglucose positron emission tomography ((18)F FDG-PET) facilitates examination of glucose metabolism. Previously, we described regional cerebral glucose hypometabolism using (18)F FDG-PET in patients with Glucose transporter 1 Deficiency Syndrome (Glut1 DS). We now expand this observation in Glut1 DS using quantitative image analysis to identify the epileptic network based on the regional distribution of glucose hypometabolism. (18)F FDG-PET scans of 16 Glut1 DS patients and 7 healthy participants were examined using Statistical parametric Mapping (SPM). Summed images were preprocessed for statistical analysis using MATLAB 7.1 and SPM 2 software. Region of interest (ROI) analysis was performed to validate SPM results. Visual analysis of the (18)F FDG-PET images demonstrated prominent regional glucose hypometabolism in the thalamus, neocortical regions and cerebellum bilaterally. Group comparison using SPM analysis confirmed that the regional distribution of glucose hypo-metabolism was present in thalamus, cerebellum, temporal cortex and central lobule. Two mildly affected patients without epilepsy had hypometabolism in cerebellum, inferior frontal cortex, and temporal lobe, but not thalamus. Glucose hypometabolism did not correlate with age at the time of PET imaging, head circumference, CSF glucose concentration at the time of diagnosis, RBC glucose uptake, or CNS score. Quantitative analysis of (18)F FDG-PET imaging in Glut1 DS patients confirmed that hypometabolism was present symmetrically in thalamus, cerebellum, frontal and temporal cortex. The hypometabolism in thalamus correlated with the clinical history of epilepsy. Copyright © 2014. Published by Elsevier B.V.

Quantitative Assessment of Regional Wall Motion Abnormalities Using Dual-Energy Digital Subtraction Intravenous Ventriculography

NASA Astrophysics Data System (ADS)

McCollough, Cynthia H.

Healthy portions of the left ventricle (LV) can often compensate for regional dysfunction, thereby masking regional disease when global indices of LV function are employed. Thus, quantitation of regional function provides a more useful method of assessing LV function, especially in diseases that have regional effects such as coronary artery disease. This dissertation studied the ability of a phase -matched dual-energy digital subtraction angiography (DE -DSA) technique to quantitate changes in regional LV systolic volume. The potential benefits and a theoretical description of the DE imaging technique are detailed. A correlated noise reduction algorithm is also presented which raises the signal-to-noise ratio of DE images by a factor of 2 -4. Ten open-chest dogs were instrumented with transmural ultrasonic crystals to assess regional LV function in terms of systolic normalized-wall-thickening rate (NWTR) and percent-systolic-thickening (PST). A pneumatic occluder was placed on the left-anterior-descending (LAD) coronary artery to temporarily reduce myocardial blood flow, thereby changing regional LV function in the LAD bed. DE-DSA intravenous left ventriculograms were obtained at control and four levels of graded myocardial ischemia, as determined by reductions in PST. Phase-matched images displaying changes in systolic contractile function were created by subtracting an end-systolic (ES) control image from ES images acquired at each level of myocardial ischemia. The resulting wall-motion difference signal (WMD), which represents a change in regional systolic volume between the control and ischemic states, was quantitated by videodensitometry and compared with changes in NWTR and PST. Regression analysis of 56 data points from 10 animals shows a linear relationship between WMD and both NWTR and PST: WMD = -2.46 NWTR + 13.9, r = 0.64, p < 0.001; WMD = -2.11 PST + 18.4, r = 0.54, p < 0.001. Thus, changes in regional ES LV volume between rest and ischemic states, as measured using the described imaging technique, appear linearly related to changes in wall-thickening, as measured using transmural ultrasonic crystals. This type of image analysis may prove useful in a variety of clinical and research applications and further investigation is proposed.

Semi-quantitative methods yield greater inter- and intraobserver agreement than subjective methods for interpreting 99m technetium-hydroxymethylene-diphosphonate uptake in equine thoracic processi spinosi.

PubMed

van Zadelhoff, Claudia; Ehrle, Anna; Merle, Roswitha; Jahn, Werner; Lischer, Christoph

2018-05-09

Scintigraphy is a standard diagnostic method for evaluating horses with back pain due to suspected thoracic processus spinosus pathology. Lesion detection is based on subjective or semi-quantitative assessments of increased uptake. This retrospective, analytical study is aimed to compare semi-quantitative and subjective methods in the evaluation of scintigraphic images of the processi spinosi in the equine thoracic spine. Scintigraphic images of 20 Warmblood horses, presented for assessment of orthopedic conditions between 2014 and 2016, were included in the study. Randomized, blinded image evaluation was performed by 11 veterinarians using subjective and semi-quantitative methods. Subjective grading was performed for the analysis of red-green-blue and grayscale scintigraphic images, which were presented in full-size or as masked images. For the semi-quantitative assessment, observers placed regions of interest over each processus spinosus. The uptake ratio of each processus spinosus in comparison to a reference region of interest was determined. Subsequently, a modified semi-quantitative calculation was developed whereby only the highest counts-per-pixel for a specified number of pixels was processed. Inter- and intraobserver agreement was calculated using intraclass correlation coefficients. Inter- and intraobserver intraclass correlation coefficients were 41.65% and 71.39%, respectively, for the subjective image assessment. Additionally, a correlation between intraobserver agreement, experience, and grayscale images was identified. The inter- and intraobserver agreement was significantly increased when using semi-quantitative analysis (97.35% and 98.36%, respectively) or the modified semi-quantitative calculation (98.61% and 98.82%, respectively). The proposed modified semi-quantitative technique showed a higher inter- and intraobserver agreement when compared to other methods, which makes it a useful tool for the analysis of scintigraphic images. The association of the findings from this study with clinical and radiological examinations requires further investigation. © 2018 American College of Veterinary Radiology.

Photo ion spectrometer

DOEpatents

Gruen, Dieter M.; Young, Charles E.; Pellin, Michael J.

1989-01-01

A method and apparatus for extracting for quantitative analysis ions of selected atomic components of a sample. A lens system is configured to provide a slowly diminishing field region for a volume containing the selected atomic components, enabling accurate energy analysis of ions generated in the slowly diminishing field region. The lens system also enables focusing on a sample of a charged particle beam, such as an ion beam, along a path length perpendicular to the sample and extraction of the charged particles along a path length also perpendicular to the sample. Improvement of signal to noise ratio is achieved by laser excitation of ions to selected autoionization states before carrying out quantitative analysis. Accurate energy analysis of energetic charged particles is assured by using a preselected resistive thick film configuration disposed on an insulator substrate for generating predetermined electric field boundary conditions to achieve for analysis the required electric field potential. The spectrometer also is applicable in the fields of SIMS, ISS and electron spectroscopy.

Photo ion spectrometer

DOEpatents

Gruen, D.M.; Young, C.E.; Pellin, M.J.

1989-08-08

A method and apparatus are described for extracting for quantitative analysis ions of selected atomic components of a sample. A lens system is configured to provide a slowly diminishing field region for a volume containing the selected atomic components, enabling accurate energy analysis of ions generated in the slowly diminishing field region. The lens system also enables focusing on a sample of a charged particle beam, such as an ion beam, along a path length perpendicular to the sample and extraction of the charged particles along a path length also perpendicular to the sample. Improvement of signal to noise ratio is achieved by laser excitation of ions to selected auto-ionization states before carrying out quantitative analysis. Accurate energy analysis of energetic charged particles is assured by using a preselected resistive thick film configuration disposed on an insulator substrate for generating predetermined electric field boundary conditions to achieve for analysis the required electric field potential. The spectrometer also is applicable in the fields of SIMS, ISS and electron spectroscopy. 8 figs.

Alzheimer disease: Quantitative analysis of I-123-iodoamphetamine SPECT brain imaging

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

Hellman, R.S.; Tikofsky, R.S.; Collier, B.D.

1989-07-01

To enable a more quantitative diagnosis of senile dementia of the Alzheimer type (SDAT), the authors developed and tested a semiautomated method to define regions of interest (ROIs) to be used in quantitating results from single photon emission computed tomography (SPECT) of regional cerebral blood flow performed with N-isopropyl iodine-123-iodoamphetamine. SPECT/IMP imaging was performed in ten patients with probable SDAT and seven healthy subjects. Multiple ROIs were manually and semiautomatically generated, and uptake was quantitated for each ROI. Mean cortical activity was estimated as the average of the mean activity in 24 semiautomatically generated ROIs; mean cerebellar activity was determinedmore » from the mean activity in separate ROIs. A ratio of parietal to cerebellar activity less than 0.60 and a ratio of parietal to mean cortical activity less than 0.90 allowed correct categorization of nine of ten and eight of ten patients, respectively, with SDAT and all control subjects. The degree of diminished mental status observed in patients with SDAT correlated with both global and regional changes in IMP uptake.« less

X-ray vision of fuel sprays.

PubMed

Wang, Jin

2005-03-01

With brilliant synchrotron X-ray sources, microsecond time-resolved synchrotron X-ray radiography and tomography have been used to elucidate the detailed three-dimensional structure and dynamics of high-pressure high-speed fuel sprays in the near-nozzle region. The measurement allows quantitative determination of the fuel distribution in the optically impenetrable region owing to the multiple scattering of visible light by small atomized fuel droplets surrounding the jet. X-radiographs of the jet-induced shock waves prove that the fuel jets become supersonic under appropriate injection conditions and that the quantitative analysis of the thermodynamic properties of the shock waves can also be derived from the most direct measurement. In other situations where extremely axial-asymmetric sprays are encountered, mass deconvolution and cross-sectional fuel distribution models can be computed based on the monochromatic and time-resolved X-radiographic images collected from various rotational orientations of the sprays. Such quantitative analysis reveals the never-before-reported characteristics and most detailed near-nozzle mass distribution of highly transient fuel sprays.

Quantitative methods in fractography; Proceedings of the Symposium on Evaluation and Techniques in Fractography, Atlanta, GA, Nov. 10, 1988

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

Strauss, B.M.; Putatunda, S.K.

1990-01-01

Papers are presented on the application of quantitative fractography and computed tomography to fracture processes in materials, the relationships between fractographic features and material toughness, the quantitative analysis of fracture surfaces using fractals, and the analysis and interpretation of aircraft component defects by means of quantitative fractography. Also discussed are the characteristics of hydrogen-assisted cracking measured by the holding-load and fractographic method, a fractographic study of isolated cleavage regions in nuclear pressure vessel steels and their weld metals, a fractographic and metallographic study of the initiation of brittle fracture in weldments, cracking mechanisms for mean stress/strain low-cycle multiaxial fatigue loadings,more » and corrosion fatigue crack arrest in Al alloys.« less

Segmentation of the Knee for Analysis of Osteoarthritis

NASA Astrophysics Data System (ADS)

Zerfass, Peter; Museyko, Oleg; Bousson, Valérie; Laredo, Jean-Denis; Kalender, Willi A.; Engelke, Klaus

Osteoarthritis changes the load distribution within joints and also changes bone density and structure. Within typical timelines of clinical studies these changes can be very small. Therefore precise definition of evaluation regions which are highly robust and show little to no interand intra-operator variance are essential for high quality quantitative analysis. To achieve this goal we have developed a system for the definition of such regions with minimal user input.

RAMP: a computer system for mapping regional areas

Treesearch

Bradley B. Nickey

1975-01-01

Until 1972, the U.S. Forest Service's Individual Fire Reports recorded locations by the section-township-range system..These earlier fire reports, therefore, lacked congruent locations. RAMP (Regional Area Mapping Procedure) was designed to make the reports more useful for quantitative analysis. This computer-based technique converts locations expressed in...

Temporal analysis of regional wall motion from cine cardiac MRI

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Didier, Dominique; Chretien, Anne; Rosset, Antoine; Magnin, Isabelle E.; Ligier, Yves

1996-04-01

The purpose of this work is to develop and to evaluate an automatic analysis technique for quantitative assessment of cardiac function from cine MRI and to identify regional alterations in synchronicity based on Fourier analysis of ventricular wall motion (WM). A temporal analysis technique of left ventricular wall displacement was developed for quantitative analysis of temporal delays in wall motion and applied to gated cine 'dark blood' cardiac MRI. This imaging technique allows the user to saturate the blood both above and below the imaging slice simultaneously by using a specially designed rf presaturation pulse. The acquisition parameters are: TR equals 25 - 60 msec, TE equals 5 - 7 msec, 0 equals 25 degrees, slice thickness equals 10 mm, 16 to 32 frames/cycle. Automatic edge detection was used to outline the ventricular cavities on all frames of a cardiac cycle. Two different segmentation techniques were applied to all studies and lead to similar results. Further improvement in edge detection accuracy was achieved by temporal interpolation of individual contours on each image of the cardiac cycle. Radial analysis of the ventricular wall motion was then performed along 64 radii drawn from the center of the ventricular cavity. The first harmonic of the Fourier transform of each radial motion curve is calculated. The phase of the fundamental Fourier component is used as an index of synchrony (delay) of regional wall motion. Results are displayed in color-coded maps of regional alterations in the amplitude and synchrony of wall motion. The temporal delays measured from individual segments are evaluated through a histogram of phase distribution, where the width of the main peak is used as an index of overall synchrony of wall motion. The variability of this technique was validated in 10 normal volunteers and was used to identify regions with asynchronous WM in 15 patients with documented CAD. The standard deviation (SD) of phase distribution measured in short axis views was calculated and used to identify regions with asynchronous wall motion in patients with coronary artery disease. Results suggest that this technique is more sensitive than global functional parameters such as ejection fraction for the detection of ventricular dysfunction. Color coded parametric display offers a more convenient way for the identification and localization of regional wall motion asynchrony. Data obtained from endocardial wall motion analysis were not significantly different from wall thickening measurements. The innovative approach of evaluating the temporal behavior of regional wall motion anomalies is expected to provide clinically relevant data about subtle alteration that cannot be detected through simple analysis of the extent (amplitude) of wall motion or myocardial thickening. Temporal analysis of regional WM abnormality from cine MRI offers an innovative and promising means for objective quantitative evaluation of subtle regional abnormalities. Color coded parametric maps allowed a better identification and localization of regional WM asynchrony.

Qualitative and quantitative interpretation of computed tomography of the lungs in healthy neonatal foals.

PubMed

Lascola, Kara M; O'Brien, Robert T; Wilkins, Pamela A; Clark-Price, Stuart C; Hartman, Susan K; Mitchell, Mark A

2013-09-01

To qualitatively describe lung CT images obtained from sedated healthy equine neonates (≤ 14 days of age), use quantitative analysis of CT images to characterize attenuation and distribution of gas and tissue volumes within the lungs, and identify differences between lung characteristics of foals ≤ 7 days of age and foals > 7 days of age. 10 Standardbred foals between 2.5 and 13 days of age. Foals were sedated with butorphanol, midazolam, and propofol and positioned in sternal recumbency for thoracic CT. Image analysis software was used to exclude lung from nonlung structures. Lung attenuation was measured in Hounsfield units (HU) for analysis of whole lung and regional changes in attenuation and lung gas and tissue components. Degree of lung attenuation was classified as follows: hyperinflated or emphysema, -1,000 to -901 HU; well aerated, -900 to -501 HU; poorly aerated, -500 to -101 HU; and nonaerated, > -100 HU. Qualitative evidence of an increase in lung attenuation and patchy alveolar patterns in the ventral lung region were more pronounced in foals ≤ 7 days of age than in older foals. Quantitative analysis revealed that mean ± SD lung attenuation was greater in foals ≤ 7 days of age (-442 ± 28 HU) than in foals > 7 days of age (-521 ± 24 HU). Lung aeration and gas volumes were lower than in other regions ventrally and in the mid lung region caudal to the heart. CONCLUSIONS AND CLINICAL RELEVANCE-Identified radiographic patterns and changes in attenuation were most consistent with atelectasis and appeared more severe in foals ≤ 7 days of age than in older neonatal foals. Recognition of these changes may have implications for accurate CT interpretation in sedated neonatal foals with pulmonary disease.

Quantitative high-resolution genomic analysis of single cancer cells.

PubMed

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

2011-01-01

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

Quantitative Analysis of the Cervical Texture by Ultrasound and Correlation with Gestational Age.

PubMed

Baños, Núria; Perez-Moreno, Alvaro; Migliorelli, Federico; Triginer, Laura; Cobo, Teresa; Bonet-Carne, Elisenda; Gratacos, Eduard; Palacio, Montse

2017-01-01

Quantitative texture analysis has been proposed to extract robust features from the ultrasound image to detect subtle changes in the textures of the images. The aim of this study was to evaluate the feasibility of quantitative cervical texture analysis to assess cervical tissue changes throughout pregnancy. This was a cross-sectional study including singleton pregnancies between 20.0 and 41.6 weeks of gestation from women who delivered at term. Cervical length was measured, and a selected region of interest in the cervix was delineated. A model to predict gestational age based on features extracted from cervical images was developed following three steps: data splitting, feature transformation, and regression model computation. Seven hundred images, 30 per gestational week, were included for analysis. There was a strong correlation between the gestational age at which the images were obtained and the estimated gestational age by quantitative analysis of the cervical texture (R = 0.88). This study provides evidence that quantitative analysis of cervical texture can extract features from cervical ultrasound images which correlate with gestational age. Further research is needed to evaluate its applicability as a biomarker of the risk of spontaneous preterm birth, as well as its role in cervical assessment in other clinical situations in which cervical evaluation might be relevant. © 2016 S. Karger AG, Basel.

Quantitative analysis of diffusion tensor orientation: theoretical framework.

PubMed

Wu, Yu-Chien; Field, Aaron S; Chung, Moo K; Badie, Benham; Alexander, Andrew L

2004-11-01

Diffusion-tensor MRI (DT-MRI) yields information about the magnitude, anisotropy, and orientation of water diffusion of brain tissues. Although white matter tractography and eigenvector color maps provide visually appealing displays of white matter tract organization, they do not easily lend themselves to quantitative and statistical analysis. In this study, a set of visual and quantitative tools for the investigation of tensor orientations in the human brain was developed. Visual tools included rose diagrams, which are spherical coordinate histograms of the major eigenvector directions, and 3D scatterplots of the major eigenvector angles. A scatter matrix of major eigenvector directions was used to describe the distribution of major eigenvectors in a defined anatomic region. A measure of eigenvector dispersion was developed to describe the degree of eigenvector coherence in the selected region. These tools were used to evaluate directional organization and the interhemispheric symmetry of DT-MRI data in five healthy human brains and two patients with infiltrative diseases of the white matter tracts. In normal anatomical white matter tracts, a high degree of directional coherence and interhemispheric symmetry was observed. The infiltrative diseases appeared to alter the eigenvector properties of affected white matter tracts, showing decreased eigenvector coherence and interhemispheric symmetry. This novel approach distills the rich, 3D information available from the diffusion tensor into a form that lends itself to quantitative analysis and statistical hypothesis testing. (c) 2004 Wiley-Liss, Inc.

The employment of FTIR spectroscopy in combination with chemometrics for analysis of rat meat in meatball formulation.

PubMed

Rahmania, Halida; Sudjadi; Rohman, Abdul

2015-02-01

For Indonesian community, meatball is one of the favorite meat food products. In order to gain economical benefits, the substitution of beef meat with rat meat can happen due to the different prices between rat meat and beef. In this present research, the feasibility of FTIR spectroscopy in combination with multivariate calibration of partial least square (PLS) was used for the quantitative analysis of rat meat in the binary mixture of beef in meatball formulation. Meanwhile, the chemometrics of principal component analysis (PCA) was used for the classification between rat meat and beef meatballs. Some frequency regions in mid infrared region were optimized, and finally, the frequency region of 750-1000 cm(-1) was selected during PLS and PCA modeling.For quantitative analysis, the relationship between actual values (x-axis) and FTIR predicted values (y-axis) of rat meat is described by the equation of y= 0.9417x+ 2.8410 with coefficient of determination (R2) of 0.993, and root mean square error of calibration (RMSEC) of 1.79%. Furthermore, PCA was successfully used for the classification of rat meat meatball and beef meatball.

Economic Impacts of a Wide Area Release of Anthrax

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

Judd, Kathleen S.; Olson, Jarrod; Stein, Steven L.

2009-05-29

This analysis explores economic impacts that might result from a wide-area release of anthrax. The intent is not to provide a quantitative analysis of such a disaster, but to: 1. Define the general categories of economic impacts that the region should be concerned about; and, 2. Explore what types of private sector businesses or industries, if any, may have the greatest impact on speeding the economic recovery of the region.

Classification of cassava genotypes based on qualitative and quantitative data.

PubMed

Oliveira, E J; Oliveira Filho, O S; Santos, V S

2015-02-02

We evaluated the genetic variation of cassava accessions based on qualitative (binomial and multicategorical) and quantitative traits (continuous). We characterized 95 accessions obtained from the Cassava Germplasm Bank of Embrapa Mandioca e Fruticultura; we evaluated these accessions for 13 continuous, 10 binary, and 25 multicategorical traits. First, we analyzed the accessions based only on quantitative traits; next, we conducted joint analysis (qualitative and quantitative traits) based on the Ward-MLM method, which performs clustering in two stages. According to the pseudo-F, pseudo-t2, and maximum likelihood criteria, we identified five and four groups based on quantitative trait and joint analysis, respectively. The smaller number of groups identified based on joint analysis may be related to the nature of the data. On the other hand, quantitative data are more subject to environmental effects in the phenotype expression; this results in the absence of genetic differences, thereby contributing to greater differentiation among accessions. For most of the accessions, the maximum probability of classification was >0.90, independent of the trait analyzed, indicating a good fit of the clustering method. Differences in clustering according to the type of data implied that analysis of quantitative and qualitative traits in cassava germplasm might explore different genomic regions. On the other hand, when joint analysis was used, the means and ranges of genetic distances were high, indicating that the Ward-MLM method is very useful for clustering genotypes when there are several phenotypic traits, such as in the case of genetic resources and breeding programs.

Subsistence strategies in Argentina during the late Pleistocene and early Holocene

NASA Astrophysics Data System (ADS)

Martínez, Gustavo; Gutiérrez, María A.; Messineo, Pablo G.; Kaufmann, Cristian A.; Rafuse, Daniel J.

2016-07-01

This paper highlights regional and temporal variation in the presence and exploitation of faunal resources from different regions of Argentina during the late Pleistocene and early Holocene. Specifically, the faunal analysis considered here includes the zooarchaeological remains from all sites older than 7500 14C years BP. We include quantitative information for each reported species (genus, family, or order) and we use the number of identified specimens (NISP per taxon and the NISPtotal by sites) as the quantitative measure of taxonomic abundance. The taxonomic richness (Ntaxatotal and Ntaxaexploited) and the taxonomic heterogeneity or Shannon-Wiener index are estimated in order to consider dietary generalization or specialization, and ternary diagrams are used to categorize subsistence patterns of particular sites and regions. The archaeological database is composed of 78 sites which are represented by 110 stratigraphic contexts. Our results demonstrate that although some quantitative differences between regions are observed, artiodactyls (camelids and deer) were the most frequently consumed animal resource in Argentina. Early hunter-gatherers did not follow a specialized predation strategy in megamammals. A variety in subsistence systems, operating in parallel with a strong regional emphasis is shown, according to specific environmental conditions and cultural trajectories.

Analysis of lard in meatball broth using Fourier transform infrared spectroscopy and chemometrics.

PubMed

Kurniawati, Endah; Rohman, Abdul; Triyana, Kuwat

2014-01-01

Meatball is one of the favorite foods in Indonesia. For the economic reason (due to the price difference), the substitution of beef meat with pork can occur. In this study, FTIR spectroscopy in combination with chemometrics of partial least square (PLS) and principal component analysis (PCA) was used for analysis of pork fat (lard) in meatball broth. Lard in meatball broth was quantitatively determined at wavenumber region of 1018-1284 cm(-1). The coefficient of determination (R(2)) and root mean square error of calibration (RMSEC) values obtained were 0.9975 and 1.34% (v/v), respectively. Furthermore, the classification of lard and beef fat in meatball broth as well as in commercial samples was performed at wavenumber region of 1200-1000 cm(-1). The results showed that FTIR spectroscopy coupled with chemometrics can be used for quantitative analysis and classification of lard in meatball broth for Halal verification studies. The developed method is simple in operation, rapid and not involving extensive sample preparation. © 2013.

A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum interspecific populations and Gossypium hirsutum x Gossypium barbadense populations

USDA-ARS?s Scientific Manuscript database

Recent Meta-analysis of quantitative trait loci (QTL) in tetraploid cotton (Gossypium spp.) has identified regions of the genome with high concentrations of various trait QTL called clusters, and specific trait QTL called hotspots. The Meta-analysis included all population types of Gossypium mixing ...

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.

Automatic registration of ICG images using mutual information and perfusion analysis

NASA Astrophysics Data System (ADS)

Kim, Namkug; Seo, Jong-Mo; Lee, June-goo; Kim, Jong Hyo; Park, Kwangsuk; Yu, Hyeong-Gon; Yu, Young Suk; Chung, Hum

2005-04-01

Introduction: Indocyanin green fundus angiographic images (ICGA) of the eyes is useful method in detecting and characterizing the choroidal neovascularization (CNV), which is the major cause of the blindness over 65 years of age. To investigate the quantitative analysis of the blood flow on ICGA, systematic approach for automatic registration of using mutual information and a quantitative analysis was developed. Methods: Intermittent sequential images of indocyanin green angiography were acquired by Heidelberg retinal angiography that uses the laser scanning system for the image acquisition. Misalignment of the each image generated by the minute eye movement of the patients was corrected by the mutual information method because the distribution of the contrast media on image is changing throughout the time sequences. Several region of interest (ROI) were selected by a physician and the intensities of the selected region were plotted according to the time sequences. Results: The registration of ICGA time sequential images is required not only translate transform but also rotational transform. Signal intensities showed variation based on gamma-variate function depending on ROIs and capillary vessels show more variance of signal intensity than major vessels. CNV showed intermediate variance of signal intensity and prolonged transit time. Conclusion: The resulting registered images can be used not only for quantitative analysis, but also for perfusion analysis. Various investigative approached on CNV using this method will be helpful in the characterization of the lesion and follow-up.

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

PubMed Central

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

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics. PMID:22140428

Quantitative representations of an exaggerated anxiety response in the brain of female spider phobics-a parametric fMRI study.

PubMed

Zilverstand, Anna; Sorger, Bettina; Kaemingk, Anita; Goebel, Rainer

2017-06-01

We employed a novel parametric spider picture set in the context of a parametric fMRI anxiety provocation study, designed to tease apart brain regions involved in threat monitoring from regions representing an exaggerated anxiety response in spider phobics. For the stimulus set, we systematically manipulated perceived proximity of threat by varying a depicted spider's context, size, and posture. All stimuli were validated in a behavioral rating study (phobics n = 20; controls n = 20; all female). An independent group participated in a subsequent fMRI anxiety provocation study (phobics n = 7; controls n = 7; all female), in which we compared a whole-brain categorical to a whole-brain parametric analysis. Results demonstrated that the parametric analysis provided a richer characterization of the functional role of the involved brain networks. In three brain regions-the mid insula, the dorsal anterior cingulate, and the ventrolateral prefrontal cortex-activation was linearly modulated by perceived proximity specifically in the spider phobia group, indicating a quantitative representation of an exaggerated anxiety response. In other regions (e.g., the amygdala), activation was linearly modulated in both groups, suggesting a functional role in threat monitoring. Prefrontal regions, such as dorsolateral prefrontal cortex, were activated during anxiety provocation but did not show a stimulus-dependent linear modulation in either group. The results confirm that brain regions involved in anxiety processing hold a quantitative representation of a pathological anxiety response and more generally suggest that parametric fMRI designs may be a very powerful tool for clinical research in the future, particularly when developing novel brain-based interventions (e.g., neurofeedback training). Hum Brain Mapp 38:3025-3038, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Estimating raw material equivalents on a macro-level: comparison of multi-regional input-output analysis and hybrid LCI-IO.

PubMed

Schoer, Karl; Wood, Richard; Arto, Iñaki; Weinzettel, Jan

2013-12-17

The mass of material consumed by a population has become a useful proxy for measuring environmental pressure. The "raw material equivalents" (RME) metric of material consumption addresses the issue of including the full supply chain (including imports) when calculating national or product level material impacts. The RME calculation suffers from data availability, however, as quantitative data on production practices along the full supply chain (in different regions) is required. Hence, the RME is currently being estimated by three main approaches: (1) assuming domestic technology in foreign economies, (2) utilizing region-specific life-cycle inventories (in a hybrid framework), and (3) utilizing multi-regional input-output (MRIO) analysis to explicitly cover all regions of the supply chain. While the first approach has been shown to give inaccurate results, this paper focuses on the benefits and costs of the latter two approaches. We analyze results from two key (MRIO and hybrid) projects modeling raw material equivalents, adjusting the models in a stepwise manner in order to quantify the effects of individual conceptual elements. We attempt to isolate the MRIO gap, which denotes the quantitative impact of calculating the RME of imports by an MRIO approach instead of the hybrid model, focusing on the RME of EU external trade imports. While, the models give quantitatively similar results, differences become more pronounced when tracking more detailed material flows. We assess the advantages and disadvantages of the two approaches and look forward to ways to further harmonize data and approaches.

An Empirical Study of Education Divide Diminishment through Online Learning Courses

ERIC Educational Resources Information Center

Hsieh, Ming-Yuan

2017-01-01

According to the swift development of education system, Taiwanese government is always devoting diminishing the educational divide between rural and urban regions. This research focuses on this educational divide by cross-employing the Grey Relational Analysis (GRA) of quantitative analysis and the Fuzzy Set Qualitative Comparative Analysis…

A quantitative analysis of inter-island telephony traffic in the Pacific Basin Region (PBR)

NASA Technical Reports Server (NTRS)

Evans, D. D.; Arth, C. H.

1980-01-01

As part of NASA's continuing assessment of future communication satellite requirements, a study was conducted to quantitatively scope current and future telecommunication traffic demand in the South Pacific Archipelagos. This demand was then converted to equivalent satellite transponder capacities. Only inter-island telephony traffic for the Pacific Basin Region was included. The results show that if all this traffic were carried by a satellite system, one-third of a satellite transponder would be needed to satisfy the base-year (1976-1977) requirement and about two-thirds of a satellite transponder would be needed to satisfy the forecasted 1985 requirement.

Identification of genomic region controlling resistance to aflatoxin contamination in a peanut recombinant inbred line population (Tifrunner x GT-C20)

USDA-ARS?s Scientific Manuscript database

Aflatoxin contamination of peanut is a significant threat to global food safety. In this study we performed quantitative trait loci (QTL) analysis to identify peanut genomic regions contributing to aflatoxin contamination resistance in a recombinant inbred line (RIL) population derived from the Tifr...

Epistasis analysis for quantitative traits by functional regression model.

PubMed

Zhang, Futao; Boerwinkle, Eric; Xiong, Momiao

2014-06-01

The critical barrier in interaction analysis for rare variants is that most traditional statistical methods for testing interactions were originally designed for testing the interaction between common variants and are difficult to apply to rare variants because of their prohibitive computational time and poor ability. The great challenges for successful detection of interactions with next-generation sequencing (NGS) data are (1) lack of methods for interaction analysis with rare variants, (2) severe multiple testing, and (3) time-consuming computations. To meet these challenges, we shift the paradigm of interaction analysis between two loci to interaction analysis between two sets of loci or genomic regions and collectively test interactions between all possible pairs of SNPs within two genomic regions. In other words, we take a genome region as a basic unit of interaction analysis and use high-dimensional data reduction and functional data analysis techniques to develop a novel functional regression model to collectively test interactions between all possible pairs of single nucleotide polymorphisms (SNPs) within two genome regions. By intensive simulations, we demonstrate that the functional regression models for interaction analysis of the quantitative trait have the correct type 1 error rates and a much better ability to detect interactions than the current pairwise interaction analysis. The proposed method was applied to exome sequence data from the NHLBI's Exome Sequencing Project (ESP) and CHARGE-S study. We discovered 27 pairs of genes showing significant interactions after applying the Bonferroni correction (P-values < 4.58 × 10(-10)) in the ESP, and 11 were replicated in the CHARGE-S study. © 2014 Zhang et al.; Published by Cold Spring Harbor Laboratory Press.

Thin-film hermeticity - A quantitative analysis of diamondlike carbon using variable angle spectroscopic ellipsometry

NASA Technical Reports Server (NTRS)

Orzeszko, S.; De, Bhola N.; Woollam, John A.; Pouch, John J.; Alterovitz, Samuel A.

1988-01-01

This paper reports on the successful application of variable-angle spectroscopic ellipsometry to quantitative thin-film hermeticity evaluation. It is shown that, under a variety of film preparations and moisture introduction conditions, water penetrates only a very thin diamondlike carbon (DLC) top surface-roughness region. Thus, DLC is an excellent candidate for use as protective coatings in adverse chemical and aqueous environments.

Geographical classification of Epimedium based on HPLC fingerprint analysis combined with multi-ingredients quantitative analysis.

PubMed

Xu, Ning; Zhou, Guofu; Li, Xiaojuan; Lu, Heng; Meng, Fanyun; Zhai, Huaqiang

2017-05-01

A reliable and comprehensive method for identifying the origin and assessing the quality of Epimedium has been developed. The method is based on analysis of HPLC fingerprints, combined with similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and multi-ingredient quantitative analysis. Nineteen batches of Epimedium, collected from different areas in the western regions of China, were used to establish the fingerprints and 18 peaks were selected for the analysis. Similarity analysis, HCA and PCA all classified the 19 areas into three groups. Simultaneous quantification of the five major bioactive ingredients in the Epimedium samples was also carried out to confirm the consistency of the quality tests. These methods were successfully used to identify the geographical origin of the Epimedium samples and to evaluate their quality. Copyright © 2016 John Wiley & Sons, Ltd.

Linkage analysis of quantitative refraction and refractive errors in the Beaver Dam Eye Study.

PubMed

Klein, Alison P; Duggal, Priya; Lee, Kristine E; Cheng, Ching-Yu; Klein, Ronald; Bailey-Wilson, Joan E; Klein, Barbara E K

2011-07-13

Refraction, as measured by spherical equivalent, is the need for an external lens to focus images on the retina. While genetic factors play an important role in the development of refractive errors, few susceptibility genes have been identified. However, several regions of linkage have been reported for myopia (2q, 4q, 7q, 12q, 17q, 18p, 22q, and Xq) and for quantitative refraction (1p, 3q, 4q, 7p, 8p, and 11p). To replicate previously identified linkage peaks and to identify novel loci that influence quantitative refraction and refractive errors, linkage analysis of spherical equivalent, myopia, and hyperopia in the Beaver Dam Eye Study was performed. Nonparametric, sibling-pair, genome-wide linkage analyses of refraction (spherical equivalent adjusted for age, education, and nuclear sclerosis), myopia and hyperopia in 834 sibling pairs within 486 extended pedigrees were performed. Suggestive evidence of linkage was found for hyperopia on chromosome 3, region q26 (empiric P = 5.34 × 10(-4)), a region that had shown significant genome-wide evidence of linkage to refraction and some evidence of linkage to hyperopia. In addition, the analysis replicated previously reported genome-wide significant linkages to 22q11 of adjusted refraction and myopia (empiric P = 4.43 × 10(-3) and 1.48 × 10(-3), respectively) and to 7p15 of refraction (empiric P = 9.43 × 10(-4)). Evidence was also found of linkage to refraction on 7q36 (empiric P = 2.32 × 10(-3)), a region previously linked to high myopia. The findings provide further evidence that genes controlling refractive errors are located on 3q26, 7p15, 7p36, and 22q11.

Quantitative analysis of ChIP-seq data uncovers dynamic and sustained H3K4me3 and H3K27me3 modulation in cancer cells under hypoxia.

PubMed

Adriaens, Michiel E; Prickaerts, Peggy; Chan-Seng-Yue, Michelle; van den Beucken, Twan; Dahlmans, Vivian E H; Eijssen, Lars M; Beck, Timothy; Wouters, Bradly G; Voncken, Jan Willem; Evelo, Chris T A

2016-01-01

A comprehensive assessment of the epigenetic dynamics in cancer cells is the key to understanding the molecular mechanisms underlying cancer and to improving cancer diagnostics, prognostics and treatment. By combining genome-wide ChIP-seq epigenomics and microarray transcriptomics, we studied the effects of oxygen deprivation and subsequent reoxygenation on histone 3 trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in a breast cancer cell line, serving as a model for abnormal oxygenation in solid tumors. A priori, epigenetic markings and gene expression levels not only are expected to vary greatly between hypoxic and normoxic conditions, but also display a large degree of heterogeneity across the cell population. Where traditionally ChIP-seq data are often treated as dichotomous data, the model and experiment here necessitate a quantitative, data-driven analysis of both datasets. We first identified genomic regions with sustained epigenetic markings, which provided a sample-specific reference enabling quantitative ChIP-seq data analysis. Sustained H3K27me3 marking was located around centromeres and intergenic regions, while sustained H3K4me3 marking is associated with genes involved in RNA binding, translation and protein transport and localization. Dynamic marking with both H3K4me3 and H3K27me3 (hypoxia-induced bivalency) was found in CpG-rich regions at loci encoding factors that control developmental processes, congruent with observations in embryonic stem cells. In silico -identified epigenetically sustained and dynamic genomic regions were confirmed through ChIP-PCR in vitro, and obtained results are corroborated by published data and current insights regarding epigenetic regulation.

Directed differential connectivity graph of interictal epileptiform discharges

PubMed Central

Amini, Ladan; Jutten, Christian; Achard, Sophie; David, Olivier; Soltanian-Zadeh, Hamid; Hossein-Zadeh, Gh. Ali; Kahane, Philippe; Minotti, Lorella; Vercueil, Laurent

2011-01-01

In this paper, we study temporal couplings between interictal events of spatially remote regions in order to localize the leading epileptic regions from intracerebral electroencephalogram (iEEG). We aim to assess whether quantitative epileptic graph analysis during interictal period may be helpful to predict the seizure onset zone of ictal iEEG. Using wavelet transform, cross-correlation coefficient, and multiple hypothesis test, we propose a differential connectivity graph (DCG) to represent the connections that change significantly between epileptic and non-epileptic states as defined by the interictal events. Post-processings based on mutual information and multi-objective optimization are proposed to localize the leading epileptic regions through DCG. The suggested approach is applied on iEEG recordings of five patients suffering from focal epilepsy. Quantitative comparisons of the proposed epileptic regions within ictal onset zones detected by visual inspection and using electrically stimulated seizures, reveal good performance of the present method. PMID:21156385

A Whole-Genome Screen of a Quantitative Trait of Age-Related Maculopathy in Sibships from the Beaver Dam Eye Study

PubMed Central

Schick, James H.; Iyengar, Sudha K.; Klein, Barbara E.; Klein, Ronald; Reading, Karlie; Liptak, Rachel; Millard, Christopher; Lee, Kristine E.; Tomany, Sandra C.; Moore, Emily L.; Fijal, Bonnie A.; Elston, Robert C.

2003-01-01

Age-related maculopathy (ARM) is a leading cause of visual impairment among the elderly in Western populations. To identify ARM-susceptibility loci, we genotyped a subset of subjects from the Beaver Dam (WI) Eye Study and performed a model-free genomewide linkage analysis for markers linked to a quantitative measure of ARM. We initially genotyped 345 autosomal markers in 325 individuals (N=263 sib pairs) from 102 pedigrees. Ten regions suggestive of linkage with ARM were observed on chromosomes 3, 5, 6, 12, 15, and 16. Prior to fine mapping, the most significant regions were an 18-cM region on chromosome 12, near D12S1300 (P=.0159); a region on chromosome 3, near D3S1763, with a P value of .0062; and a 6-cM region on chromosome 16, near D16S769, with a P value of .0086. After expanding our analysis to include 25 additional fine-mapping markers, we found that a 14-cM region on chromosome 12, near D12S346 (located at 106.89 cM), showed the strongest indication of linkage, with a P value of .004. Three other regions, on chromosomes 5, 6, and 15, that were nominally significant at P⩽.01 are also appropriate for fine mapping. PMID:12717633

Evaluation of cerebral maturation by visual and quantitative analysis of resting electroencephalography in children with primary nocturnal enuresis.

PubMed

Hallioğlu, O; Ozge, A; Comelekoglu, U; Topaloglu, A K; Kanik, A; Duzovali, O; Yilgor, E

2001-10-01

This study was undertaken to evaluate resting electroencephalographic (EEG) changes and their relations to cerebral maturation in children with primary nocturnal enuresis. Cerebral maturation is known to be important in the pathogenesis of this disorder. Twenty-five right-handed patients with primary nocturnal enuresis, aged 6 to 14 years, and 23 age- and sex-matched healthy children were included in this cross-sectional case-control study. The abnormalities detected using such techniques as hemispheral asymmetry, regional differences, and hyperventilation response in addition to visual and quantitative EEG analysis were examined statistically by multivariate analysis. A decrease in alpha activity in the left (dominant hemisphere) temporal lobe and in the frontal lobes bilaterally and an increase in delta activity in the right temporal region were observed. We concluded that insufficient cerebral maturation is an important factor in the pathogenesis of primary nocturnal enuresis, and EEG, as a noninvasive and inexpensive method, could be used in evaluating cerebral maturation.

Is there a core neural network in empathy? An fMRI based quantitative meta-analysis.

PubMed

Fan, Yan; Duncan, Niall W; de Greck, Moritz; Northoff, Georg

2011-01-01

Whilst recent neuroimaging studies have identified a series of different brain regions as being involved in empathy, it remains unclear concerning the activation consistence of these brain regions and their specific functional roles. Using MKDA, a whole-brain based quantitative meta-analysis of recent fMRI studies of empathy was performed. This analysis identified the dACC-aMCC-SMA and bilateral anterior insula as being consistently activated in empathy. Hypothesizing that what are here termed affective-perceptual and cognitive-evaluative forms of empathy might be characterized by different activity patterns, the neural activations in these forms of empathy were compared. The dorsal aMCC was demonstrated to be recruited more frequently in the cognitive-evaluative form of empathy, whilst the right anterior insula was found to be involved in the affective-perceptual form of empathy only. The left anterior insula was active in both forms of empathy. It was concluded that the dACC-aMCC-SMA and bilateral insula can be considered as forming a core network in empathy, and that cognitive-evaluative and affective-perceptual empathy can be distinguished at the level of regional activation. Copyright © 2010 Elsevier Ltd. All rights reserved.

Dominant Epistasis Between Two Quantitative Trait Loci Governing Sporulation Efficiency in Yeast Saccharomyces cerevisiae

PubMed Central

Bergman, Juraj; Mitrikeski, Petar T.

2015-01-01

Summary Sporulation efficiency in the yeast Saccharomyces cerevisiae is a well-established model for studying quantitative traits. A variety of genes and nucleotides causing different sporulation efficiencies in laboratory, as well as in wild strains, has already been extensively characterised (mainly by reciprocal hemizygosity analysis and nucleotide exchange methods). We applied a different strategy in order to analyze the variation in sporulation efficiency of laboratory yeast strains. Coupling classical quantitative genetic analysis with simulations of phenotypic distributions (a method we call phenotype modelling) enabled us to obtain a detailed picture of the quantitative trait loci (QTLs) relationships underlying the phenotypic variation of this trait. Using this approach, we were able to uncover a dominant epistatic inheritance of loci governing the phenotype. Moreover, a molecular analysis of known causative quantitative trait genes and nucleotides allowed for the detection of novel alleles, potentially responsible for the observed phenotypic variation. Based on the molecular data, we hypothesise that the observed dominant epistatic relationship could be caused by the interaction of multiple quantitative trait nucleotides distributed across a 60--kb QTL region located on chromosome XIV and the RME1 locus on chromosome VII. Furthermore, we propose a model of molecular pathways which possibly underlie the phenotypic variation of this trait. PMID:27904371

Texture analysis of T1-w and T2-w MR images allows a quantitative evaluation of radiation-induced changes of internal obturator muscles after radiotherapy for prostate cancer.

PubMed

Scalco, Elisa; Rancati, Tiziana; Pirovano, Ileana; Mastropietro, Alfonso; Palorini, Federica; Cicchetti, Alessandro; Messina, Antonella; Avuzzi, Barbara; Valdagni, Riccardo; Rizzo, Giovanna

2018-04-01

To investigate the potential of texture analysis applied on T2-w and postcontrast T1-w images acquired before radiotherapy for prostate cancer (PCa) and 12 months after its completion in quantitatively characterizing local radiation effect on the muscular component of internal obturators, as organs potentially involved in urinary toxicity. T2-w and postcontrast T1-w MR images were acquired at 1.5 T before treatment (MRI1) and at 12 months of follow-up (MRI2) in 13 patients treated with radiotherapy for PCa. Right and left internal obturator muscle contours were manually delineated upon MRI1 and then automatically propagated on MRI2 by an elastic registration method. Planning CT images were coregistered to both MRIs and dose maps were deformed accordingly. A high-dose region receiving >55 Gy and a low-dose region receiving <55 Gy were identified in each muscle volume. Eighteen textural features were extracted from each region of interest and differences between MRI1 and MRI2 were evaluated. A signal increase was highlighted in both T2-w and T1-w images in the portion of the obturators near the prostate, i.e., in the region receiving medium-high doses. A change in the spatial organization was identified, as an increase in homogeneity and a decrease in contrast and complexity, compatible with an inflammatory status. In particular, the region receiving medium-high doses presented more significant or, at least, stronger differences. Texture analysis applied on T1-w and T2-w MR images has demonstrated its ability in quantitative evaluating radiation-induced changes in obturator muscles after PCa radiotherapy. © 2018 American Association of Physicists in Medicine.

QEEG Spectral and Coherence Assessment of Autistic Children in Three Different Experimental Conditions

ERIC Educational Resources Information Center

Machado, Calixto; Estévez, Mario; Leisman, Gerry; Melillo, Robert; Rodríguez, Rafael; DeFina, Phillip; Hernández, Adrián; Pérez-Nellar, Jesús; Naranjo, Rolando; Chinchilla, Mauricio; Garófalo, Nicolás; Vargas, José; Beltrán, Carlos

2015-01-01

We studied autistics by quantitative EEG spectral and coherence analysis during three experimental conditions: basal, watching a cartoon with audio (V-A), and with muted audio band (VwA). Significant reductions were found for the absolute power spectral density (PSD) in the central region for delta and theta, and in the posterior region for sigma…

An Empirical Study of the Distributional Changes in Higher Education among East, Middle and West China

ERIC Educational Resources Information Center

Jiang, Chunjiao; Li, Song

2008-01-01

Based on the quantitative research and comparative study method, this paper attempts to make a systematic study and analysis of regional differences which have existed since 1949 in higher education among East, Middle and West China. The study is intended to explore the causes, regional differences, social changes, and their co-related…

Model-free arterial spin labelling for cerebral blood flow quantification: introduction of regional arterial input functions identified by factor analysis.

PubMed

Knutsson, Linda; Bloch, Karin Markenroth; Holtås, Stig; Wirestam, Ronnie; Ståhlberg, Freddy

2008-05-01

To identify regional arterial input functions (AIFs) using factor analysis of dynamic studies (FADS) when quantification of perfusion is performed using model-free arterial spin labelling. Five healthy volunteers and one patient were examined on a 3-T Philips unit using quantitative STAR labelling of arterial regions (QUASAR). Two sets of images were retrieved, one where the arterial signal had been crushed and another where it was retained. FADS was applied to the arterial signal curves to acquire the AIFs. Perfusion maps were obtained using block-circulant SVD deconvolution and regional AIFs obtained by FADS. In the volunteers, the ASL experiment was repeated within 24 h. The patient was also examined using dynamic susceptibility contrast MRI. In the healthy volunteers, CBF was 64+/-10 ml/[min 100 g] (mean+/-S.D.) in GM and 24+/-4 ml/[min 100 g] in WM, while the mean aBV was 0.94% in GM and 0.25% in WM. Good CBF image quality and reasonable quantitative CBF values were obtained using the combined QUASAR/FADS technique. We conclude that FADS may be a useful supplement in the evaluation of ASL data using QUASAR.

Combinational pixel-by-pixel and object-level classifying, segmenting, and agglomerating in performing quantitative image analysis that distinguishes between healthy non-cancerous and cancerous cell nuclei and delineates nuclear, cytoplasm, and stromal material objects from stained biological tissue materials

DOEpatents

Boucheron, Laura E

2013-07-16

Quantitative object and spatial arrangement-level analysis of tissue are detailed using expert (pathologist) input to guide the classification process. A two-step method is disclosed for imaging tissue, by classifying one or more biological materials, e.g. nuclei, cytoplasm, and stroma, in the tissue into one or more identified classes on a pixel-by-pixel basis, and segmenting the identified classes to agglomerate one or more sets of identified pixels into segmented regions. Typically, the one or more biological materials comprises nuclear material, cytoplasm material, and stromal material. The method further allows a user to markup the image subsequent to the classification to re-classify said materials. The markup is performed via a graphic user interface to edit designated regions in the image.

Geospatial Resource Access Analysis In Hedaru, Tanzania

NASA Astrophysics Data System (ADS)

Clark, Dylan G.; Premkumar, Deepak; Mazur, Robert; Kisimbo, Elibariki

2013-12-01

Populations around the world are facing increased impacts of anthropogenic-induced environmental changes and rapid population movements. These environmental and social shifts are having an elevated impact on the livelihoods of agriculturalists and pastoralists in developing countries. This appraisal integrates various tools—usually used independently— to gain a comprehensive understanding of the regional livelihood constraints in the rural Hedaru Valley of northeastern Tanzania. Conducted in three villages with different natural resources, using three primary methods: 1) participatory mapping of infrastructures; 2) administration of quantitative, spatially-tied surveys (n=80) and focus groups (n=14) that examined land use, household health, education, and demographics; 3) conducting quantitative time series analysis of Landsat- based Normalized Difference Vegetation Index images. Through various geospatial and multivariate linear regression analyses, significant geospatial trends emerged. This research added to the academic understanding of the region while establishing pathways for climate change adaptation strategies.

Regional fringe analysis for improving depth measurement in phase-shifting fringe projection profilometry

NASA Astrophysics Data System (ADS)

Chien, Kuang-Che Chang; Tu, Han-Yen; Hsieh, Ching-Huang; Cheng, Chau-Jern; Chang, Chun-Yen

2018-01-01

This study proposes a regional fringe analysis (RFA) method to detect the regions of a target object in captured shifted images to improve depth measurement in phase-shifting fringe projection profilometry (PS-FPP). In the RFA method, region-based segmentation is exploited to segment the de-fringed image of a target object, and a multi-level fuzzy-based classification with five presented features is used to analyze and discriminate the regions of an object from the segmented regions, which were associated with explicit fringe information. Then, in the experiment, the performance of the proposed method is tested and evaluated on 26 test cases made of five types of materials. The qualitative and quantitative results demonstrate that the proposed RFA method can effectively detect the desired regions of an object to improve depth measurement in the PS-FPP system.

Quantitative background parenchymal uptake on molecular breast imaging and breast cancer risk: a case-control study.

PubMed

Hruska, Carrie B; Geske, Jennifer R; Swanson, Tiffinee N; Mammel, Alyssa N; Lake, David S; Manduca, Armando; Conners, Amy Lynn; Whaley, Dana H; Scott, Christopher G; Carter, Rickey E; Rhodes, Deborah J; O'Connor, Michael K; Vachon, Celine M

2018-06-05

Background parenchymal uptake (BPU), which refers to the level of Tc-99m sestamibi uptake within normal fibroglandular tissue on molecular breast imaging (MBI), has been identified as a breast cancer risk factor, independent of mammographic density. Prior analyses have used subjective categories to describe BPU. We evaluate a new quantitative method for assessing BPU by testing its reproducibility, comparing quantitative results with previously established subjective BPU categories, and determining the association of quantitative BPU with breast cancer risk. Two nonradiologist operators independently performed region-of-interest analysis on MBI images viewed in conjunction with corresponding digital mammograms. Quantitative BPU was defined as a unitless ratio of the average pixel intensity (counts/pixel) within the fibroglandular tissue versus the average pixel intensity in fat. Operator agreement and the correlation of quantitative BPU measures with subjective BPU categories assessed by expert radiologists were determined. Percent density on mammograms was estimated using Cumulus. The association of quantitative BPU with breast cancer (per one unit BPU) was examined within an established case-control study of 62 incident breast cancer cases and 177 matched controls. Quantitative BPU ranged from 0.4 to 3.2 across all subjects and was on average higher in cases compared to controls (1.4 versus 1.2, p < 0.007 for both operators). Quantitative BPU was strongly correlated with subjective BPU categories (Spearman's r = 0.59 to 0.69, p < 0.0001, for each paired combination of two operators and two radiologists). Interoperator and intraoperator agreement in the quantitative BPU measure, assessed by intraclass correlation, was 0.92 and 0.98, respectively. Quantitative BPU measures showed either no correlation or weak negative correlation with mammographic percent density. In a model adjusted for body mass index and percent density, higher quantitative BPU was associated with increased risk of breast cancer for both operators (OR = 4.0, 95% confidence interval (CI) 1.6-10.1, and 2.4, 95% CI 1.2-4.7). Quantitative measurement of BPU, defined as the ratio of average counts in fibroglandular tissue relative to that in fat, can be reliably performed by nonradiologist operators with a simple region-of-interest analysis tool. Similar to results obtained with subjective BPU categories, quantitative BPU is a functional imaging biomarker of breast cancer risk, independent of mammographic density and hormonal factors.

Fatigue crack growth in an aluminum alloy-fractographic study

NASA Astrophysics Data System (ADS)

Salam, I.; Muhammad, W.; Ejaz, N.

2016-08-01

A two-fold approach was adopted to understand the fatigue crack growth process in an Aluminum alloy; fatigue crack growth test of samples and analysis of fractured surfaces. Fatigue crack growth tests were conducted on middle tension M(T) samples prepared from an Aluminum alloy cylinder. The tests were conducted under constant amplitude loading at R ratio 0.1. The stress applied was from 20,30 and 40 per cent of the yield stress of the material. The fatigue crack growth data was recorded. After fatigue testing, the samples were subjected to detailed scanning electron microscopic (SEM) analysis. The resulting fracture surfaces were subjected to qualitative and quantitative fractographic examinations. Quantitative fracture analysis included an estimation of crack growth rate (CGR) in different regions. The effect of the microstructural features on fatigue crack growth was examined. It was observed that in stage II (crack growth region), the failure mode changes from intergranular to transgranular as the stress level increases. In the region of intergranular failure the localized brittle failure was observed and fatigue striations are difficult to reveal. However, in the region of transgranular failure the crack path is independent of the microstructural features. In this region, localized ductile failure mode was observed and well defined fatigue striations were present in the wake of fatigue crack. The effect of interaction of growing fatigue crack with microstructural features was not substantial. The final fracture (stage III) was ductile in all the cases.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells.

PubMed

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W; Gautier, Virginie W

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip.

MATtrack: A MATLAB-Based Quantitative Image Analysis Platform for Investigating Real-Time Photo-Converted Fluorescent Signals in Live Cells

PubMed Central

Courtney, Jane; Woods, Elena; Scholz, Dimitri; Hall, William W.; Gautier, Virginie W.

2015-01-01

We introduce here MATtrack, an open source MATLAB-based computational platform developed to process multi-Tiff files produced by a photo-conversion time lapse protocol for live cell fluorescent microscopy. MATtrack automatically performs a series of steps required for image processing, including extraction and import of numerical values from Multi-Tiff files, red/green image classification using gating parameters, noise filtering, background extraction, contrast stretching and temporal smoothing. MATtrack also integrates a series of algorithms for quantitative image analysis enabling the construction of mean and standard deviation images, clustering and classification of subcellular regions and injection point approximation. In addition, MATtrack features a simple user interface, which enables monitoring of Fluorescent Signal Intensity in multiple Regions of Interest, over time. The latter encapsulates a region growing method to automatically delineate the contours of Regions of Interest selected by the user, and performs background and regional Average Fluorescence Tracking, and automatic plotting. Finally, MATtrack computes convenient visualization and exploration tools including a migration map, which provides an overview of the protein intracellular trajectories and accumulation areas. In conclusion, MATtrack is an open source MATLAB-based software package tailored to facilitate the analysis and visualization of large data files derived from real-time live cell fluorescent microscopy using photoconvertible proteins. It is flexible, user friendly, compatible with Windows, Mac, and Linux, and a wide range of data acquisition software. MATtrack is freely available for download at eleceng.dit.ie/courtney/MATtrack.zip. PMID:26485569

Accelerated Brain DCE-MRI Using Iterative Reconstruction With Total Generalized Variation Penalty for Quantitative Pharmacokinetic Analysis: A Feasibility Study.

PubMed

Wang, Chunhao; Yin, Fang-Fang; Kirkpatrick, John P; Chang, Zheng

2017-08-01

To investigate the feasibility of using undersampled k-space data and an iterative image reconstruction method with total generalized variation penalty in the quantitative pharmacokinetic analysis for clinical brain dynamic contrast-enhanced magnetic resonance imaging. Eight brain dynamic contrast-enhanced magnetic resonance imaging scans were retrospectively studied. Two k-space sparse sampling strategies were designed to achieve a simulated image acquisition acceleration factor of 4. They are (1) a golden ratio-optimized 32-ray radial sampling profile and (2) a Cartesian-based random sampling profile with spatiotemporal-regularized sampling density constraints. The undersampled data were reconstructed to yield images using the investigated reconstruction technique. In quantitative pharmacokinetic analysis on a voxel-by-voxel basis, the rate constant K trans in the extended Tofts model and blood flow F B and blood volume V B from the 2-compartment exchange model were analyzed. Finally, the quantitative pharmacokinetic parameters calculated from the undersampled data were compared with the corresponding calculated values from the fully sampled data. To quantify each parameter's accuracy calculated using the undersampled data, error in volume mean, total relative error, and cross-correlation were calculated. The pharmacokinetic parameter maps generated from the undersampled data appeared comparable to the ones generated from the original full sampling data. Within the region of interest, most derived error in volume mean values in the region of interest was about 5% or lower, and the average error in volume mean of all parameter maps generated through either sampling strategy was about 3.54%. The average total relative error value of all parameter maps in region of interest was about 0.115, and the average cross-correlation of all parameter maps in region of interest was about 0.962. All investigated pharmacokinetic parameters had no significant differences between the result from original data and the reduced sampling data. With sparsely sampled k-space data in simulation of accelerated acquisition by a factor of 4, the investigated dynamic contrast-enhanced magnetic resonance imaging pharmacokinetic parameters can accurately estimate the total generalized variation-based iterative image reconstruction method for reliable clinical application.

Acoustic Facies Analysis of Side-Scan Sonar Data

NASA Astrophysics Data System (ADS)

Dwan, Fa Shu

Acoustic facies analysis methods have allowed the generation of system-independent values for the quantitative seafloor acoustic parameter, backscattering strength, from GLORIA and (TAMU) ^2 side-scan sonar data. The resulting acoustic facies parameters enable quantitative comparisons of data collected by different sonar systems, data from different environments, and measurements made with survey geometries. Backscattering strength values were extracted from the sonar amplitude data by inversion based on the sonar equation. Image processing products reveal seafloor features and patterns of relative intensity. To quantitatively compare data collected at different times or by different systems, and to ground truth-measurements and geoacoustic models, quantitative corrections must be made on any given data set for system source level, beam pattern, time-varying gain, processing gain, transmission loss, absorption, insonified area contribution, and grazing angle effects. In the sonar equation, backscattering strength is the sonar parameter which is directly related to seafloor properties. The GLORIA data used in this study are from the edge of a distal lobe of the Monterey Fan. An interfingered region of strong and weak seafloor signal returns from a flat seafloor region provides an ideal data set for this study. Inversion of imagery data from the region allows the quantitative definition of different acoustic facies. The (TAMU) ^2 data used are from a calibration site near the Green Canyon area of the Gulf of Mexico. Acoustic facies analysis techniques were implemented to generate statistical information for acoustic facies based on the estimates of backscattering strength. The backscattering strength values have been compared with Lambert's Law and other functions to parameterize the description of the acoustic facies. The resulting Lambertian constant values range from -26 dB to -36 dB. A modified Lambert relationship, which consists of both intercept and slope terms, appears to represent the BSS versus grazing angle profiles better based on chi^2 testing and error ellipse generation. Different regression functions, composed of trigonometric functions, were analyzed for different segments of the BSS profiles. A cotangent or sine/cosine function shows promising results for representing the entire grazing angle span of the BSS profiles.

The health impact of trade and investment agreements: a quantitative systematic review and network co-citation analysis.

PubMed

Barlow, Pepita; McKee, Martin; Basu, Sanjay; Stuckler, David

2017-03-08

Regional trade agreements are major international policy instruments that shape macro-economic and political systems. There is widespread debate as to whether and how these agreements pose risks to public health. Here we perform a comprehensive systematic review of quantitative studies of the health impact of trade and investment agreements. We identified studies from searches in PubMed, Web of Science, EMBASE, and Global Health Online. Research articles were eligible for inclusion if they were quantitative studies of the health impacts of trade and investment agreements or policy. We systematically reviewed study findings, evaluated quality using the Quality Assessment Tool from the Effective Public Health Practice Project, and performed network citation analysis to study disciplinary siloes. Seventeen quantitative studies met our inclusion criteria. There was consistent evidence that implementing trade agreements was associated with increased consumption of processed foods and sugar-sweetened beverages. Granting import licenses for patented drugs was associated with increased access to pharmaceuticals. Implementing trade agreements and associated policies was also correlated with higher cardiovascular disease incidence and higher Body Mass Index (BMI), whilst correlations with tobacco consumption, under-five mortality, maternal mortality, and life expectancy were inconclusive. Overall, the quality of studies is weak or moderately weak, and co-citation analysis revealed a relative isolation of public health from economics. We identified limitations in existing studies which preclude definitive conclusions of the health impacts of regional trade and investment agreements. Few address unobserved confounding, and many possible consequences and mechanisms linking trade and investment agreements to health remain poorly understood. Results from our co-citation analysis suggest scope for greater interdisciplinary collaboration. Notwithstanding these limitations, our results find evidence that trade agreements pose some significant health risks. Health protections in trade and investment treaties may mitigate these impacts.

An innovative expression model of human health risk based on the quantitative analysis of soil metals sources contribution in different spatial scales.

PubMed

Zhang, Yimei; Li, Shuai; Wang, Fei; Chen, Zhuang; Chen, Jie; Wang, Liqun

2018-09-01

Toxicity of heavy metals from industrialization poses critical concern, and analysis of sources associated with potential human health risks is of unique significance. Assessing human health risk of pollution sources (factored health risk) concurrently in the whole and the sub region can provide more instructive information to protect specific potential victims. In this research, we establish a new expression model of human health risk based on quantitative analysis of sources contribution in different spatial scales. The larger scale grids and their spatial codes are used to initially identify the level of pollution risk, the type of pollution source and the sensitive population at high risk. The smaller scale grids and their spatial codes are used to identify the contribution of various sources of pollution to each sub region (larger grid) and to assess the health risks posed by each source for each sub region. The results of case study show that, for children (sensitive populations, taking school and residential area as major region of activity), the major pollution source is from the abandoned lead-acid battery plant (ALP), traffic emission and agricultural activity. The new models and results of this research present effective spatial information and useful model for quantifying the hazards of source categories and human health a t complex industrial system in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

Atmospheric Environment Vulnerability Cause Analysis for the Beijing-Tianjin-Hebei Metropolitan Region

PubMed Central

Zhang, Yang; Shen, Jing; Li, Yu

2018-01-01

Assessing and quantifying atmospheric vulnerability is a key issue in urban environmental protection and management. This paper integrated the Analytical hierarchy process (AHP), fuzzy synthesis evaluation and Geographic Information System (GIS) spatial analysis into an Exposure-Sensitivity-Adaptive capacity (ESA) framework to quantitatively assess atmospheric environment vulnerability in the Beijing-Tianjin-Hebei (BTH) region with spatial and temporal comparisons. The elaboration of the relationships between atmospheric environment vulnerability and indices of exposure, sensitivity, and adaptive capacity supports enable analysis of the atmospheric environment vulnerability. Our findings indicate that the atmospheric environment vulnerability of 13 cities in the BTH region exhibits obvious spatial heterogeneity, which is caused by regional diversity in exposure, sensitivity, and adaptive capacity indices. The results of atmospheric environment vulnerability assessment and the cause analysis can provide guidance to pick out key control regions and recognize vulnerable indicators for study sites. The framework developed in this paper can also be replicated at different spatial and temporal scales using context-specific datasets to support environmental management. PMID:29342852

Atmospheric Environment Vulnerability Cause Analysis for the Beijing-Tianjin-Hebei Metropolitan Region.

PubMed

Zhang, Yang; Shen, Jing; Li, Yu

2018-01-13

Assessing and quantifying atmospheric vulnerability is a key issue in urban environmental protection and management. This paper integrated the Analytical hierarchy process (AHP), fuzzy synthesis evaluation and Geographic Information System (GIS) spatial analysis into an Exposure-Sensitivity-Adaptive capacity (ESA) framework to quantitatively assess atmospheric environment vulnerability in the Beijing-Tianjin-Hebei (BTH) region with spatial and temporal comparisons. The elaboration of the relationships between atmospheric environment vulnerability and indices of exposure, sensitivity, and adaptive capacity supports enable analysis of the atmospheric environment vulnerability. Our findings indicate that the atmospheric environment vulnerability of 13 cities in the BTH region exhibits obvious spatial heterogeneity, which is caused by regional diversity in exposure, sensitivity, and adaptive capacity indices. The results of atmospheric environment vulnerability assessment and the cause analysis can provide guidance to pick out key control regions and recognize vulnerable indicators for study sites. The framework developed in this paper can also be replicated at different spatial and temporal scales using context-specific datasets to support environmental management.

Genome-wide Linkage Analysis for Identifying Quantitative Trait Loci Involved in the Regulation of Lipoprotein a (Lpa) Levels

PubMed Central

López, Sonia; Buil, Alfonso; Ordoñez, Jordi; Souto, Juan Carlos; Almasy, Laura; Lathrop, Mark; Blangero, John; Blanco-Vaca, Francisco; Fontcuberta, Jordi; Soria, José Manuel

2009-01-01

Lipoprotein Lp(a) levels are highly heritable and are associated with cardiovascular risk. We performed a genome-wide linkage analysis to delineate the genomic regions that influence the concentration of Lp(a) in families from the Genetic Analysis of Idiopathic Thrombophilia (GAIT) Project. Lp(a) levels were measured in 387 individuals belonging to 21 extended Spanish families. A total of 485 DNA microsatellite markers were genotyped to provide a 7.1 cM genetic map. A variance component linkage method was used to evaluate linkage and to detect quantitative trait loci (QTLs). The main QTL that showed strong evidence of linkage with Lp(a) levels was located at the structural gene for apo(a) on Chromosome 6 (LOD score=13.8). Interestingly, another QTL influencing Lp(a) concentration was located on Chromosome 2 with a LOD score of 2.01. This region contains several candidate genes. One of them is the tissue factor pathway inhibitor (TFPI), which has antithrombotic action and also has the ability to bind lipoproteins. However, quantitative trait association analyses performed with 12 SNPs in TFPI gene revealed no association with Lp(a) levels. Our study confirms previous results on the genetic basis of Lp(a) levels. In addition, we report a new QTL on Chromosome 2 involved in the quantitative variation of Lp(a). These data should serve as the basis for further detection of candidate genes and to elucidate the relationship between the concentration of Lp(a) and cardiovascular risk. PMID:18560444

PET brain kinetics studies of 11C-ITMM and 11C-ITDM,radioprobes for metabotropic glutamate receptor type 1, in a nonhuman primate

PubMed Central

Yamasaki, Tomoteru; Maeda, Jun; Fujinaga, Masayuki; Nagai, Yuji; Hatori, Akiko; Yui, Joji; Xie, Lin; Nengaki, Nobuki; Zhang, Ming-Rong

2014-01-01

The metabotropic glutamate receptor type 1 (mGluR1) is a novel target protein for the development of new drugs against central nervous system disorders. Recently, we have developed 11C-labeled PET probes 11C-ITMM and 11C-ITDM, which demonstrate similar profiles, for imaging of mGluR1. In the present study, we compared 11C-ITMM and 11C-ITDM PET imaging and quantitative analysis in the monkey brain. Respective PET images showed similar distribution of uptake in the cerebellum, thalamus, and cingulate cortex. Slightly higher uptake was detected with 11C-ITDM than with 11C-ITMM. For the kinetic analysis using the two-tissue compartment model (2-TCM), the distribution volume (VT) in the cerebellum, an mGluR1-rich region in the brain, was 2.5 mL∙cm-3 for 11C-ITMM and 3.6 mL∙cm-3 for 11C-ITDM. By contrast, the VT in the pons, a region with negligible mGluR1 expression, was similarly low for both radiopharmaceuticals. Based on these results, we performed noninvasive PET quantitative analysis with general reference tissue models using the time-activity curve of the pons as a reference region. We confirmed the relationship and differences between the reference tissue models and 2-TCM using correlational scatter plots and Bland-Altman plots analyses. Although the scattergrams of both radiopharmaceuticals showed over- or underestimations of reference tissue model-based the binding potentials against 2-TCM, there were no significant differences between the two kinetic analysis models. In conclusion, we first demonstrated the potentials of 11C-ITMM and 11C-ITDM for noninvasive PET quantitative analysis using reference tissue models. In addition, our findings suggest that 11C-ITDM may be superior to 11C-ITMM as a PET probe for imaging of mGluR1, because regional VT values in PET with 11C-ITDM were higher than those of 11C-ITMM. Clinical studies of 11C-ITDM in humans will be necessary in the future. PMID:24795840

PET brain kinetics studies of (11)C-ITMM and (11)C-ITDM,radioprobes for metabotropic glutamate receptor type 1, in a nonhuman primate.

PubMed

Yamasaki, Tomoteru; Maeda, Jun; Fujinaga, Masayuki; Nagai, Yuji; Hatori, Akiko; Yui, Joji; Xie, Lin; Nengaki, Nobuki; Zhang, Ming-Rong

2014-01-01

The metabotropic glutamate receptor type 1 (mGluR1) is a novel target protein for the development of new drugs against central nervous system disorders. Recently, we have developed (11)C-labeled PET probes (11)C-ITMM and (11)C-ITDM, which demonstrate similar profiles, for imaging of mGluR1. In the present study, we compared (11)C-ITMM and (11)C-ITDM PET imaging and quantitative analysis in the monkey brain. Respective PET images showed similar distribution of uptake in the cerebellum, thalamus, and cingulate cortex. Slightly higher uptake was detected with (11)C-ITDM than with (11)C-ITMM. For the kinetic analysis using the two-tissue compartment model (2-TCM), the distribution volume (VT) in the cerebellum, an mGluR1-rich region in the brain, was 2.5 mL∙cm(-3) for (11)C-ITMM and 3.6 mL∙cm(-3) for (11)C-ITDM. By contrast, the VT in the pons, a region with negligible mGluR1 expression, was similarly low for both radiopharmaceuticals. Based on these results, we performed noninvasive PET quantitative analysis with general reference tissue models using the time-activity curve of the pons as a reference region. We confirmed the relationship and differences between the reference tissue models and 2-TCM using correlational scatter plots and Bland-Altman plots analyses. Although the scattergrams of both radiopharmaceuticals showed over- or underestimations of reference tissue model-based the binding potentials against 2-TCM, there were no significant differences between the two kinetic analysis models. In conclusion, we first demonstrated the potentials of (11)C-ITMM and (11)C-ITDM for noninvasive PET quantitative analysis using reference tissue models. In addition, our findings suggest that (11)C-ITDM may be superior to (11)C-ITMM as a PET probe for imaging of mGluR1, because regional VT values in PET with (11)C-ITDM were higher than those of (11)C-ITMM. Clinical studies of (11)C-ITDM in humans will be necessary in the future.

Quantitative Imaging in Cancer Evolution and Ecology

PubMed Central

Grove, Olya; Gillies, Robert J.

2013-01-01

Cancer therapy, even when highly targeted, typically fails because of the remarkable capacity of malignant cells to evolve effective adaptations. These evolutionary dynamics are both a cause and a consequence of cancer system heterogeneity at many scales, ranging from genetic properties of individual cells to large-scale imaging features. Tumors of the same organ and cell type can have remarkably diverse appearances in different patients. Furthermore, even within a single tumor, marked variations in imaging features, such as necrosis or contrast enhancement, are common. Similar spatial variations recently have been reported in genetic profiles. Radiologic heterogeneity within tumors is usually governed by variations in blood flow, whereas genetic heterogeneity is typically ascribed to random mutations. However, evolution within tumors, as in all living systems, is subject to Darwinian principles; thus, it is governed by predictable and reproducible interactions between environmental selection forces and cell phenotype (not genotype). This link between regional variations in environmental properties and cellular adaptive strategies may permit clinical imaging to be used to assess and monitor intratumoral evolution in individual patients. This approach is enabled by new methods that extract, report, and analyze quantitative, reproducible, and mineable clinical imaging data. However, most current quantitative metrics lack spatialness, expressing quantitative radiologic features as a single value for a region of interest encompassing the whole tumor. In contrast, spatially explicit image analysis recognizes that tumors are heterogeneous but not well mixed and defines regionally distinct habitats, some of which appear to harbor tumor populations that are more aggressive and less treatable than others. By identifying regional variations in key environmental selection forces and evidence of cellular adaptation, clinical imaging can enable us to define intratumoral Darwinian dynamics before and during therapy. Advances in image analysis will place clinical imaging in an increasingly central role in the development of evolution-based patient-specific cancer therapy. © RSNA, 2013 PMID:24062559

Non-destructive and fast identification of cotton-polyester blend fabrics by the portable near-infrared spectrometer.

PubMed

Li, Wen-xia; Li, Feng; Zhao, Guo-liang; Tang, Shi-jun; Liu, Xiao-ying

2014-12-01

A series of 376 cotton-polyester (PET) blend fabrics were studied by a portable near-infrared (NIR) spectrometer. A NIR semi-quantitative-qualitative calibration model was established by Partial Least Squares (PLS) method combined with qualitative identification coefficient. In this process, PLS method in a quantitative analysis was used as a correction method, and the qualitative identification coefficient was set by the content of cotton and polyester in blend fabrics. Cotton-polyester blend fabrics were identified qualitatively by the model and their relative contents were obtained quantitatively, the model can be used for semi-quantitative identification analysis. In the course of establishing the model, the noise and baseline drift of the spectra were eliminated by Savitzky-Golay(S-G) derivative. The influence of waveband selection and different pre-processing method was also studied in the qualitative calibration model. The major absorption bands of 100% cotton samples were in the 1400~1600 nm region, and the one for 100% polyester were around 1600~1800 nm, the absorption intensity was enhancing with the content increasing of cotton or polyester. Therefore, the cotton-polyester's major absorption region was selected as the base waveband, the optimal waveband (1100~2500 nm) was found by expanding the waveband in two directions (the correlation coefficient was 0.6, and wave-point number was 934). The validation samples were predicted by the calibration model, the results showed that the model evaluation parameters was optimum in the 1100~2500 nm region, and the combination of S-G derivative, multiplicative scatter correction (MSC) and mean centering was used as the pre-processing method. RC (relational coefficient of calibration) value was 0.978, RP (relational coefficient of prediction) value was 0.940, SEC (standard error of calibration) value was 1.264, SEP (standard error of prediction) value was 1.590, and the sample's recognition accuracy was up to 93.4%. It showed that the cotton-polyester blend fabrics could be predicted by the semi-quantitative-qualitative calibration model.

Effect of vision, touch and stance on cerebellar vermian-related sway and tremor: a quantitative physiological and MRI study.

PubMed

Sullivan, Edith V; Rose, Jessica; Pfefferbaum, Adolf

2006-08-01

Postural balance is impaired in individuals with pathology of the anterior superior vermis of the cerebellum. Chronic alcoholism, with its known vermian pathology, provides a viable model for studying the relationship between cerebellar pathology and postural stability. Decades of separate study of recovering alcoholics and post-mortem neuroanatomical analysis have demonstrated vermian pathology but few studies have used quantitative posturography, acquired concurrently with quantitative neuroimaging, to establish whether this brain structure-function relationship is selective in vivo. Here, 30 healthy men and 39 chronic alcoholic men, abstinent from alcohol for several months, underwent MRI for volumetric quantitation of the cerebellar vermis and three comparison brain regions, the cerebellar hemispheres, supratentorial cortex and corpus callosum. All subjects also participated in an experiment involving a force platform that measured sway path length and tremor during static standing balance under four sensory conditions and two stance conditions. Three novel findings emerged: (i) sway path length, a physiological index of postural control, was selectively related to volume of the cerebellar vermis and not to any comparison brain region in the alcoholics; (ii) spectral analysis revealed sway prominence in the 2-5 Hz band, another physiological sign of vermian lesions and also selectively related to vermian volume in the alcoholics; and (iii) despite substantial postural sway in the patients, they successfully used vision, touch and stance to normalize sway and reduce tremor. The selective relationship of sway path to vermian but not lateral cerebellar volume provides correlational evidence for functional differentiation of these cerebellar regions. Improvement to virtual normal levels in balance and reduction in sway and tremor with changes in vision, touch and stance provide evidence that adaptive mechanisms recruiting sensorimotor integration can be invoked to compensate for underlying cerebellar vermian-related dysfunction.

Association analysis of rare variants near the APOE region with CSF and neuroimaging biomarkers of Alzheimer's disease.

PubMed

Nho, Kwangsik; Kim, Sungeun; Horgusluoglu, Emrin; Risacher, Shannon L; Shen, Li; Kim, Dokyoon; Lee, Seunggeun; Foroud, Tatiana; Shaw, Leslie M; Trojanowski, John Q; Aisen, Paul S; Petersen, Ronald C; Jack, Clifford R; Weiner, Michael W; Green, Robert C; Toga, Arthur W; Saykin, Andrew J

2017-05-24

The APOE ε4 allele is the most significant common genetic risk factor for late-onset Alzheimer's disease (LOAD). The region surrounding APOE on chromosome 19 has also shown consistent association with LOAD. However, no common variants in the region remain significant after adjusting for APOE genotype. We report a rare variant association analysis of genes in the vicinity of APOE with cerebrospinal fluid (CSF) and neuroimaging biomarkers of LOAD. Whole genome sequencing (WGS) was performed on 817 blood DNA samples from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Sequence data from 757 non-Hispanic Caucasian participants was used in the present analysis. We extracted all rare variants (MAF (minor allele frequency) < 0.05) within a 312 kb window in APOE's vicinity encompassing 12 genes. We assessed CSF and neuroimaging (MRI and PET) biomarkers as LOAD-related quantitative endophenotypes. Gene-based analyses of rare variants were performed using the optimal Sequence Kernel Association Test (SKAT-O). A total of 3,334 rare variants (MAF < 0.05) were found within the APOE region. Among them, 72 rare non-synonymous variants were observed. Eight genes spanning the APOE region were significantly associated with CSF Aβ 1-42 (p < 1.0 × 10 -3 ). After controlling for APOE genotype and adjusting for multiple comparisons, 4 genes (CBLC, BCAM, APOE, and RELB) remained significant. Whole-brain surface-based analysis identified highly significant clusters associated with rare variants of CBLC in the temporal lobe region including the entorhinal cortex, as well as frontal lobe regions. Whole-brain voxel-wise analysis of amyloid PET identified significant clusters in the bilateral frontal and parietal lobes showing associations of rare variants of RELB with cortical amyloid burden. Rare variants within genes spanning the APOE region are significantly associated with LOAD-related CSF Aβ 1-42 and neuroimaging biomarkers after adjusting for APOE genotype. These findings warrant further investigation and illustrate the role of next generation sequencing and quantitative endophenotypes in assessing rare variants which may help explain missing heritability in AD and other complex diseases.

Teaching bioinformatics and neuroinformatics by using free web-based tools.

PubMed

Grisham, William; Schottler, Natalie A; Valli-Marill, Joanne; Beck, Lisa; Beatty, Jackson

2010-01-01

This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). Instructors can use these various websites in concert to teach genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, quantitative trait locus analysis, and molecular biology (including in situ hybridization and microarray analysis), and to introduce bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the phenotypic trait, 2) a list of candidate genes-narrowed by expression data, 3) the in situ pattern of a given gene in the region of interest, 4) the nucleotide sequence of the candidate gene, and 5) articles describing the gene. Teaching materials such as a detailed student/instructor's manual, PowerPoints, sample exams, and links to free Web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.

Simultaneous qualitative and quantitative analysis of flavonoids and alkaloids from the leaves of Nelumbo nucifera Gaertn. using high-performance liquid chromatography with quadrupole time-of-flight mass spectrometry.

PubMed

Guo, Yujie; Chen, Xi; Qi, Jin; Yu, Boyang

2016-07-01

A reliable method, combining qualitative analysis by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry and quantitative assessment by high-performance liquid chromatography with photodiode array detection, has been developed to simultaneously analyze flavonoids and alkaloids in lotus leaf extracts. In the qualitative analysis, a total of 30 compounds, including 12 flavonoids, 16 alkaloids, and two proanthocyanidins, were identified. The fragmentation behaviors of four types of flavone glycoside and three types of alkaloid are summarized. The mass spectra of four representative components, quercetin 3-O-glucuronide, norcoclaurine, nuciferine, and neferine, are shown to illustrate their fragmentation pathways. Five pairs of isomers were detected and three of them were distinguished by comparing the elution order with reference substances and the mass spectrometry data with reported data. In the quantitative analysis, 30 lotus leaf samples from different regions were analyzed to investigate the proportion of eight representative compounds. Quercetin 3-O-glucuronide was found to be the predominant constituent of lotus leaf extracts. For further discrimination among the samples, hierarchical cluster analysis, and principal component analysis, based on the areas of the eight quantitative peaks, were carried out. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Application of Classification Algorithm of Machine Learning and Buffer Analysis in Torism Regional Planning

NASA Astrophysics Data System (ADS)

Zhang, T. H.; Ji, H. W.; Hu, Y.; Ye, Q.; Lin, Y.

2018-04-01

Remote Sensing (RS) and Geography Information System (GIS) technologies are widely used in ecological analysis and regional planning. With the advantages of large scale monitoring, combination of point and area, multiple time-phases and repeated observation, they are suitable for monitoring and analysis of environmental information in a large range. In this study, support vector machine (SVM) classification algorithm is used to monitor the land use and land cover change (LUCC), and then to perform the ecological evaluation for Chaohu lake tourism area quantitatively. The automatic classification and the quantitative spatial-temporal analysis for the Chaohu Lake basin are realized by the analysis of multi-temporal and multispectral satellite images, DEM data and slope information data. Furthermore, the ecological buffer zone analysis is also studied to set up the buffer width for each catchment area surrounding Chaohu Lake. The results of LUCC monitoring from 1992 to 2015 has shown obvious affections by human activities. Since the construction of the Chaohu Lake basin is in the crucial stage of the rapid development of urbanization, the application of RS and GIS technique can effectively provide scientific basis for land use planning, ecological management, environmental protection and tourism resources development in the Chaohu Lake Basin.

Quantitative analysis of interfacial chemistry in TiC/Ti composite using electron-energy-loss spectroscopy

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

Gu, M.; Jiang, W.; Zhang, G.

Due to titanium carbide`s physical and elastic properties, titanium carbide particles are widely used as a reinforcement in titanium-alloy-based composites. Previous studies have shown that no obvious reaction products were detected on the interface region in TiC/Ti alloy systems; instead, a nonstoichiometric region in the TiC particle between the Ti{sub 6}Al{sub 4}V alloy and the stoichiometric TiC was found. However, the nature and the extent of the nonstoichiometric zone have not been quantitatively described. The present communication reports some results of a parallel electron-energy-loss spectroscopy (PEELS) study on a 10 vol pct TiC-particle-reinforced IMI-829 metal-matrix composite.

Quantitative 3D analysis of bone in hip osteoarthritis using clinical computed tomography.

PubMed

Turmezei, Tom D; Treece, Graham M; Gee, Andrew H; Fotiadou, Anastasia F; Poole, Kenneth E S

2016-07-01

To assess the relationship between proximal femoral cortical bone thickness and radiological hip osteoarthritis using quantitative 3D analysis of clinical computed tomography (CT) data. Image analysis was performed on clinical CT imaging data from 203 female volunteers with a technique called cortical bone mapping (CBM). Colour thickness maps were created for each proximal femur. Statistical parametric mapping was performed to identify statistically significant differences in cortical bone thickness that corresponded with the severity of radiological hip osteoarthritis. Kellgren and Lawrence (K&L) grade, minimum joint space width (JSW) and a novel CT-based osteophyte score were also blindly assessed from the CT data. For each increase in K&L grade, cortical thickness increased by up to 25 % in distinct areas of the superolateral femoral head-neck junction and superior subchondral bone plate. For increasing severity of CT osteophytes, the increase in cortical thickness was more circumferential, involving a wider portion of the head-neck junction, with up to a 7 % increase in cortical thickness per increment in score. Results were not significant for minimum JSW. These findings indicate that quantitative 3D analysis of the proximal femur can identify changes in cortical bone thickness relevant to structural hip osteoarthritis. • CT is being increasingly used to assess bony involvement in osteoarthritis • CBM provides accurate and reliable quantitative analysis of cortical bone thickness • Cortical bone is thicker at the superior femoral head-neck with worse osteoarthritis • Regions of increased thickness co-locate with impingement and osteophyte formation • Quantitative 3D bone analysis could enable clinical disease prediction and therapy development.

MANPOWER REQUIREMENTS AND DEMAND IN AGRICULTURE BY REGIONS AND NATIONALLY, WITH ESTIMATION OF VOCATIONAL TRAINING AND EDUCATIONAL NEEDS AND PRODUCTIVITY.

ERIC Educational Resources Information Center

ARCUS, PETER; HEADY, EARL O.

THE PURPOSE OF THIS STUDY IS TO ESTIMATE THE MANPOWER REQUIREMENTS FOR THE NATION FOR 144 REGIONS THE TYPES OF SKILLS AND WORK ABILITIES REQUIRED BY AGRICULTURE IN THE NEXT 15 YEARS, AND THE TYPES AND AMOUNTS OF EDUCATION NEEDED. THE QUANTITATIVE ANALYSIS IS BEING MADE BY METHODS APPROPRIATE TO THE PHASES OF THE STUDY--(1) INTERRELATIONS AMONG…

Descriptive approaches to landscape analysis

Treesearch

R. Burton Litton Jr.

1979-01-01

Descriptive landscape analyses include various procedures used to document visual/scenic resources. Historic and regional examples of landscape description represent desirable insight for contemporary professional inventory work. Routed and areal landscape inventories are discussed as basic tools. From them, qualitative and quantitative evaluations can be developed...

Soil cover patterns and dynamics impact on GHG fluxes in RF native and man-changed ecosystems

NASA Astrophysics Data System (ADS)

Vasenev, Ivan; Nesterova, Olga

2017-04-01

The increased soil spatial-temporal variability is mutual feature for most mature natural and particularly man-changed terrestrial ecosystems in Central and Far-East regions of Russia with soil cover strongly pronounced bioclimatic zoning and landscape-geomorphologic differentiation. Soil cover patterns (SCP) detailed morphogenetic analysis and typification is useful tool for soil forming and degradation processes quantitative evaluation, land ecological state and functional quality quantitative assessment. Quantitative analysis and functional-ecological interpretation of representative SCP spatial variability is especially important for environmentally friendly and demand-driven land-use planning and decision making. The carried out 33-years region- and local-scale researches of the wide zonal-provincial set of representative ecosystems and SCP with different types and history of land-use (forest, meadow-steppe, agricultural and recreational ones) give us the interregional multi-factorial matrix of elementary soil cover patterns (ESCP) with different land-use practices and history, soil-geomorphologic features, environmental and microclimate conditions. Succession process-based analysis of modern evolution of man-changed and natural soils and ESCP essentially increases accuracy of quantitative assessments of dominant soil forming and degradation processes rate and potential, their influence on land and soil cover quality and ecosystem services. Their results allow developing the regional and landscape adapted versions of automated land evaluation systems and land-use DSS. The validation and ranging of the limiting factors of ESCP regulation and develop¬ment, ecosystem principal services (with especial attention on greenhouse gases emissions, soil carbon dynamics and sequestration potential, biodiversity and productivity, hydrological regimes and geomorphologic stabilization), land functional qualities and agroecological state have been done for dominating and most dynamical components of ESCP regional-typological forms - with application of regional/local GIS, ESCP mapping, kriging, correlation tree models and adapted to region DSS. Key-site monitoring results and regional generalized data showed 1-1.5 % Corg lost during last 50 years period, active processes of CO2, CH4 and N2O emission (2-4-time variability in frame of one farm and of one vegetation season) and humus redistribution throw soil profile and soil cover patterns. Forest-steppe Chernozem ecosystems are usually characterized by more stable SCP than forest or steppe ones. The ratio between erosive and biological losses in humus supplies is estimated as fifty-fifty with strong spatial varia¬bility due to slope and land-use parameters. These problem agroecological situations can be essentially improved by climate-smart agriculture practice development with DSS-based landscape-adaptive land-use systems and organic farming stimulation with environmentally friendly technologies, adapted to conditions of concrete agrolandscapes in Central and Far-East Russia.

Linkage Analysis of Quantitative Refraction and Refractive Errors in the Beaver Dam Eye Study

PubMed Central

Duggal, Priya; Lee, Kristine E.; Cheng, Ching-Yu; Klein, Ronald; Bailey-Wilson, Joan E.; Klein, Barbara E. K.

2011-01-01

Purpose. Refraction, as measured by spherical equivalent, is the need for an external lens to focus images on the retina. While genetic factors play an important role in the development of refractive errors, few susceptibility genes have been identified. However, several regions of linkage have been reported for myopia (2q, 4q, 7q, 12q, 17q, 18p, 22q, and Xq) and for quantitative refraction (1p, 3q, 4q, 7p, 8p, and 11p). To replicate previously identified linkage peaks and to identify novel loci that influence quantitative refraction and refractive errors, linkage analysis of spherical equivalent, myopia, and hyperopia in the Beaver Dam Eye Study was performed. Methods. Nonparametric, sibling-pair, genome-wide linkage analyses of refraction (spherical equivalent adjusted for age, education, and nuclear sclerosis), myopia and hyperopia in 834 sibling pairs within 486 extended pedigrees were performed. Results. Suggestive evidence of linkage was found for hyperopia on chromosome 3, region q26 (empiric P = 5.34 × 10−4), a region that had shown significant genome-wide evidence of linkage to refraction and some evidence of linkage to hyperopia. In addition, the analysis replicated previously reported genome-wide significant linkages to 22q11 of adjusted refraction and myopia (empiric P = 4.43 × 10−3 and 1.48 × 10−3, respectively) and to 7p15 of refraction (empiric P = 9.43 × 10−4). Evidence was also found of linkage to refraction on 7q36 (empiric P = 2.32 × 10−3), a region previously linked to high myopia. Conclusions. The findings provide further evidence that genes controlling refractive errors are located on 3q26, 7p15, 7p36, and 22q11. PMID:21571680

Neurofilament protein defines regional patterns of cortical organization in the macaque monkey visual system: a quantitative immunohistochemical analysis

NASA Technical Reports Server (NTRS)

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

1995-01-01

Visual function in monkeys is subserved at the cortical level by a large number of areas defined by their specific physiological properties and connectivity patterns. For most of these cortical fields, a precise index of their degree of anatomical specialization has not yet been defined, although many regional patterns have been described using Nissl or myelin stains. In the present study, an attempt has been made to elucidate the regional characteristics, and to varying degrees boundaries, of several visual cortical areas in the macaque monkey using an antibody to neurofilament protein (SMI32). This antibody labels a subset of pyramidal neurons with highly specific regional and laminar distribution patterns in the cerebral cortex. Based on the staining patterns and regional quantitative analysis, as many as 28 cortical fields were reliably identified. Each field had a homogeneous distribution of labeled neurons, except area V1, where increases in layer IVB cell and in Meynert cell counts paralleled the increase in the degree of eccentricity in the visual field representation. Within the occipitotemporal pathway, areas V3 and V4 and fields in the inferior temporal cortex were characterized by a distinct population of neurofilament-rich neurons in layers II-IIIa, whereas areas located in the parietal cortex and part of the occipitoparietal pathway had a consistent population of large labeled neurons in layer Va. The mediotemporal areas MT and MST displayed a distinct population of densely labeled neurons in layer VI. Quantitative analysis of the laminar distribution of the labeled neurons demonstrated that the visual cortical areas could be grouped in four hierarchical levels based on the ratio of neuron counts between infragranular and supragranular layers, with the first (areas V1, V2, V3, and V3A) and third (temporal and parietal regions) levels characterized by low ratios and the second (areas MT, MST, and V4) and fourth (frontal regions) levels characterized by high to very high ratios. Such density trends may correspond to differential representation of corticocortically (and corticosubcortically) projecting neurons at several functional steps in the integration of the visual stimuli. In this context, it is possible that neurofilament protein is crucial for the unique capacity of certain subsets of neurons to perform the highly precise mapping functions of the monkey visual system.

Augmenting Amyloid PET Interpretations With Quantitative Information Improves Consistency of Early Amyloid Detection.

PubMed

Harn, Nicholas R; Hunt, Suzanne L; Hill, Jacqueline; Vidoni, Eric; Perry, Mark; Burns, Jeffrey M

2017-08-01

Establishing reliable methods for interpreting elevated cerebral amyloid-β plaque on PET scans is increasingly important for radiologists, as availability of PET imaging in clinical practice increases. We examined a 3-step method to detect plaque in cognitively normal older adults, focusing on the additive value of quantitative information during the PET scan interpretation process. Fifty-five F-florbetapir PET scans were evaluated by 3 experienced raters. Scans were first visually interpreted as having "elevated" or "nonelevated" plaque burden ("Visual Read"). Images were then processed using a standardized quantitative analysis software (MIMneuro) to generate whole brain and region of interest SUV ratios. This "Quantitative Read" was considered elevated if at least 2 of 6 regions of interest had an SUV ratio of more than 1.1. The final interpretation combined both visual and quantitative data together ("VisQ Read"). Cohen kappa values were assessed as a measure of interpretation agreement. Plaque was elevated in 25.5% to 29.1% of the 165 total Visual Reads. Interrater agreement was strong (kappa = 0.73-0.82) and consistent with reported values. Quantitative Reads were elevated in 45.5% of participants. Final VisQ Reads changed from initial Visual Reads in 16 interpretations (9.7%), with most changing from "nonelevated" Visual Reads to "elevated." These changed interpretations demonstrated lower plaque quantification than those initially read as "elevated" that remained unchanged. Interrater variability improved for VisQ Reads with the addition of quantitative information (kappa = 0.88-0.96). Inclusion of quantitative information increases consistency of PET scan interpretations for early detection of cerebral amyloid-β plaque accumulation.

Quantitative analysis of naphthenic acids in water by liquid chromatography-accurate mass time-of-flight mass spectrometry.

PubMed

Hindle, Ralph; Noestheden, Matthew; Peru, Kerry; Headley, John

2013-04-19

This study details the development of a routine method for quantitative analysis of oil sands naphthenic acids, which are a complex class of compounds found naturally and as contaminants in oil sands process waters from Alberta's Athabasca region. Expanding beyond classical naphthenic acids (CnH2n-zO2), those compounds conforming to the formula CnH2n-zOx (where 2≥x≤4) were examined in commercial naphthenic acid and environmental water samples. HPLC facilitated a five-fold reduction in ion suppression when compared to the more commonly used flow injection analysis. A comparison of 39 model naphthenic acids revealed significant variability in response factors, demonstrating the necessity of using naphthenic acid mixtures for quantitation, rather than model compounds. It was also demonstrated that naphthenic acidic heterogeneity (commercial and environmental) necessitates establishing a single NA mix as the standard against which all quantitation is performed. The authors present the first ISO17025 accredited method for the analysis of naphthenic acids in water using HPLC high resolution accurate mass time-of-flight mass spectrometry. The method detection limit was 1mg/L total oxy-naphthenic acids (Sigma technical mix). Copyright © 2013 Elsevier B.V. All rights reserved.

Three-dimensional modeling and quantitative analysis of gap junction distributions in cardiac tissue.

PubMed

Lackey, Daniel P; Carruth, Eric D; Lasher, Richard A; Boenisch, Jan; Sachse, Frank B; Hitchcock, Robert W

2011-11-01

Gap junctions play a fundamental role in intercellular communication in cardiac tissue. Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions. Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements. In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions. In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing. We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes. The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles. The methodology was tested in rat ventricular myocardium. Our analysis yielded novel quantitative data on gap junction distributions. In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis. We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium. Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction.

Spatial data analysis for exploration of regional scale geothermal resources

NASA Astrophysics Data System (ADS)

Moghaddam, Majid Kiavarz; Noorollahi, Younes; Samadzadegan, Farhad; Sharifi, Mohammad Ali; Itoi, Ryuichi

2013-10-01

Defining a comprehensive conceptual model of the resources sought is one of the most important steps in geothermal potential mapping. In this study, Fry analysis as a spatial distribution method and 5% well existence, distance distribution, weights of evidence (WofE), and evidential belief function (EBFs) methods as spatial association methods were applied comparatively to known geothermal occurrences, and to publicly-available regional-scale geoscience data in Akita and Iwate provinces within the Tohoku volcanic arc, in northern Japan. Fry analysis and rose diagrams revealed similar directional patterns of geothermal wells and volcanoes, NNW-, NNE-, NE-trending faults, hotsprings and fumaroles. Among the spatial association methods, WofE defined a conceptual model correspondent with the real world situations, approved with the aid of expert opinion. The results of the spatial association analyses quantitatively indicated that the known geothermal occurrences are strongly spatially-associated with geological features such as volcanoes, craters, NNW-, NNE-, NE-direction faults and geochemical features such as hotsprings, hydrothermal alteration zones and fumaroles. Geophysical data contains temperature gradients over 100 °C/km and heat flow over 100 mW/m2. In general, geochemical and geophysical data were better evidence layers than geological data for exploring geothermal resources. The spatial analyses of the case study area suggested that quantitative knowledge from hydrothermal geothermal resources was significantly useful for further exploration and for geothermal potential mapping in the case study region. The results can also be extended to the regions with nearly similar characteristics.

Palaeoclimate records 60-8 ka in the Austrian and Swiss Alps and their forelands

NASA Astrophysics Data System (ADS)

Heiri, Oliver; Koinig, Karin A.; Spötl, Christoph; Barrett, Sam; Brauer, Achim; Drescher-Schneider, Ruth; Gaar, Dorian; Ivy-Ochs, Susan; Kerschner, Hanns; Luetscher, Marc; Moran, Andrew; Nicolussi, Kurt; Preusser, Frank; Schmidt, Roland; Schoeneich, Philippe; Schwörer, Christoph; Sprafke, Tobias; Terhorst, Birgit; Tinner, Willy

2014-12-01

The European Alps and their forelands provide a range of different archives and climate proxies for developing climate records in the time interval 60-8 thousand years (ka) ago. We review quantitative and semi-quantitative approaches for reconstructing climatic variables in the Austrian and Swiss sector of the Alpine region within this time interval. Available quantitative to semi-quantitative climate records in this region are mainly based on fossil assemblages of biota such as chironomids, cladocerans, coleopterans, diatoms and pollen preserved in lake sediments and peat, the analysis of oxygen isotopes in speleothems and lake sediment records, the reconstruction of past variations in treeline altitude, the reconstruction of past equilibrium line altitude and extent of glaciers based on geomorphological evidence, and the interpretation of past soil formation processes, dust deposition and permafrost as apparent in loess-palaeosol sequences. Palaeoclimate reconstructions in the Alpine region are affected by dating uncertainties increasing with age, the fragmentary nature of most of the available records, which typically only incorporate a fraction of the time interval of interest, and the limited replication of records within and between regions. Furthermore, there have been few attempts to cross-validate different approaches across this time interval to confirm reconstructed patterns of climatic change by several independent lines of evidence. Based on our review we identify a number of developments that would provide major advances for palaeoclimate reconstruction for the period 60-8 ka in the Alps and their forelands. These include (1) the compilation of individual, fragmentary records to longer and continuous reconstructions, (2) replication of climate records and the development of regional reconstructions for different parts of the Alps, (3) the cross-validation of different proxy-types and approaches, and (4) the reconstruction of past variations in climate gradients across the Alps and their forelands. Furthermore, the development of downscaled climate model runs for the Alpine region 60-8 ka, and of forward modelling approaches for climate proxies would expand the opportunities for quantitative assessments of climatic conditions in Europe within this time-interval.

Quantitation of stress echocardiography by tissue Doppler and strain rate imaging: a dream come true?

PubMed

Galderisi, Maurizio; Mele, Donato; Marino, Paolo Nicola

2005-01-01

Tissue Doppler (TD) is an ultrasound tool providing a quantitative agreement of left ventricular regional myocardial function in different modalities. Spectral pulsed wave (PW) TD, performed online during the examination, measures instantaneous myocardial velocities. By means of color TD, velocity images are digitally stored for subsequent off-line analysis and mean myocardial velocities are measured. An implementation of color TD includes strain rate imaging (SRI), based on post-processing conversion of regional velocities in local myocardial deformation rate (strain rate) and percent deformation (strain). These three modalities have been applied to stress echocardiography for quantitative evaluation of regional left ventricular function and detection of ischemia and viability. They present advantages and limitations. PWTD does not permit the simultaneous assessment of multiple walls and therefore is not compatible with clinical stress echocardiography while it could be used in a laboratory setting. Color TD provides a spatial map of velocity throughout the myocardium but its results are strongly affected by the frame rate. Both color TD and PWTD are also influenced by overall cardiac motion and tethering from adjacent segments and require reference velocity values for interpretation of regional left ventricular function. High frame rate (i.e. > 150 ms) post-processing-derived SRI can potentially overcome these limitations, since measurements of myocardial deformation have not any significant apex-to-base gradient. Preliminary studies have shown encouraging results about the ability of SRI to detect ischemia and viability, in terms of both strain rate changes and/or evidence of post-systolic thickening. SRI is, however, Doppler-dependent and time-consuming. Further technical refinements are needed to improve its application and introduce new ultrasound modalities to overcome the limitations of the Doppler-derived deformation analysis.

Socioeconomic influences on biodiversity, ecosystem services and human well-being: a quantitative application of the DPSIR model in Jiangsu, China.

PubMed

Hou, Ying; Zhou, Shudong; Burkhard, Benjamin; Müller, Felix

2014-08-15

One focus of ecosystem service research is the connection between biodiversity, ecosystem services and human well-being as well as the socioeconomic influences on them. Despite existing investigations, exact impacts from the human system on the dynamics of biodiversity, ecosystem services and human well-being are still uncertain because of the insufficiency of the respective quantitative analyses. Our research aims are discerning the socioeconomic influences on biodiversity, ecosystem services and human well-being and demonstrating mutual impacts between these items. We propose a DPSIR framework coupling ecological integrity, ecosystem services as well as human well-being and suggest DPSIR indicators for the case study area Jiangsu, China. Based on available statistical and surveying data, we revealed the factors significantly impacting biodiversity, ecosystem services and human well-being in the research area through factor analysis and correlation analysis, using the 13 prefecture-level cities of Jiangsu as samples. The results show that urbanization and industrialization in the urban areas have predominant positive influences on regional biodiversity, agricultural productivity and tourism services as well as rural residents' living standards. Additionally, the knowledge, technology and finance inputs for agriculture also have generally positive impacts on these system components. Concerning regional carbon storage, non-cropland vegetation cover obviously plays a significant positive role. Contrarily, the expansion of farming land and the increase of total food production are two important negative influential factors of biodiversity, ecosystem's food provisioning service capacity, regional tourism income and the well-being of the rural population. Our study provides a promising approach based on the DPSIR model to quantitatively capture the socioeconomic influential factors of biodiversity, ecosystem services and human well-being for human-environmental systems at regional scales. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative and qualitative analysis of groundwater in aguanaval and chupaderos aquifers (Mexico)

USDA-ARS?s Scientific Manuscript database

Adequate regional groundwater assessment studies are essential for the correct groundwater management by policy/decision makers; increased use of groundwater resources and drought have led to concern about the future availability of groundwater to meet domestic, agricultural, industrial, and environ...

Dahl (S × R) rat congenic strain analysis confirms and defines a chromosome 17 spatial navigation quantitative trait locus to <10 Mbp.

PubMed

Herrera, Victoria L; Pasion, Khristine A; Tan, Glaiza A; Ruiz-Opazo, Nelson

2013-01-01

A quantitative trait locus (QTL) linked with ability to find a platform in the Morris Water Maze (MWM) was located on chromosome 17 (Nav-5 QTL) using intercross between Dahl S and Dahl R rats. We developed two congenic strains, S.R17A and S.R17B introgressing Dahl R-chromosome 17 segments into Dahl S chromosome 17 region spanning putative Nav-5 QTL. Performance analysis of S.R17A, S.R17B and Dahl S rats in the Morris water maze (MWM) task showed a significantly decreased spatial navigation performance in S.R17B congenic rats when compared with Dahl S controls (P = 0.02). The S.R17A congenic segment did not affect MWM performance delimiting Nav-5 to the chromosome 17 65.02-74.66 Mbp region. Additional fine mapping is necessary to identify the specific gene variant accounting for Nav-5 effect on spatial learning and memory in Dahl rats.

Causal functional contributions and interactions in the attention network of the brain: an objective multi-perturbation analysis.

PubMed

Zavaglia, Melissa; Hilgetag, Claus C

2016-06-01

Spatial attention is a prime example for the distributed network functions of the brain. Lesion studies in animal models have been used to investigate intact attentional mechanisms as well as perspectives for rehabilitation in the injured brain. Here, we systematically analyzed behavioral data from cooling deactivation and permanent lesion experiments in the cat, where unilateral deactivation of the posterior parietal cortex (in the vicinity of the posterior middle suprasylvian cortex, pMS) or the superior colliculus (SC) cause a severe neglect in the contralateral hemifield. Counterintuitively, additional deactivation of structures in the opposite hemisphere reverses the deficit. Using such lesion data, we employed a game-theoretical approach, multi-perturbation Shapley value analysis (MSA), for inferring functional contributions and network interactions of bilateral pMS and SC from behavioral performance in visual attention studies. The approach provides an objective theoretical strategy for lesion inferences and allows a unique quantitative characterization of regional functional contributions and interactions on the basis of multi-perturbations. The quantitative analysis demonstrated that right posterior parietal cortex and superior colliculus made the strongest positive contributions to left-field orienting, while left brain regions had negative contributions, implying that their perturbation may reverse the effects of contralateral lesions or improve normal function. An analysis of functional modulations and interactions among the regions revealed redundant interactions (implying functional overlap) between regions within each hemisphere, and synergistic interactions between bilateral regions. To assess the reliability of the MSA method in the face of variable and incomplete input data, we performed a sensitivity analysis, investigating how much the contribution values of the four regions depended on the performance of specific configurations and on the prediction of unknown performances. The results suggest that the MSA approach is sensitive to categorical, but insensitive to gradual changes in the input data. Finally, we created a basic network model that was based on the known anatomical interactions among cortical-tectal regions and reproduced the experimentally observed behavior in visual orienting. We discuss the structural organization of the network model relative to the causal modulations identified by MSA, to aid a mechanistic understanding of the attention network of the brain.

An Automated Solar Synoptic Analysis Software System

NASA Astrophysics Data System (ADS)

Hong, S.; Lee, S.; Oh, S.; Kim, J.; Lee, J.; Kim, Y.; Lee, J.; Moon, Y.; Lee, D.

2012-12-01

We have developed an automated software system of identifying solar active regions, filament channels, and coronal holes, those are three major solar sources causing the space weather. Space weather forecasters of NOAA Space Weather Prediction Center produce the solar synoptic drawings as a daily basis to predict solar activities, i.e., solar flares, filament eruptions, high speed solar wind streams, and co-rotating interaction regions as well as their possible effects to the Earth. As an attempt to emulate this process with a fully automated and consistent way, we developed a software system named ASSA(Automated Solar Synoptic Analysis). When identifying solar active regions, ASSA uses high-resolution SDO HMI intensitygram and magnetogram as inputs and providing McIntosh classification and Mt. Wilson magnetic classification of each active region by applying appropriate image processing techniques such as thresholding, morphology extraction, and region growing. At the same time, it also extracts morphological and physical properties of active regions in a quantitative way for the short-term prediction of flares and CMEs. When identifying filament channels and coronal holes, images of global H-alpha network and SDO AIA 193 are used for morphological identification and also SDO HMI magnetograms for quantitative verification. The output results of ASSA are routinely checked and validated against NOAA's daily SRS(Solar Region Summary) and UCOHO(URSIgram code for coronal hole information). A couple of preliminary scientific results are to be presented using available output results. ASSA will be deployed at the Korean Space Weather Center and serve its customers in an operational status by the end of 2012.

Regional reliability of quantitative signal targeting with alternating radiofrequency (STAR) labeling of arterial regions (QUASAR).

PubMed

Tatewaki, Yasuko; Higano, Shuichi; Taki, Yasuyuki; Thyreau, Benjamin; Murata, Takaki; Mugikura, Shunji; Ito, Daisuke; Takase, Kei; Takahashi, Shoki

2014-01-01

Quantitative signal targeting with alternating radiofrequency labeling of arterial regions (QUASAR) is a recent spin labeling technique that could improve the reliability of brain perfusion measurements. Although it is considered reliable for measuring gray matter as a whole, it has never been evaluated regionally. Here we assessed this regional reliability. Using a 3-Tesla Philips Achieva whole-body system, we scanned four times 10 healthy volunteers, in two sessions 2 weeks apart, to obtain QUASAR images. We computed perfusion images and ran a voxel-based analysis within all brain structures. We also calculated mean regional cerebral blood flow (rCBF) within regions of interest configured for each arterial territory distribution. The mean CBF over whole gray matter was 37.74 with intraclass correlation coefficient (ICC) of .70. In white matter, it was 13.94 with an ICC of .30. Voxel-wise ICC and coefficient-of-variation maps showed relatively lower reliability in watershed areas and white matter especially in deeper white matter. The absolute mean rCBF values were consistent with the ones reported from PET, as was the relatively low variability in different feeding arteries. Thus, QUASAR reliability for regional perfusion is high within gray matter, but uncertain within white matter. © 2014 The Authors. Journal of Neuroimaging published by the American Society of Neuroimaging.

Regional Reliability of Quantitative Signal Targeting with Alternating Radiofrequency (STAR) Labeling of Arterial Regions (QUASAR)

PubMed Central

Tatewaki, Yasuko; Higano, Shuichi; Taki, Yasuyuki; Thyreau, Benjamin; Murata, Takaki; Mugikura, Shunji; Ito, Daisuke; Takase, Kei; Takahashi, Shoki

2014-01-01

BACKGROUND AND PURPOSE Quantitative signal targeting with alternating radiofrequency labeling of arterial regions (QUASAR) is a recent spin labeling technique that could improve the reliability of brain perfusion measurements. Although it is considered reliable for measuring gray matter as a whole, it has never been evaluated regionally. Here we assessed this regional reliability. METHODS Using a 3-Tesla Philips Achieva whole-body system, we scanned four times 10 healthy volunteers, in two sessions 2 weeks apart, to obtain QUASAR images. We computed perfusion images and ran a voxel-based analysis within all brain structures. We also calculated mean regional cerebral blood flow (rCBF) within regions of interest configured for each arterial territory distribution. RESULTS The mean CBF over whole gray matter was 37.74 with intraclass correlation coefficient (ICC) of .70. In white matter, it was 13.94 with an ICC of .30. Voxel-wise ICC and coefficient-of-variation maps showed relatively lower reliability in watershed areas and white matter especially in deeper white matter. The absolute mean rCBF values were consistent with the ones reported from PET, as was the relatively low variability in different feeding arteries. CONCLUSIONS Thus, QUASAR reliability for regional perfusion is high within gray matter, but uncertain within white matter. PMID:25370338

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. © The Author(s) 2016.

Quantitative analysis for peripheral vascularity assessment based on clinical photoacoustic and ultrasound images

NASA Astrophysics Data System (ADS)

Murakoshi, Dai; Hirota, Kazuhiro; Ishii, Hiroyasu; Hashimoto, Atsushi; Ebata, Tetsurou; Irisawa, Kaku; Wada, Takatsugu; Hayakawa, Toshiro; Itoh, Kenji; Ishihara, Miya

2018-02-01

Photoacoustic (PA) imaging technology is expected to be applied to clinical assessment for peripheral vascularity. We started a clinical evaluation with the prototype PA imaging system we recently developed. Prototype PA imaging system was composed with in-house Q-switched Alexandrite laser system which emits short-pulsed laser with 750 nm wavelength, handheld ultrasound transducer where illumination optics were integrated and signal processing for PA image reconstruction implemented in the clinical ultrasound (US) system. For the purpose of quantitative assessment of PA images, an image analyzing function has been developed and applied to clinical PA images. In this analyzing function, vascularity derived from PA signal intensity ranged for prescribed threshold was defined as a numerical index of vessel fulfillment and calculated for the prescribed region of interest (ROI). Skin surface was automatically detected by utilizing B-mode image acquired simultaneously with PA image. Skinsurface position is utilized to place the ROI objectively while avoiding unwanted signals such as artifacts which were imposed due to melanin pigment in the epidermal layer which absorbs laser emission and generates strong PA signals. Multiple images were available to support the scanned image set for 3D viewing. PA images for several fingers of patients with systemic sclerosis (SSc) were quantitatively assessed. Since the artifact region is trimmed off in PA images, the visibility of vessels with rather low PA signal intensity on the 3D projection image was enhanced and the reliability of the quantitative analysis was improved.

Passive-solar homes for Texas

NASA Astrophysics Data System (ADS)

Garrison, M. L.

1982-06-01

Acceptance of passive solar technologies has been slow within the conventional building trades in Texas because it is a common misconception that solar is expensive, and data on local applications is severely limited or nonexistent. It is the purpose of this solar development to move passive solar design into the mainstream of public acceptance by helping to overcome and eliminate these barriers. Specifically, the goal is to develop a set of regional climatic building standards to help guide the conventional building trade toward the utilization of soft energy systems which will reduce overall consumption at a price and convenience most Texans can afford. To meet this objective, eight sample passive design structures are presented. These designs represent state of the art regional applications of passive solar space conditioning. The methodology used in the passive solar design process included: analysis of regional climatic data; analysis of historical regional building prototypes; determination of regional climatic design priorities and assets; prototypical design models for the discretionary housing market; quantitative thermal analysis of prototypical designs; and construction drawings of building prototypes.

[The development of a computer model in the quantitative assessment of thallium-201 myocardial scintigraphy].

PubMed

Raineri, M; Traina, M; Rotolo, A; Candela, B; Lombardo, R M; Raineri, A A

1993-05-01

Thallium-201 scintigraphy is a widely used noninvasive procedure for the detection and prognostic assessment of patients with suspected or proven coronary artery disease. Thallium uptake can be evaluated by a visual analysis or by a quantitative interpretation. Quantitative scintigraphy enhances disease detection in individual coronary arteries, provides a more precise estimate of the amount of ischemic myocardium, distinguishing scar from hypoperfused tissue. Due to the great deal of data, analysis, interpretation and comparison of thallium uptake can be very complex. We designed a computer-based system for the interpretation of quantitative thallium-201 scintigraphy data uptake. We used a database (DataEase 4.2-DataEase Italia). Our software has the following functions: data storage; calculation; conversion of numerical data into different definitions classifying myocardial perfusion; uptake data comparison; automatic conclusion; comparison of different scintigrams for the same patient. Our software is made up by 4 sections: numeric analysis, descriptive analysis, automatic conclusion, clinical remarks. We introduced in the computer system appropriate information, "logical paths", that use the "IF ... THEN" rules. The software executes these rules in order to analyze the myocardial regions in the 3 phases of scintigraphic analysis (stress, redistribution, re-injection), in the 3 projections (LAO 45 degrees, LAT,ANT), considering our uptake cutoff, obtaining, finally, the automatic conclusions. For these reasons, our computer-based system could be considered a real "expert system".

Risk assessment in the North Caucasus ski resorts

NASA Astrophysics Data System (ADS)

Komarov, Anton Y.; Seliverstov, Yury G.; Glazovskaya, Tatyana G.; Turchaninova, Alla S.

2016-10-01

Avalanches pose a significant problem in most mountain regions of Russia. The constant growth of economic activity, and therefore the increased avalanche hazard, in the North Caucasus region lead to demand for the development of large-scale avalanche risk assessment methods. Such methods are needed for the determination of appropriate avalanche protection measures as well as for economic assessments.The requirement of natural hazard risk assessments is determined by the Federal Law of the Russian Federation (Federal Law 21.12.1994 N 68-FZ, 2016). However, Russian guidelines (SNIP 11-02-96, 2013; SNIP 22-02-2003, 2012) are not clearly presented concerning avalanche risk assessment calculations. Thus, we discuss these problems by presenting a new avalanche risk assessment approach, with the example of developing but poorly researched ski resort areas. The suggested method includes the formulas to calculate collective and individual avalanche risk. The results of risk analysis are shown in quantitative data that can be used to determine levels of avalanche risk (appropriate, acceptable and inappropriate) and to suggest methods to decrease the individual risk to an acceptable level or better. The analysis makes it possible to compare risk quantitative data obtained from different regions, analyze them and evaluate the economic feasibility of protection measures.

Simplex and duplex event-specific analytical methods for functional biotech maize.

PubMed

Lee, Seong-Hun; Kim, Su-Jeong; Yi, Bu-Young

2009-08-26

Analytical methods are very important in the control of genetically modified organism (GMO) labeling systems or living modified organism (LMO) management for biotech crops. Event-specific primers and probes were developed for qualitative and quantitative analysis for biotech maize event 3272 and LY 038 on the basis of the 3' flanking regions, respectively. The qualitative primers confirmed the specificity by a single PCR product and sensitivity to 0.05% as a limit of detection (LOD). Simplex and duplex quantitative methods were also developed using TaqMan real-time PCR. One synthetic plasmid was constructed from two taxon-specific DNA sequences of maize and two event-specific 3' flanking DNA sequences of event 3272 and LY 038 as reference molecules. In-house validation of the quantitative methods was performed using six levels of mixing samples, from 0.1 to 10.0%. As a result, the biases from the true value and the relative deviations were all within the range of +/-30%. Limits of quantitation (LOQs) of the quantitative methods were all 0.1% for simplex real-time PCRs of event 3272 and LY 038 and 0.5% for duplex real-time PCR of LY 038. This study reports that event-specific analytical methods were applicable for qualitative and quantitative analysis for biotech maize event 3272 and LY 038.

Using normalization 3D model for automatic clinical brain quantative analysis and evaluation

NASA Astrophysics Data System (ADS)

Lin, Hong-Dun; Yao, Wei-Jen; Hwang, Wen-Ju; Chung, Being-Tau; Lin, Kang-Ping

2003-05-01

Functional medical imaging, such as PET or SPECT, is capable of revealing physiological functions of the brain, and has been broadly used in diagnosing brain disorders by clinically quantitative analysis for many years. In routine procedures, physicians manually select desired ROIs from structural MR images and then obtain physiological information from correspondent functional PET or SPECT images. The accuracy of quantitative analysis thus relies on that of the subjectively selected ROIs. Therefore, standardizing the analysis procedure is fundamental and important in improving the analysis outcome. In this paper, we propose and evaluate a normalization procedure with a standard 3D-brain model to achieve precise quantitative analysis. In the normalization process, the mutual information registration technique was applied for realigning functional medical images to standard structural medical images. Then, the standard 3D-brain model that shows well-defined brain regions was used, replacing the manual ROIs in the objective clinical analysis. To validate the performance, twenty cases of I-123 IBZM SPECT images were used in practical clinical evaluation. The results show that the quantitative analysis outcomes obtained from this automated method are in agreement with the clinical diagnosis evaluation score with less than 3% error in average. To sum up, the method takes advantage of obtaining precise VOIs, information automatically by well-defined standard 3-D brain model, sparing manually drawn ROIs slice by slice from structural medical images in traditional procedure. That is, the method not only can provide precise analysis results, but also improve the process rate for mass medical images in clinical.

Landscape Characterization and Representativeness Analysis for Understanding Sampling Network Coverage

DOE Data Explorer

Maddalena, Damian; Hoffman, Forrest; Kumar, Jitendra; Hargrove, William

2014-08-01

Sampling networks rarely conform to spatial and temporal ideals, often comprised of network sampling points which are unevenly distributed and located in less than ideal locations due to access constraints, budget limitations, or political conflict. Quantifying the global, regional, and temporal representativeness of these networks by quantifying the coverage of network infrastructure highlights the capabilities and limitations of the data collected, facilitates upscaling and downscaling for modeling purposes, and improves the planning efforts for future infrastructure investment under current conditions and future modeled scenarios. The work presented here utilizes multivariate spatiotemporal clustering analysis and representativeness analysis for quantitative landscape characterization and assessment of the Fluxnet, RAINFOR, and ForestGEO networks. Results include ecoregions that highlight patterns of bioclimatic, topographic, and edaphic variables and quantitative representativeness maps of individual and combined networks.

Chemical Fingerprint and Quantitative Analysis for the Quality Evaluation of Platycladi cacumen by Ultra-performance Liquid Chromatography Coupled with Hierarchical Cluster Analysis.

PubMed

Shan, Mingqiu; Li, Sam Fong Yau; Yu, Sheng; Qian, Yan; Guo, Shuchen; Zhang, Li; Ding, Anwei

2018-01-01

Platycladi cacumen (dried twigs and leaves of Platycladus orientalis (L.) Franco) is a frequently utilized Chinese medicinal herb. To evaluate the quality of the phytomedcine, an ultra-performance liquid chromatographic method with diode array detection was established for chemical fingerprinting and quantitative analysis. In this study, 27 batches of P. cacumen from different regions were collected for analysis. A chemical fingerprint with 20 common peaks was obtained using Similarity Evaluation System for Chromatographic Fingerprint of Traditional Chinese Medicine (Version 2004A). Among these 20 components, seven flavonoids (myricitrin, isoquercitrin, quercitrin, afzelin, cupressuflavone, amentoflavone and hinokiflavone) were identified and determined simultaneously. In the method validation, the seven analytes showed good regressions (R ≥ 0.9995) within linear ranges and good recoveries from 96.4% to 103.3%. Furthermore, with the contents of these seven flavonoids, hierarchical clustering analysis was applied to distinguish the 27 batches into five groups. The chemometric results showed that these groups were almost consistent with geographical positions and climatic conditions of the production regions. Integrating fingerprint analysis, simultaneous determination and hierarchical clustering analysis, the established method is rapid, sensitive, accurate and readily applicable, and also provides a significant foundation for quality control of P. cacumen efficiently. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Spring 1991 Meeting outstanding papers

NASA Astrophysics Data System (ADS)

The Atmospheric Sciences Committee has presented Kaye Brubaker and Jichun Shi with Outstanding Student Paper awards for presentations given at the AGU 1991 Spring Meeting, held in Baltimore May 28-31.Brubaker's paper, “Precipitation Recycling Estimated from Atmospheric Data,” presented quantitative estimates of the contribution of locallyevaporated moisture to precipitation over several large continental regions. Recycled precipitation is defined as water that evaporates from the land surface of a specified region and falls again as precipitation within the region. Brubaker applied a control volume analysis based on a model proposed by Budyko.

Development of quantitative analysis method for stereotactic brain image: assessment of reduced accumulation in extent and severity using anatomical segmentation.

PubMed

Mizumura, Sunao; Kumita, Shin-ichiro; Cho, Keiichi; Ishihara, Makiko; Nakajo, Hidenobu; Toba, Masahiro; Kumazaki, Tatsuo

2003-06-01

Through visual assessment by three-dimensional (3D) brain image analysis methods using stereotactic brain coordinates system, such as three-dimensional stereotactic surface projections and statistical parametric mapping, it is difficult to quantitatively assess anatomical information and the range of extent of an abnormal region. In this study, we devised a method to quantitatively assess local abnormal findings by segmenting a brain map according to anatomical structure. Through quantitative local abnormality assessment using this method, we studied the characteristics of distribution of reduced blood flow in cases with dementia of the Alzheimer type (DAT). Using twenty-five cases with DAT (mean age, 68.9 years old), all of whom were diagnosed as probable Alzheimer's disease based on NINCDS-ADRDA, we collected I-123 iodoamphetamine SPECT data. A 3D brain map using the 3D-SSP program was compared with the data of 20 cases in the control group, who age-matched the subject cases. To study local abnormalities on the 3D images, we divided the whole brain into 24 segments based on anatomical classification. We assessed the extent of an abnormal region in each segment (rate of the coordinates with a Z-value that exceeds the threshold value, in all coordinates within a segment), and severity (average Z-value of the coordinates with a Z-value that exceeds the threshold value). This method clarified orientation and expansion of reduced accumulation, through classifying stereotactic brain coordinates according to the anatomical structure. This method was considered useful for quantitatively grasping distribution abnormalities in the brain and changes in abnormality distribution.

A quantitative spatiotemporal analysis of microglia morphology during ischemic stroke and reperfusion

PubMed Central

2013-01-01

Background Microglia cells continuously survey the healthy brain in a ramified morphology and, in response to injury, undergo progressive morphological and functional changes that encompass microglia activation. Although ideally positioned for immediate response to ischemic stroke (IS) and reperfusion, their progressive morphological transformation into activated cells has not been quantified. In addition, it is not well understood if diverse microglia morphologies correlate to diverse microglia functions. As such, the dichotomous nature of these cells continues to confound our understanding of microglia-mediated injury after IS and reperfusion. The purpose of this study was to quantitatively characterize the spatiotemporal pattern of microglia morphology during the evolution of cerebral injury after IS and reperfusion. Methods Male C57Bl/6 mice were subjected to focal cerebral ischemia and periods of reperfusion (0, 8 and 24 h). The microglia process length/cell and number of endpoints/cell was quantified from immunofluorescent confocal images of brain regions using a skeleton analysis method developed for this study. Live cell morphology and process activity were measured from movies acquired in acute brain slices from GFP-CX3CR1 transgenic mice after IS and 24-h reperfusion. Regional CD11b and iNOS expressions were measured from confocal images and Western blot, respectively, to assess microglia proinflammatory function. Results Quantitative analysis reveals a significant spatiotemporal relationship between microglia morphology and evolving cerebral injury in the ipsilateral hemisphere after IS and reperfusion. Microglia were both hyper- and de-ramified in striatal and cortical brain regions (respectively) after 60 min of focal cerebral ischemia. However, a de-ramified morphology was prominent when ischemia was coupled to reperfusion. Live microglia were de-ramified, and, in addition, process activity was severely blunted proximal to the necrotic core after IS and 24 h of reperfusion. CD11b expression, but not iNOS expression, was increased in regions of hyper- and de-ramified microglia during the course of ischemic stroke and 24 h of reperfusion. Conclusions Our findings illustrate that microglia activation after stroke includes both increased and decreased cell ramification. Importantly, quantitative analyses of microglial morphology and activity are feasible and, in future studies, would assist in the comprehensive identification and stratification of their dichotomous contribution toward cerebral injury and recovery during IS and reperfusion. PMID:23311642

Mass- and energy-analyses of ions from plasma by means of a miniature Thomson spectrometer.

PubMed

Sadowski, M J; Czaus, K; Malinowski, K; Skladnik-Sadowska, E; Zebrowski, J

2009-05-01

The paper presents an improved version of a miniature mass-spectrometer of the Thomson-type, which has been adopted for ion analysis near the dense plasma region inside a vacuum chamber. Problems connected with the separation of ions from plasma streams are considered. Input diaphragms and pumping systems, needed to ensure good vacuum inside the analyzing region, are described. The application of the miniature Thomson-type analyzer is illustrated by ion parabolas recorded in plasma-focus facility and rod plasma injector experiment. A quantitative analysis of the recorded ion parabolas is presented. Factors influencing accuracy of the ion analysis are discussed and methods of the spectrometer calibration are described.

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 continental platform and its lack of proto-oceanic crust northward.

Social Network Analysis and Qualitative Interviews for Assessing Geographic Characteristics of Tourism Business Networks.

PubMed

Kelman, Ilan; Luthe, Tobias; Wyss, Romano; Tørnblad, Silje H; Evers, Yvette; Curran, Marina Martin; Williams, Richard J; Berlow, Eric L

2016-01-01

This study integrates quantitative social network analysis (SNA) and qualitative interviews for understanding tourism business links in isolated communities through analysing spatial characteristics. Two case studies are used, the Surselva-Gotthard region in the Swiss Alps and Longyearbyen in the Arctic archipelago of Svalbard, to test the spatial characteristics of physical proximity, isolation, and smallness for understanding tourism business links. In the larger Surselva-Gotthard region, we found a strong relationship between geographic separation of the three communities on compartmentalization of the collaboration network. A small set of businesses played a central role in steering collaborative decisions for this community, while a group of structurally 'peripheral' actors were less influential. By contrast, the business community in Svalbard showed compartmentalization that was independent of geographic distance between actors. Within towns of similar size and governance scale, Svalbard is more compartmentalized, and those compartments are not driven by geographic separation of the collaboration clusters. This compartmentalization in Svalbard was reflected in a lower density of formal business collaboration ties compared to the communities of the Alps. We infer that the difference is due to Svalbard having higher cultural diversity and population turnover than the Alps communities. We propose that integrating quantitative network analysis from simple surveys with qualitative interviews targeted from the network results is an efficient general approach to identify regionally specific constraints and opportunities for effective governance.

Differentiating invasive and pre-invasive lung cancer by quantitative analysis of histopathologic images

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Sun, Hongliu; Chan, Heang-Ping; Chughtai, Aamer; Wei, Jun; Hadjiiski, Lubomir; Kazerooni, Ella

2018-02-01

We are developing automated radiopathomics method for diagnosis of lung nodule subtypes. In this study, we investigated the feasibility of using quantitative methods to analyze the tumor nuclei and cytoplasm in pathologic wholeslide images for the classification of pathologic subtypes of invasive nodules and pre-invasive nodules. We developed a multiscale blob detection method with watershed transform (MBD-WT) to segment the tumor cells. Pathomic features were extracted to characterize the size, morphology, sharpness, and gray level variation in each segmented nucleus and the heterogeneity patterns of tumor nuclei and cytoplasm. With permission of the National Lung Screening Trial (NLST) project, a data set containing 90 digital haematoxylin and eosin (HE) whole-slide images from 48 cases was used in this study. The 48 cases contain 77 regions of invasive subtypes and 43 regions of pre-invasive subtypes outlined by a pathologist on the HE images using the pathological tumor region description provided by NLST as reference. A logistic regression model (LRM) was built using leave-one-case-out resampling and receiver operating characteristic (ROC) analysis for classification of invasive and pre-invasive subtypes. With 11 selected features, the LRM achieved a test area under the ROC curve (AUC) value of 0.91+/-0.03. The results demonstrated that the pathologic invasiveness of lung adenocarcinomas could be categorized with high accuracy using pathomics analysis.

Social Network Analysis and Qualitative Interviews for Assessing Geographic Characteristics of Tourism Business Networks

PubMed Central

Luthe, Tobias; Wyss, Romano; Tørnblad, Silje H.; Evers, Yvette; Curran, Marina Martin; Williams, Richard J.; Berlow, Eric L.

2016-01-01

This study integrates quantitative social network analysis (SNA) and qualitative interviews for understanding tourism business links in isolated communities through analysing spatial characteristics. Two case studies are used, the Surselva-Gotthard region in the Swiss Alps and Longyearbyen in the Arctic archipelago of Svalbard, to test the spatial characteristics of physical proximity, isolation, and smallness for understanding tourism business links. In the larger Surselva-Gotthard region, we found a strong relationship between geographic separation of the three communities on compartmentalization of the collaboration network. A small set of businesses played a central role in steering collaborative decisions for this community, while a group of structurally ‘peripheral’ actors were less influential. By contrast, the business community in Svalbard showed compartmentalization that was independent of geographic distance between actors. Within towns of similar size and governance scale, Svalbard is more compartmentalized, and those compartments are not driven by geographic separation of the collaboration clusters. This compartmentalization in Svalbard was reflected in a lower density of formal business collaboration ties compared to the communities of the Alps. We infer that the difference is due to Svalbard having higher cultural diversity and population turnover than the Alps communities. We propose that integrating quantitative network analysis from simple surveys with qualitative interviews targeted from the network results is an efficient general approach to identify regionally specific constraints and opportunities for effective governance. PMID:27258007

MR morphology of triangular fibrocartilage complex: correlation with quantitative MR and biomechanical properties.

PubMed

Bae, Won C; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda; Chung, Christine B

2016-04-01

To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high-resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Five cadaveric wrists (22-70 years) were imaged at 3 T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques.

Assessing present and future climate changes in Siberia and their regional socioeconomic consequences using a web-based big data geoprocessing platform

NASA Astrophysics Data System (ADS)

Alexeev, V. A.; Gordov, E. P.

2016-12-01

Recently initiated collaborative research project is presented. Its main objective is to develop high spatial and temporal resolution datasets for studying the ongoing and future climate changes in Siberia, caused by global and regional processes in the atmosphere and the ocean. This goal will be achieved by using a set of regional and global climate models for the analysis of the mechanisms of climate change and quantitative assessment of changes in key climate variables, including analysis of extreme weather and climate events and their dynamics, evaluation of the frequency, amplitude and the risks caused by the extreme events in the region. The main practical application of the project is to provide experts, stakeholders and the public with quantitative information about the future climate change in Siberia obtained on the base of a computational web- geoinformation platform. The thematic platform will be developed in order to facilitate processing and analysis of high resolution georeferenced datasets that will be delivered and made available to scientific community, policymakes and other end users as a result of the project. Software packages will be developed to implement calculation of various climatological indicators in order to characterize and diagnose climate change and its dynamics, as well as to archive results in digital form of electronic maps (GIS layers). By achieving these goals the project will provide science based tools necessary for developing mitigation measures for adapting to climate change and reducing negative impact on the population and infrastructure of the region. Financial support of the computational web- geoinformation platform prototype development by the RF Ministry of Education and Science under Agreement 14.613.21.0037 (RFMEFI61315X0037) is acknowledged.

Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis

NASA Astrophysics Data System (ADS)

Woolfrey, John R.; Avery, Mitchell A.; Doweyko, Arthur M.

1998-03-01

Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.

General Staining and Segmentation Procedures for High Content Imaging and Analysis.

PubMed

Chambers, Kevin M; Mandavilli, Bhaskar S; Dolman, Nick J; Janes, Michael S

2018-01-01

Automated quantitative fluorescence microscopy, also known as high content imaging (HCI), is a rapidly growing analytical approach in cell biology. Because automated image analysis relies heavily on robust demarcation of cells and subcellular regions, reliable methods for labeling cells is a critical component of the HCI workflow. Labeling of cells for image segmentation is typically performed with fluorescent probes that bind DNA for nuclear-based cell demarcation or with those which react with proteins for image analysis based on whole cell staining. These reagents, along with instrument and software settings, play an important role in the successful segmentation of cells in a population for automated and quantitative image analysis. In this chapter, we describe standard procedures for labeling and image segmentation in both live and fixed cell samples. The chapter will also provide troubleshooting guidelines for some of the common problems associated with these aspects of HCI.

Increasing Information Sharing Among Independent Police Departments

DTIC Science & Technology

2009-03-01

the operational level . 50 Robert Fox (Lieutenant, Los Angeles Police Department – Assigned to the Joint Regional... Angeles Police Department ( LAPD ) is the largest independent police department in Los Angeles County. The department is responsible for patrolling...agencies operating in metropolitan areas based on a quantitative analysis of the 46 independent police

Application of Particle Image Velocimetry and Reference Image Topography to jet shock cells using the hydraulic analogy

NASA Astrophysics Data System (ADS)

Kumar, Vaibhav; Ng, Ivan; Sheard, Gregory J.; Brocher, Eric; Hourigan, Kerry; Fouras, Andreas

2011-08-01

This paper examines the shock cell structure, vorticity and velocity field at the exit of an underexpanded jet nozzle using a hydraulic analogy and the Reference Image Topography technique. Understanding the flow in this region is important for the mitigation of screech, an aeroacoustic problem harmful to aircraft structures. Experiments are conducted on a water table, allowing detailed quantitative investigation of this important flow regime at a greatly reduced expense. Conventional Particle Image Velocimetry is employed to determine the velocity and vorticity fields of the nozzle exit region. Applying Reference Image Topography, the wavy water surface is reconstructed and when combined with the hydraulic analogy, provides a pressure map of the region. With this approach subtraction of surfaces is used to highlight the unsteady regions of the flow, which is not as convenient or quantitative with conventional Schlieren techniques. This allows a detailed analysis of the shock cell structures and their interaction with flow instabilities in the shear layer that are the underlying cause of jet screech.

Anthropogenic activities and coastal environmental quality: a regional quantitative analysis in southeast China with management implications.

PubMed

Chen, Kai; Liu, Yan; Huang, Dongren; Ke, Hongwei; Chen, Huorong; Zhang, Songbin; Yang, Shengyun; Cai, Minggang

2018-02-01

Regional analysis of environmental issues has always been a hot topic in the field of sustainable development. Because the different levels of economic growth, urbanization, resource endowments, etc. in different regions generate apparently different ecological responses, a better description and comparison across different regions will provide more valuable implications for ecological improvement and policymaking. In this study, seven typical bays in southeast China that are a rapid developing area were selected to quantitatively analyze the relationship between socioeconomic development and coastal environmental quality. Based on the water quality data from 2007 to 2015, the multivariate statistical method was applied to analyze the potential environmental risks and to classify the seven bays based on their environmental quality status. The possible variation trends of environmental indices were predicted based on the cross-regional panel data by Environmental Kuznets Curve. The results showed that there were significant regional differences among the seven bays, especially Quanzhou, Xiamen, and Luoyuan Bays, suffered from severer artificial disturbances than other bays, despite their different development patterns. Socioeconomic development level was significantly associated with some water quality indices (pH, DIN, PO 4 -P); the association was roughly positive: the areas with higher GDP per capita have some worse water quality indices. In addition, the decreasing trend of pH values and the increasing trend of nutrient concentration in the seven bays will continue in the foreseeable future. In consideration of the variation trends, the limiting nutrient strategy should be implemented to mitigate the deterioration of the coastal environments.

Quantitative analysis of Argyrophilic Nucleolar organizer regions in odontogenic cysts and tumor - A comparative study.

PubMed

Gupta, Bhavana; Chandra, Shaleen; Raj, Vineet; Gupta, Vivek

2018-01-01

The nucleolar organizer region (NOR) is by definition part of a chromosome, and nucleolus is a structure containing this chromosomal part and in addition the material which accumulate around the NOR, mostly rRNAs and their precursors as well as specific ribosomal proteins. Argyrophilic Nucleolar organizing region (AgNOR) are silver binding NORs often used to study cell proliferation in various types of tumors. Quantitative assessment of Argyrophilic Nucleolar organizing region count and its comparison among dentigerous cyst, keratocystic odontogenic tumor and ameloblastoma. Forty-five histologically confirmed cases, 15 cases each of keratocystic odontogenic tumor, dentigerous cysts and ameloblastomas were examined for Argyrophilic Nucleolar organizing region. The sections were obtained and Argyrophilic Nucleolar organizer regions staining was done for comparing the proliferative capacity among these lesions. Post hoc analysis for inter-group comparison and one way ANOVA were done in all three groups in this study. P  < 0.001 was considered significant. The results of AgNOR counts were higher in KCOTs as compared to ameloblastoma and least in dentigerous cysts. The mean AgNOR counts between the study groups were compared using one way ANOVA test and the differences were found to be significant ( P  < 0.001). AgNOR counts were significantly higher in KCOT and ameloblastoma as compared to dentigerous cyst suggesting that these lesions have a higher proliferative capacity than dentigerous cyst. The finding of a significantly higher AgNOR counts in KCOT as compared to ameloblastoma represent a difference in proliferative activity and greater growth potential between these two lesions.

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

PubMed

Mansur, Sanawar; Abdulla, Rahima; Ayupbec, Amatjan; Aisa, Haji Akbar

2016-12-21

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

The genetic architecture of photosynthesis and plant growth-related traits in tomato.

PubMed

de Oliveira Silva, Franklin Magnum; Lichtenstein, Gabriel; Alseekh, Saleh; Rosado-Souza, Laise; Conte, Mariana; Suguiyama, Vanessa Fuentes; Lira, Bruno Silvestre; Fanourakis, Dimitrios; Usadel, Björn; Bhering, Leonardo Lopes; DaMatta, Fábio M; Sulpice, Ronan; Araújo, Wagner L; Rossi, Magdalena; de Setta, Nathalia; Fernie, Alisdair R; Carrari, Fernando; Nunes-Nesi, Adriano

2018-02-01

To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis and respiration, a population of Solanum pennellii introgression lines was analyzed. We determined phenotypes for physiological, metabolic, and growth related traits, including gas exchange and chlorophyll fluorescence parameters. Data analysis allowed the identification of 208 physiological and metabolic quantitative trait loci with 33 of these being associated to smaller intervals of the genomic regions, termed BINs. Eight BINs were identified that were associated with higher assimilation rates than the recurrent parent M82. Two and 10 genomic regions were related to shoot and root dry matter accumulation, respectively. Nine genomic regions were associated with starch levels, whereas 12 BINs were associated with the levels of other metabolites. Additionally, a comprehensive and detailed annotation of the genomic regions spanning these quantitative trait loci allowed us to identify 87 candidate genes that putatively control the investigated traits. We confirmed 8 of these at the level of variance in gene expression. Taken together, our results allowed the identification of candidate genes that most likely regulate photosynthesis, primary metabolism, and plant growth and as such provide new avenues for crop improvement. © 2017 John Wiley & Sons Ltd.

Improving the geological interpretation of magnetic and gravity satellite anomalies

NASA Technical Reports Server (NTRS)

Hinze, William J.; Braile, Lawrence W.; Vonfrese, Ralph R. B.

1987-01-01

Quantitative analysis of the geologic component of observed satellite magnetic and gravity fields requires accurate isolation of the geologic component of the observations, theoretically sound and viable inversion techniques, and integration of collateral, constraining geologic and geophysical data. A number of significant contributions were made which make quantitative analysis more accurate. These include procedures for: screening and processing orbital data for lithospheric signals based on signal repeatability and wavelength analysis; producing accurate gridded anomaly values at constant elevations from the orbital data by three-dimensional least squares collocation; increasing the stability of equivalent point source inversion and criteria for the selection of the optimum damping parameter; enhancing inversion techniques through an iterative procedure based on the superposition theorem of potential fields; and modeling efficiently regional-scale lithospheric sources of satellite magnetic anomalies. In addition, these techniques were utilized to investigate regional anomaly sources of North and South America and India and to provide constraints to continental reconstruction. Since the inception of this research study, eleven papers were presented with associated published abstracts, three theses were completed, four papers were published or accepted for publication, and an additional manuscript was submitted for publication.

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.

Quantitative evaluation of morphological changes in activated platelets in vitro using digital holographic microscopy.

PubMed

Kitamura, Yutaka; Isobe, Kazushige; Kawabata, Hideo; Tsujino, Tetsuhiro; Watanabe, Taisuke; Nakamura, Masayuki; Toyoda, Toshihisa; Okudera, Hajime; Okuda, Kazuhiro; Nakata, Koh; Kawase, Tomoyuki

2018-06-18

Platelet activation and aggregation have been conventionally evaluated using an aggregometer. However, this method is suitable for short-term but not long-term quantitative evaluation of platelet aggregation, morphological changes, and/or adhesion to specific materials. The recently developed digital holographic microscopy (DHM) has enabled the quantitative evaluation of cell size and morphology without labeling or destruction. Thus, we aim to validate its applicability in quantitatively evaluating changes in cell morphology, especially in the aggregation and spreading of activated platelets, thus modifying typical image analysis procedures to suit aggregated platelets. Freshly prepared platelet-rich plasma was washed with phosphate-buffered saline and treated with 0.1% CaCl 2 . Platelets were then fixed and subjected to DHM, scanning electron microscopy (SEM), atomic force microscopy, optical microscopy, and flow cytometry (FCM). Tightly aggregated platelets were identified as single cells. Data obtained from time-course experiments were plotted two-dimensionally according to the average optical thickness versus attachment area and divided into four regions. The majority of the control platelets, which supposedly contained small and round platelets, were distributed in the lower left region. As activation time increased, however, this population dispersed toward the upper right region. The distribution shift demonstrated by DHM was essentially consistent with data obtained from SEM and FCM. Therefore, DHM was validated as a promising device for testing platelet function given that it allows for the quantitative evaluation of activation-dependent morphological changes in platelets. DHM technology will be applicable to the quality assurance of platelet concentrates, as well as diagnosis and drug discovery related to platelet functions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative muscle ultrasound in Duchenne muscular dystrophy: a comparison of techniques.

PubMed

Shklyar, Irina; Geisbush, Tom R; Mijialovic, Aleksandar S; Pasternak, Amy; Darras, Basil T; Wu, Jim S; Rutkove, Seward B; Zaidman, Craig M

2015-02-01

Muscle pathology in Duchenne muscular dystrophy (DMD) can be quantified using ultrasound by measuring either the amplitudes of sound-waves scattered back from the tissue [quantitative backscatter analysis (QBA)] or by measuring these backscattered amplitudes after compression into grayscale levels (GSL) obtained from the images. We measured and compared QBA and GSL from 6 muscles of 25 boys with DMD and 25 healthy subjects, aged 2-14 years, with age and, in DMD, with function (North Star Ambulatory Assessment). Both QBA and GSL were measured reliably (intraclass correlation ≥ 0.87) and were higher in DMD than controls (P < 0.0001). In DMD, average QBA and GSL measured from superficial regions of muscle increased (rho ≥ 0.47, P < 0.05) with both higher age and worse function; in contrast, GSL measured from whole regions of muscle did not. QBA and GSL measured from superficial regions of muscle can similarly quantify muscle pathology in DMD. © 2014 Wiley Periodicals, Inc.

Electrophysiological evidence during episodic prospection implicates medial prefrontal and bilateral middle temporal gyrus.

PubMed

Hsu, Chia-Fen; Sonuga-Barke, Edmund J S

2016-08-01

fMRI studies have implicated the medial prefrontal cortex and medial temporal lobe, components of the default mode network (DMN), in episodic prospection. This study compared quantitative EEG localized to these DMN regions during prospection and during resting and while waiting for rewards. EEG was recorded in twenty-two adults while they were asked to (i) envision future monetary episodes; (ii) wait for rewards and (iii) rest. Activation sources were localized to core DMN regions. EEG power and phase coherence were compared across conditions. Prospection, compared to resting and waiting, was associated with reduced power in the medial prefrontal gyrus and increased power in the bilateral medial temporal gyrus across frequency bands as well as greater phase synchrony between these regions in the delta band. The current quantitative EEG analysis confirms prior fMRI research suggesting that medial prefrontal and medial temporal gyrus interactions are central to the capacity for episodic prospection. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluation of the default-mode network by quantitative 15O-PET: comparative study between cerebral blood flow and oxygen consumption.

PubMed

Aoe, Jo; Watabe, Tadashi; Shimosegawa, Eku; Kato, Hiroki; Kanai, Yasukazu; Naka, Sadahiro; Matsunaga, Keiko; Isohashi, Kayako; Tatsumi, Mitsuaki; Hatazawa, Jun

2018-06-22

Resting-state functional MRI (rs-fMRI) has revealed the existence of a default-mode network (DMN) based on spontaneous oscillations of the blood oxygenation level-dependent (BOLD) signal. The BOLD signal reflects the deoxyhemoglobin concentration, which depends on the relationship between the regional cerebral blood flow (CBF) and the cerebral metabolic rate of oxygen (CMRO 2 ). However, these two factors cannot be separated in BOLD rs-fMRI. In this study, we attempted to estimate the functional correlations in the DMN by means of quantitative 15 O-labeled gases and water PET, and to compare the contribution of the CBF and CMRO 2 to the DMN. Nine healthy volunteers (5 men and 4 women; mean age, 47.0 ± 1.2 years) were studied by means of 15 O-O 2 , 15 O-CO gases and 15 O-water PET. Quantitative CBF and CMRO 2 images were generated by an autoradiographic method and transformed into MNI standardized brain template. Regions of interest were placed on normalized PET images according to the previous rs-fMRI study. For the functional correlation analysis, the intersubject Pearson's correlation coefficients (r) were calculated for all pairs in the brain regions and correlation matrices were obtained for CBF and CMRO 2 , respectively. We defined r > 0.7 as a significant positive correlation and compared the correlation matrices of CBF and CMRO 2 . Significant positive correlations (r > 0.7) were observed in 24 pairs of brain regions for the CBF and 22 pairs of brain regions for the CMRO 2 . Among them, 12 overlapping networks were observed between CBF and CMRO 2 . Correlation analysis of CBF led to the detection of more brain networks as compared to that of CMRO 2 , indicating that the CBF can capture the state of the spontaneous activity with a higher sensitivity. We estimated the functional correlations in the DMN by means of quantitative PET using 15 O-labeled gases and water. The correlation matrix derived from the CBF revealed a larger number of brain networks as compared to that derived from the CMRO 2 , indicating that contribution to the functional correlation in the DMN is higher in the blood flow more than the oxygen consumption.

Retinal status analysis method based on feature extraction and quantitative grading in OCT images.

PubMed

Fu, Dongmei; Tong, Hejun; Zheng, Shuang; Luo, Ling; Gao, Fulin; Minar, Jiri

2016-07-22

Optical coherence tomography (OCT) is widely used in ophthalmology for viewing the morphology of the retina, which is important for disease detection and assessing therapeutic effect. The diagnosis of retinal diseases is based primarily on the subjective analysis of OCT images by trained ophthalmologists. This paper describes an OCT images automatic analysis method for computer-aided disease diagnosis and it is a critical part of the eye fundus diagnosis. This study analyzed 300 OCT images acquired by Optovue Avanti RTVue XR (Optovue Corp., Fremont, CA). Firstly, the normal retinal reference model based on retinal boundaries was presented. Subsequently, two kinds of quantitative methods based on geometric features and morphological features were proposed. This paper put forward a retinal abnormal grading decision-making method which was used in actual analysis and evaluation of multiple OCT images. This paper showed detailed analysis process by four retinal OCT images with different abnormal degrees. The final grading results verified that the analysis method can distinguish abnormal severity and lesion regions. This paper presented the simulation of the 150 test images, where the results of analysis of retinal status showed that the sensitivity was 0.94 and specificity was 0.92.The proposed method can speed up diagnostic process and objectively evaluate the retinal status. This paper aims on studies of retinal status automatic analysis method based on feature extraction and quantitative grading in OCT images. The proposed method can obtain the parameters and the features that are associated with retinal morphology. Quantitative analysis and evaluation of these features are combined with reference model which can realize the target image abnormal judgment and provide a reference for disease diagnosis.

CALIPSO: an interactive image analysis software package for desktop PACS workstations

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Huang, H. K.

1990-07-01

The purpose of this project is to develop a low cost workstation for quantitative analysis of multimodality images using a Macintosh II personal computer. In the current configuration the Macintosh operates as a stand alone workstation where images are imported either from a central PACS server through a standard Ethernet network or recorded through video digitizer board. The CALIPSO software developed contains a large variety ofbasic image display and manipulation tools. We focused our effort however on the design and implementation ofquantitative analysis methods that can be applied to images from different imaging modalities. Analysis modules currently implemented include geometric and densitometric volumes and ejection fraction calculation from radionuclide and cine-angiograms Fourier analysis ofcardiac wall motion vascular stenosis measurement color coded parametric display of regional flow distribution from dynamic coronary angiograms automatic analysis ofmyocardial distribution ofradiolabelled tracers from tomoscintigraphic images. Several of these analysis tools were selected because they use similar color coded andparametric display methods to communicate quantitative data extracted from the images. 1. Rationale and objectives of the project Developments of Picture Archiving and Communication Systems (PACS) in clinical environment allow physicians and radiologists to assess radiographic images directly through imaging workstations (''). This convenient access to the images is often limited by the number of workstations available due in part to their high cost. There is also an increasing need for quantitative analysis ofthe images. During thepast decade

Quantitative analysis of ex vivo colorectal epithelium using an automated feature extraction algorithm for microendoscopy image data

PubMed Central

Prieto, Sandra P.; Lai, Keith K.; Laryea, Jonathan A.; Mizell, Jason S.; Muldoon, Timothy J.

2016-01-01

Abstract. Qualitative screening for colorectal polyps via fiber bundle microendoscopy imaging has shown promising results, with studies reporting high rates of sensitivity and specificity, as well as low interobserver variability with trained clinicians. A quantitative image quality control and image feature extraction algorithm (QFEA) was designed to lessen the burden of training and provide objective data for improved clinical efficacy of this method. After a quantitative image quality control step, QFEA extracts field-of-view area, crypt area, crypt circularity, and crypt number per image. To develop and validate this QFEA, a training set of microendoscopy images was collected from freshly resected porcine colon epithelium. The algorithm was then further validated on ex vivo image data collected from eight human subjects, selected from clinically normal appearing regions distant from grossly visible tumor in surgically resected colorectal tissue. QFEA has proven flexible in application to both mosaics and individual images, and its automated crypt detection sensitivity ranges from 71 to 94% despite intensity and contrast variation within the field of view. It also demonstrates the ability to detect and quantify differences in grossly normal regions among different subjects, suggesting the potential efficacy of this approach in detecting occult regions of dysplasia. PMID:27335893

Regional patterns of total nitrogen concentrations in the National Rivers and Streams Assessment

USGS Publications Warehouse

Omernik, James M.; Paulsen, Steven G.; Griffith, Glenn E.; Weber, Marc H.

2016-01-01

Patterns of nitrogen (N) concentrations in streams sampled by the National Rivers and Streams Assessment (NRSA) were examined semiquantitatively to identify regional differences in stream N levels. The data were categorized and analyzed by watershed size classes to reveal patterns of the concentrations that are consistent with the spatial homogeneity in natural and anthropogenic characteristics associated with regional differences in N levels. Ecoregions and mapped information on human activities including agricultural practices were used to determine the resultant regions. Marked differences in N levels were found among the nine aggregations of ecoregions used to report the results of the NRSA. We identified distinct regional patterns of stream N concentrations within the reporting regions that are associated with the characteristics of specific Level III ecoregions, groups of Level III ecoregions, groups of Level IV ecoregions, certain geographic characteristics within ecoregions, and/or particular watershed size classes. We described each of these regions and illustrated their areal extent and median and range in N concentrations. Understanding the spatial variability of nutrient concentrations in flowing waters and the apparent contributions that human and nonhuman factors have on different sizes of streams and rivers is critical to the development of effective water quality assessment and management plans. This semi-quantitative analysis is also intended to identify areas within which more detailed quantitative work can be conducted to determine specific regional factors associated with variations in stream N concentrations.

Survival Prediction in Pancreatic Ductal Adenocarcinoma by Quantitative Computed Tomography Image Analysis.

PubMed

Attiyeh, Marc A; Chakraborty, Jayasree; Doussot, Alexandre; Langdon-Embry, Liana; Mainarich, Shiana; Gönen, Mithat; Balachandran, Vinod P; D'Angelica, Michael I; DeMatteo, Ronald P; Jarnagin, William R; Kingham, T Peter; Allen, Peter J; Simpson, Amber L; Do, Richard K

2018-04-01

Pancreatic cancer is a highly lethal cancer with no established a priori markers of survival. Existing nomograms rely mainly on post-resection data and are of limited utility in directing surgical management. This study investigated the use of quantitative computed tomography (CT) features to preoperatively assess survival for pancreatic ductal adenocarcinoma (PDAC) patients. A prospectively maintained database identified consecutive chemotherapy-naive patients with CT angiography and resected PDAC between 2009 and 2012. Variation in CT enhancement patterns was extracted from the tumor region using texture analysis, a quantitative image analysis tool previously described in the literature. Two continuous survival models were constructed, with 70% of the data (training set) using Cox regression, first based only on preoperative serum cancer antigen (CA) 19-9 levels and image features (model A), and then on CA19-9, image features, and the Brennan score (composite pathology score; model B). The remaining 30% of the data (test set) were reserved for independent validation. A total of 161 patients were included in the analysis. Training and test sets contained 113 and 48 patients, respectively. Quantitative image features combined with CA19-9 achieved a c-index of 0.69 [integrated Brier score (IBS) 0.224] on the test data, while combining CA19-9, imaging, and the Brennan score achieved a c-index of 0.74 (IBS 0.200) on the test data. We present two continuous survival prediction models for resected PDAC patients. Quantitative analysis of CT texture features is associated with overall survival. Further work includes applying the model to an external dataset to increase the sample size for training and to determine its applicability.

Quantitative local analysis of nonlinear systems

NASA Astrophysics Data System (ADS)

Topcu, Ufuk

This thesis investigates quantitative methods for local robustness and performance analysis of nonlinear dynamical systems with polynomial vector fields. We propose measures to quantify systems' robustness against uncertainties in initial conditions (regions-of-attraction) and external disturbances (local reachability/gain analysis). S-procedure and sum-of-squares relaxations are used to translate Lyapunov-type characterizations to sum-of-squares optimization problems. These problems are typically bilinear/nonconvex (due to local analysis rather than global) and their size grows rapidly with state/uncertainty space dimension. Our approach is based on exploiting system theoretic interpretations of these optimization problems to reduce their complexity. We propose a methodology incorporating simulation data in formal proof construction enabling more reliable and efficient search for robustness and performance certificates compared to the direct use of general purpose solvers. This technique is adapted both to region-of-attraction and reachability analysis. We extend the analysis to uncertain systems by taking an intentionally simplistic and potentially conservative route, namely employing parameter-independent rather than parameter-dependent certificates. The conservatism is simply reduced by a branch-and-hound type refinement procedure. The main thrust of these methods is their suitability for parallel computing achieved by decomposing otherwise challenging problems into relatively tractable smaller ones. We demonstrate proposed methods on several small/medium size examples in each chapter and apply each method to a benchmark example with an uncertain short period pitch axis model of an aircraft. Additional practical issues leading to a more rigorous basis for the proposed methodology as well as promising further research topics are also addressed. We show that stability of linearized dynamics is not only necessary but also sufficient for the feasibility of the formulations in region-of-attraction analysis. Furthermore, we generalize an upper bound refinement procedure in local reachability/gain analysis which effectively generates non-polynomial certificates from polynomial ones. Finally, broader applicability of optimization-based tools stringently depends on the availability of scalable/hierarchial algorithms. As an initial step toward this direction, we propose a local small-gain theorem and apply to stability region analysis in the presence of unmodeled dynamics.

MR Morphology of Triangular Fibrocartilage Complex: Correlation with Quantitative MR and Biomechanical Properties

PubMed Central

Bae, Won C.; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda

2016-01-01

Objective To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Materials and Methods Five cadaveric wrists (22 to 70 yrs) were imaged at 3T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. Results On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. Conclusion These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques. PMID:26691643

RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.

PubMed

Sheffler, Will; Baker, David

2009-01-01

We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation

PubMed Central

Sheffler, Will; Baker, David

2009-01-01

We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures. PMID:19177366

3-D Quantitative Dynamic Contrast Ultrasound for Prostate Cancer Localization.

PubMed

Schalk, Stefan G; Huang, Jing; Li, Jia; Demi, Libertario; Wijkstra, Hessel; Huang, Pintong; Mischi, Massimo

2018-04-01

To investigate quantitative 3-D dynamic contrast-enhanced ultrasound (DCE-US) and, in particular 3-D contrast-ultrasound dispersion imaging (CUDI), for prostate cancer detection and localization, 43 patients referred for 10-12-core systematic biopsy underwent 3-D DCE-US. For each 3-D DCE-US recording, parametric maps of CUDI-based and perfusion-based parameters were computed. The parametric maps were divided in regions, each corresponding to a biopsy core. The obtained parameters were validated per biopsy location and after combining two or more adjacent regions. For CUDI by correlation (r) and for the wash-in time (WIT), a significant difference in parameter values between benign and malignant biopsy cores was found (p < 0.001). In a per-prostate analysis, sensitivity and specificity were 94% and 50% for r, and 53% and 81% for WIT. Based on these results, it can be concluded that quantitative 3-D DCE-US could aid in localizing prostate cancer. Therefore, we recommend follow-up studies to investigate its value for targeting biopsies. Copyright © 2018 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

Bimolecular reaction dynamics from photoelectron spectroscopy of negative ions

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

Bradforth, S.E.

1992-11-01

The transition state region of a neutral bimolecular reaction may be experimentally investigated by photoelectron spectroscopy of an appropriate negative ion. The photoelectron spectrum provides information on the spectroscopy and dynamics of the short lived transition state and may be used to develop model potential energy surfaces that are semi-quantitative in this important region. The principles of bound [yields] bound negative ion photoelectron spectroscopy are illustrated by way of an example: a full analysis of the photoelectron bands of CN[sup [minus

Brain size regulations by cbp haploinsufficiency evaluated by in-vivo MRI based volumetry

NASA Astrophysics Data System (ADS)

Ateca-Cabarga, Juan C.; Cosa, Alejandro; Pallarés, Vicente; López-Atalaya, José P.; Barco, Ángel; Canals, Santiago; Moratal, David

2015-11-01

The Rubinstein-Taybi Syndrome (RSTS) is a congenital disease that affects brain development causing severe cognitive deficits. In most cases the disease is associated with dominant mutations in the gene encoding the CREB binding protein (CBP). In this work, we present the first quantitative analysis of brain abnormalities in a mouse model of RSTS using magnetic resonance imaging (MRI) and two novel self-developed automated algorithms for image volumetric analysis. Our results quantitatively confirm key syndromic features observed in RSTS patients, such as reductions in brain size (-16.31%, p < 0.05), white matter volume (-16.00%, p < 0.05), and corpus callosum (-12.40%, p < 0.05). Furthermore, they provide new insight into the developmental origin of the disease. By comparing brain tissues in a region by region basis between cbp+/- and cbp+/+ littermates, we found that cbp haploinsufficiency is specifically associated with significant reductions in prosencephalic tissue, such us in the olfactory bulb and neocortex, whereas regions evolved from the embryonic rhombencephalon were spared. Despite the large volume reductions, the proportion between gray-, white-matter and cerebrospinal fluid were conserved, suggesting a role of CBP in brain size regulation. The commonalities with holoprosencephaly and arhinencephaly conditions suggest the inclusion of RSTS in the family of neuronal migration disorders.

Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis.

PubMed

Bentsink, Leónie; Jowett, Jemma; Hanhart, Corrie J; Koornneef, Maarten

2006-11-07

Genetic variation for seed dormancy in nature is a typical quantitative trait controlled by multiple loci on which environmental factors have a strong effect. Finding the genes underlying dormancy quantitative trait loci is a major scientific challenge, which also has relevance for agriculture and ecology. In this study we describe the identification of the DELAY OF GERMINATION 1 (DOG1) gene previously identified as a quantitative trait locus involved in the control of seed dormancy. This gene was isolated by a combination of positional cloning and mutant analysis and is absolutely required for the induction of seed dormancy. DOG1 is a member of a small gene family of unknown molecular function, with five members in Arabidopsis. The functional natural allelic variation present in Arabidopsis is caused by polymorphisms in the cis-regulatory region of the DOG1 gene and results in considerable expression differences between the DOG1 alleles of the accessions analyzed.

Prediction of Coronal Mass Ejections From Vector Magnetograms: Quantitative Measures as Predictors

NASA Technical Reports Server (NTRS)

Falconer, D. A.; Moore, R. L.; Gary, G. A.; Rose, M. Franklin (Technical Monitor)

2001-01-01

We derived two quantitative measures of an active region's global nonpotentiality from the region's vector magnetogram, 1) the net current (I(sub N)), and 2) the length of strong-shear, strong-field main neutral line (Lss), and used these two measures in a pilot study of the CME productivity of 4 active regions. We compared the global nonpotentiality measures to the active regions' CME productivity determined from GOES and Yohkoh/SXT observations. We found that two of the active regions were highly globally nonpotential and were CME productive, while the other two active regions had little global nonpotentiality and produced no CMEs. At the Fall 2000 AGU, we reported on an expanded study (12 active regions and 17 magnetograms) in which we evaluated four quantitative global measures of an active region's magnetic field and compared these measures with the CME productivity. The four global measures (all derived from MSFC vector magnetograms) included our two previous measures (I(sub N) and L(sub ss)) as well as two new ones, the total magnetic flux (PHI) (a measure of an active region's size), and the normalized twist (alpha (bar)= muIN/PHI). We found that the three quantitative measures of global nonpotentiality (I(sub N), L(sub ss), alpha (bar)) were all well correlated (greater than 99% confidence level) with an active region's CME productivity within plus or minus 2 days of the day of the magnetogram. We will now report on our findings of how good our quantitative measures are as predictors of active-region CME productivity, using only CMEs that occurred after the magnetogram. We report the preliminary skill test of these quantitative measures as predictors. We compare the CME prediction success of our quantitative measures to the CME prediction success based on an active region's past CME productivity. We examine the cases of the handful of false positive and false negatives to look for improvements to our predictors. This work is funded by NSF through the Space Weather Program and by NASA through the Solar Physics Supporting Research and Technology Program.

Characteristics of lip-mouth region in smiling position from 80 persons with acceptable faces and individual normal occlusions.

PubMed

Zhang, Jiangheng; Chen, Yangxi; Zhou, Xiukun

2002-09-01

The characteristics of lip-mouth region including the soft and hard tissues in smiling position with frontal fixed position photographic computer-aided analysis were studied. The subjects were 80 persons (40 male and 40 females, age range: 17 to approximately 25 years) with acceptable faces and individual normal occlusions. The subjects were asked to take maximum smiling position to accept photographic measurement with computer-aided analysis. The maximum smile line could be divided into 3 categories: low smile line (16.25%), average smile line (68.75%), and high smile line (15%). The method adopting maximum smiling position to study the lip-month region is reproducible and comparable. This study would be helpful to provide a quantitative reference for clinical investigation, diagnosis, treatment and efficacy appraisal.

Modeling Dynamic Functional Neuroimaging Data Using Structural Equation Modeling

ERIC Educational Resources Information Center

Price, Larry R.; Laird, Angela R.; Fox, Peter T.; Ingham, Roger J.

2009-01-01

The aims of this study were to present a method for developing a path analytic network model using data acquired from positron emission tomography. Regions of interest within the human brain were identified through quantitative activation likelihood estimation meta-analysis. Using this information, a "true" or population path model was then…

Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine

NASA Astrophysics Data System (ADS)

Candeo, Alessia; Sana, Ilenia; Ferrari, Eleonora; Maiuri, Luigi; D'Andrea, Cosimo; Valentini, Gianluca; Bassi, Andrea

2016-05-01

Light sheet fluorescence microscopy has proven to be a powerful tool to image fixed and chemically cleared samples, providing in depth and high resolution reconstructions of intact mouse organs. We applied light sheet microscopy to image the mouse intestine. We found that large portions of the sample can be readily visualized, assessing the organ status and highlighting the presence of regions with impaired morphology. Yet, three-dimensional (3-D) sectioning of the intestine leads to a large dataset that produces unnecessary storage and processing overload. We developed a routine that extracts the relevant information from a large image stack and provides quantitative analysis of the intestine morphology. This result was achieved by a three step procedure consisting of: (1) virtually unfold the 3-D reconstruction of the intestine; (2) observe it layer-by-layer; and (3) identify distinct villi and statistically analyze multiple samples belonging to different intestinal regions. Even if the procedure has been developed for the murine intestine, most of the underlying concepts have a general applicability.

Markov chain Monte Carlo linkage analysis: effect of bin width on the probability of linkage.

PubMed

Slager, S L; Juo, S H; Durner, M; Hodge, S E

2001-01-01

We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the "probability of linkage" (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a "location estimate" for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths.

The Functional Neuroanatomy of Male Psychosexual and Physiosexual Arousal: A Quantitative Meta-Analysis

PubMed Central

Poeppl, Timm B.; Langguth, Berthold; Laird, Angela R.; Eickhoff, Simon B.

2016-01-01

Reproductive behavior is mandatory for conservation of species and mediated by a state of sexual arousal (SA), involving both complex mental processes and bodily reactions. An early neurobehavioral model of SA proposes cognitive, emotional, motivational, and autonomic components. In a comprehensive quantitative meta-analysis on previous neuroimaging findings, we provide here evidence for distinct brain networks underlying psychosexual and physiosexual arousal. Psychosexual (i.e., mental sexual) arousal recruits brain areas crucial for cognitive evaluation, top-down modulation of attention and exteroceptive sensory processing, relevance detection and affective evaluation, as well as regions implicated in the representation of urges and in triggering autonomic processes. In contrast, physiosexual (i.e., physiological sexual) arousal is mediated by regions responsible for regulation and monitoring of initiated autonomic processes and emotions and for somatosensory processing. These circuits are interconnected by subcortical structures (putamen and claustrum) that provide exchange of sensorimotor information and crossmodal processing between and within the networks. Brain deactivations may imply attenuation of introspective processes and social cognition, but be necessary to release intrinsic inhibition of SA. PMID:23674246

Dahl (S × R) Rat Congenic Strain Analysis Confirms and Defines a Chromosome 17 Spatial Navigation Quantitative Trait Locus to <10 Mbp

PubMed Central

Herrera, Victoria L.; Pasion, Khristine A.; Tan, Glaiza A.; Ruiz-Opazo, Nelson

2013-01-01

A quantitative trait locus (QTL) linked with ability to find a platform in the Morris Water Maze (MWM) was located on chromosome 17 (Nav-5 QTL) using intercross between Dahl S and Dahl R rats. We developed two congenic strains, S.R17A and S.R17B introgressing Dahl R-chromosome 17 segments into Dahl S chromosome 17 region spanning putative Nav-5 QTL. Performance analysis of S.R17A, S.R17B and Dahl S rats in the Morris water maze (MWM) task showed a significantly decreased spatial navigation performance in S.R17B congenic rats when compared with Dahl S controls (P = 0.02). The S.R17A congenic segment did not affect MWM performance delimiting Nav-5 to the chromosome 17 65.02–74.66 Mbp region. Additional fine mapping is necessary to identify the specific gene variant accounting for Nav-5 effect on spatial learning and memory in Dahl rats. PMID:23469157

Bispectral infrared forest fire detection and analysis using classification techniques

NASA Astrophysics Data System (ADS)

Aranda, Jose M.; Melendez, Juan; de Castro, Antonio J.; Lopez, Fernando

2004-01-01

Infrared cameras are well established as a useful tool for fire detection, but their use for quantitative forest fire measurements faces difficulties, due to the complex spatial and spectral structure of fires. In this work it is shown that some of these difficulties can be overcome by applying classification techniques, a standard tool for the analysis of satellite multispectral images, to bi-spectral images of fires. Images were acquired by two cameras that operate in the medium infrared (MIR) and thermal infrared (TIR) bands. They provide simultaneous and co-registered images, calibrated in brightness temperatures. The MIR-TIR scatterplot of these images can be used to classify the scene into different fire regions (background, ashes, and several ember and flame regions). It is shown that classification makes possible to obtain quantitative measurements of physical fire parameters like rate of spread, embers temperature, and radiated power in the MIR and TIR bands. An estimation of total radiated power and heat release per unit area is also made and compared with values derived from heat of combustion and fuel consumption.

A preliminary study of DTI Fingerprinting on stroke analysis.

PubMed

Ma, Heather T; Ye, Chenfei; Wu, Jun; Yang, Pengfei; Chen, Xuhui; Yang, Zhengyi; Ma, Jingbo

2014-01-01

DTI (Diffusion Tensor Imaging) is a well-known MRI (Magnetic Resonance Imaging) technique which provides useful structural information about human brain. However, the quantitative measurement to physiological variation of subtypes of ischemic stroke is not available. An automatically quantitative method for DTI analysis will enhance the DTI application in clinics. In this study, we proposed a DTI Fingerprinting technology to quantitatively analyze white matter tissue, which was applied in stroke classification. The TBSS (Tract Based Spatial Statistics) method was employed to generate mask automatically. To evaluate the clustering performance of the automatic method, lesion ROI (Region of Interest) is manually drawn on the DWI images as a reference. The results from the DTI Fingerprinting were compared with those obtained from the reference ROIs. It indicates that the DTI Fingerprinting could identify different states of ischemic stroke and has promising potential to provide a more comprehensive measure of the DTI data. Further development should be carried out to improve DTI Fingerprinting technology in clinics.

QEEG and LORETA in Teenagers With Conduct Disorder and Psychopathic Traits.

PubMed

Calzada-Reyes, Ana; Alvarez-Amador, Alfredo; Galán-García, Lídice; Valdés-Sosa, Mitchell

2017-05-01

Few studies have investigated the impact of the psychopathic traits on the EEG of teenagers with conduct disorder (CD). To date, there is no other research studying low-resolution brain electromagnetic tomography (LORETA) technique using quantitative EEG (QEEG) analysis in adolescents with CD and psychopathic traits. To find electrophysiological differences specifically related to the psychopathic traits. The current investigation compares the QEEG and the current source density measures between adolescents with CD and psychopathic traits and adolescents with CD without psychopathic traits. The resting EEG activity and LORETA for the EEG fast spectral bands were evaluated in 42 teenagers with CD, 25 with and 17 without psychopathic traits according to the Antisocial Process Screening Device. All adolescents were assessed using the DSM-IV-TR criteria. The EEG visual inspection characteristics and the use of frequency domain quantitative analysis techniques (narrow band spectral parameters) are described. QEEG analysis showed a pattern of beta activity excess on the bilateral frontal-temporal regions and decreases of alpha band power on the left central-temporal and right frontal-central-temporal regions in the psychopathic traits group. Current source density calculated at 17.18 Hz showed an increase within fronto-temporo-striatal regions in the psychopathic relative to the nonpsychopathic traits group. These findings indicate that QEEG analysis and techniques of source localization may reveal differences in brain electrical activity among teenagers with CD and psychopathic traits, which was not obvious to visual inspection. Taken together, these results suggest that abnormalities in a fronto-temporo-striatal network play a relevant role in the neurobiological basis of psychopathic behavior.

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos.

PubMed

Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E; Pierce, Niles A

2018-01-08

For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting and/or homogenization. Here, we eliminate the trade-off between quantitation and anatomical context, using quantitative in situ hybridization chain reaction (qHCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable bi-directional queries that open a new era for in situ hybridization. © 2018. Published by The Company of Biologists Ltd.

Quantitative Changes in Cerebral Perfusion during Urinary Urgency in Women with Overactive Bladder

PubMed Central

Weissbart, Steven J.; Xu, Sihua; Bhavsar, Rupal; Rao, Hengyi

2017-01-01

Purpose To quantitatively measure changes in cerebral perfusion in select regions of interest in the brain during urinary urgency in women with overactive bladder (OAB) using arterial spin labeling (ASL). Methods Twelve women with OAB and 10 controls underwent bladder filling and rated urinary urgency (scale 0–10). ASL fMRI scans were performed (1) in the low urgency state after voiding and (2) high urgency state after drinking oral fluids. Absolute regional cerebral blood flow (rCBF) in select regions of interest was compared between the low and high urgency states. Results There were no significant differences in rCBF between the low and high urgency states in the control group. In the OAB group, rCBF (mean ± SE, ml/100 g/min) increased by 10–14% from the low to the high urgency state in the right anterior cingulate cortex (ACC) (44.56 ± 0.59 versus 49.52 ± 1.49, p < 0.05), left ACC (49.29 ± 0.85 versus 54.02 ± 1.46, p < 0.05), and left insula (50.46 ± 1.72 versus 54.99 ± 1.09, p < 0.05). Whole-brain analysis identified additional areas of activation in the right insula, right dorsolateral prefrontal cortex, and pons/midbrain area. Conclusions Urinary urgency is associated with quantitative increase in cerebral perfusion in regions of the brain associated with processing emotional response to discomfort. PMID:28904950

Non-Ionic Highly Permeable Polymer Shells for Encapsulation of Living Cells

DTIC Science & Technology

2011-05-01

I would like to thank Irina Drachuk for her extensive assistance in data collection and analysis , and Drs. Veronika Kozlovskaya and Olga Shchepelina...considered complete when the intensity of the photobleached region stabilized. The quantitative analysis was performed using ImageJ software, and curve...E., Tannin -protein complexes as radical scavengers and radical sinks. J Agric Food Chem 2001, 49 (10), 4917-23. 53. Lopes, G. K.; Schulman, H. M

Critical considerations for the qualitative and quantitative determination of process-induced disorder in crystalline solids.

PubMed

Newman, Ann; Zografi, George

2014-09-01

Solid-state instabilities in crystalline solids arise during processing primarily because a certain level of structural disorder has been introduced into the crystal. Many physical instabilities appear to be associated with the recrystallization of molecules from these disordered regions, while chemical instabilities arise from sufficient molecular mobility to allow solid-state chemical reactivity. In this Commentary we discuss the various forms of structural disorder, processing which can produce disorder, the quantitative analysis of process-induced order, and strategies to limit disorder and its effects. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

5-ALA induced fluorescent image analysis of actinic keratosis

NASA Astrophysics Data System (ADS)

Cho, Yong-Jin; Bae, Youngwoo; Choi, Eung-Ho; Jung, Byungjo

2010-02-01

In this study, we quantitatively analyzed 5-ALA induced fluorescent images of actinic keratosis using digital fluorescent color and hyperspectral imaging modalities. UV-A was utilized to induce fluorescent images and actinic keratosis (AK) lesions were demarcated from surrounding the normal region with different methods. Eight subjects with AK lesion were participated in this study. In the hyperspectral imaging modality, spectral analysis method was utilized for hyperspectral cube image and AK lesions were demarcated from the normal region. Before image acquisition, we designated biopsy position for histopathology of AK lesion and surrounding normal region. Erythema index (E.I.) values on both regions were calculated from the spectral cube data. Image analysis of subjects resulted in two different groups: the first group with the higher fluorescence signal and E.I. on AK lesion than the normal region; the second group with lower fluorescence signal and without big difference in E.I. between two regions. In fluorescent color image analysis of facial AK, E.I. images were calculated on both normal and AK lesions and compared with the results of hyperspectral imaging modality. The results might indicate that the different intensity of fluorescence and E.I. among the subjects with AK might be interpreted as different phases of morphological and metabolic changes of AK lesions.

Application of array-comparative genomic hybridization in tetralogy of Fallot

PubMed Central

Liu, Lin; Wang, Hong-Dan; Cui, Cun-Ying; Wu, Dong; Li, Tao; Fan, Tai-Bing; Peng, Bang-Tian; Zhang, Lian-Zhong; Wang, Cheng-Zeng

2016-01-01

Abstract To explore the underlying pathogenesis and provide references for genetic counseling and prenatal gene diagnosis, we analyzed the chromosome karyotypes and genome-wide copy number variations (CNVs) in 86 patients with tetralogy of Fallot (TOF) by G-banding karyotype analysis and array-comparative genomic hybridization (aCGH), respectively. And then quantitative polymerase chain reaction was used to validate these candidate CNVs. Based on their different properties, CNVs were categorized into benign CNVs, suspiciously pathogenic CNVs, and indefinite CNVs. Data analysis was based on public databases such as UCSC, DECIPHER, DGV, ISCA, and OMIM. The karyotype was normal in all the 86 patients with TOF. CNVs were detected in 11 patients by aCGH and quantitative polymerase chain reaction. Patient no. 0001, 0010, and 0029 had 2.52-Mb deletion in the chromosome 22q11.21 region; patient no. 0008 had both 595- and 428-kb duplications, respectively, in 12p12.3p12.2 and 14q23.2q23.3 regions; patient no. 0009 had 1.46-Mb duplication in the 1q21.1q21.2 region; patient no. 0016 had 513-kb duplication in the 1q42.13 region; patient no. 0024 had 292-kb duplication in the 16q11.2 region; patient no. 0026 had 270-kb duplication in the 16q24.1 region; patient no. 0028 had 222-kb deletion in the 7q31.1 region; patient no. 0033 had 1.73-Mb duplication in the 17q12 region; and patient no. 0061 had 5.79-Mb deletion in the 1p36.33p36.31 region. aCGH can accurately detect CNVs in the patients with TOF. This is conducive to genetic counseling and prenatal diagnosis for TOF and provides a new clue and theoretical basis for exploring the pathogenesis of congenital heart disease. PMID:27930557

Application of array-comparative genomic hybridization in tetralogy of Fallot.

PubMed

Liu, Lin; Wang, Hong-Dan; Cui, Cun-Ying; Wu, Dong; Li, Tao; Fan, Tai-Bing; Peng, Bang-Tian; Zhang, Lian-Zhong; Wang, Cheng-Zeng

2016-12-01

To explore the underlying pathogenesis and provide references for genetic counseling and prenatal gene diagnosis, we analyzed the chromosome karyotypes and genome-wide copy number variations (CNVs) in 86 patients with tetralogy of Fallot (TOF) by G-banding karyotype analysis and array-comparative genomic hybridization (aCGH), respectively. And then quantitative polymerase chain reaction was used to validate these candidate CNVs. Based on their different properties, CNVs were categorized into benign CNVs, suspiciously pathogenic CNVs, and indefinite CNVs. Data analysis was based on public databases such as UCSC, DECIPHER, DGV, ISCA, and OMIM.The karyotype was normal in all the 86 patients with TOF. CNVs were detected in 11 patients by aCGH and quantitative polymerase chain reaction. Patient no. 0001, 0010, and 0029 had 2.52-Mb deletion in the chromosome 22q11.21 region; patient no. 0008 had both 595- and 428-kb duplications, respectively, in 12p12.3p12.2 and 14q23.2q23.3 regions; patient no. 0009 had 1.46-Mb duplication in the 1q21.1q21.2 region; patient no. 0016 had 513-kb duplication in the 1q42.13 region; patient no. 0024 had 292-kb duplication in the 16q11.2 region; patient no. 0026 had 270-kb duplication in the 16q24.1 region; patient no. 0028 had 222-kb deletion in the 7q31.1 region; patient no. 0033 had 1.73-Mb duplication in the 17q12 region; and patient no. 0061 had 5.79-Mb deletion in the 1p36.33p36.31 region.aCGH can accurately detect CNVs in the patients with TOF. This is conducive to genetic counseling and prenatal diagnosis for TOF and provides a new clue and theoretical basis for exploring the pathogenesis of congenital heart disease.

Segmentation, Splitting, and Classification of Overlapping Bacteria in Microscope Images for Automatic Bacterial Vaginosis Diagnosis.

PubMed

Song, Youyi; He, Liang; Zhou, Feng; Chen, Siping; Ni, Dong; Lei, Baiying; Wang, Tianfu

2017-07-01

Quantitative analysis of bacterial morphotypes in the microscope images plays a vital role in diagnosis of bacterial vaginosis (BV) based on the Nugent score criterion. However, there are two main challenges for this task: 1) It is quite difficult to identify the bacterial regions due to various appearance, faint boundaries, heterogeneous shapes, low contrast with the background, and small bacteria sizes with regards to the image. 2) There are numerous bacteria overlapping each other, which hinder us to conduct accurate analysis on individual bacterium. To overcome these challenges, we propose an automatic method in this paper to diagnose BV by quantitative analysis of bacterial morphotypes, which consists of a three-step approach, i.e., bacteria regions segmentation, overlapping bacteria splitting, and bacterial morphotypes classification. Specifically, we first segment the bacteria regions via saliency cut, which simultaneously evaluates the global contrast and spatial weighted coherence. And then Markov random field model is applied for high-quality unsupervised segmentation of small object. We then decompose overlapping bacteria clumps into markers, and associate a pixel with markers to identify evidence for eventual individual bacterium splitting. Next, we extract morphotype features from each bacterium to learn the descriptors and to characterize the types of bacteria using an Adaptive Boosting machine learning framework. Finally, BV diagnosis is implemented based on the Nugent score criterion. Experiments demonstrate that our proposed method achieves high accuracy and efficiency in computation for BV diagnosis.

Asian couples in negotiation: a mixed-method observational study of cultural variations across five Asian regions.

PubMed

Lee, Wai-Yung; Nakamura, Shin-Ichi; Chung, Moon Ja; Chun, Young Ju; Fu, Meng; Liang, Shu-Chuan; Liu, Cui-Lian

2013-09-01

The purpose of this study was to explore variations in how contemporary couples from five different Asian regions negotiate disagreements. Video recordings of 50 couples (10 each from Japan, Korea, Mainland China, Taiwan, and Hong Kong) discussing unresolved disagreements provided raw data for quantitative and qualitative analyses. First, teams of coders from each region used a common protocol to make quantitative ratings of content themes and interaction patterns for couples from their own region. An interregional panel of investigators then performed in-depth qualitative reviews for half of these cases, noting cultural differences not only in observed patterns of couple behavior but also in their own perceptions of these patterns. Both quantitative and qualitative analyses revealed clear regional differences on dimensions such as overt negativity, demand-withdraw interaction, and collaboration. The qualitative results also provided a richer, more nuanced view of other (e.g., gender-linked) conflict management patterns that the quantitative analyses did not capture. Inconsistencies between qualitative and quantitative data and between the qualitative observations of investigators from different regions were most pronounced for couples from Korea and Japan, whose conflict styles were subtler and less direct than those of couples from the other regions. © FPI, Inc.

Clinical significance of quantitative analysis of facial nerve enhancement on MRI in Bell's palsy.

PubMed

Song, Mee Hyun; Kim, Jinna; Jeon, Ju Hyun; Cho, Chang Il; Yoo, Eun Hye; Lee, Won-Sang; Lee, Ho-Ki

2008-11-01

Quantitative analysis of the facial nerve on the lesion side as well as the normal side, which allowed for more accurate measurement of facial nerve enhancement in patients with facial palsy, showed statistically significant correlation with the initial severity of facial nerve inflammation, although little prognostic significance was shown. This study investigated the clinical significance of quantitative measurement of facial nerve enhancement in patients with Bell's palsy by analyzing the enhancement pattern and correlating MRI findings with initial severity of facial palsy and clinical outcome. Facial nerve enhancement was measured quantitatively by using the region of interest on pre- and postcontrast T1-weighted images in 44 patients diagnosed with Bell's palsy. The signal intensity increase on the lesion side was first compared with that of the contralateral side and then correlated with the initial degree of facial palsy and prognosis. The lesion side showed significantly higher signal intensity increase compared with the normal side in all of the segments except for the mastoid segment. Signal intensity increase at the internal auditory canal and labyrinthine segments showed correlation with the initial degree of facial palsy but no significant difference was found between different prognostic groups.

The effects of AVIRIS atmospheric calibration methodology on identification and quantitative mapping of surface mineralogy, Drum Mountains, Utah

NASA Technical Reports Server (NTRS)

Kruse, Fred A.; Dwyer, John L.

1993-01-01

The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) measures reflected light in 224 contiguous spectra bands in the 0.4 to 2.45 micron region of the electromagnetic spectrum. Numerous studies have used these data for mineralogic identification and mapping based on the presence of diagnostic spectral features. Quantitative mapping requires conversion of the AVIRIS data to physical units (usually reflectance) so that analysis results can be compared and validated with field and laboratory measurements. This study evaluated two different AVIRIS calibration techniques to ground reflectance: an empirically-based method and an atmospheric model based method to determine their effects on quantitative scientific analyses. Expert system analysis and linear spectral unmixing were applied to both calibrated data sets to determine the effect of the calibration on the mineral identification and quantitative mapping results. Comparison of the image-map results and image reflectance spectra indicate that the model-based calibrated data can be used with automated mapping techniques to produce accurate maps showing the spatial distribution and abundance of surface mineralogy. This has positive implications for future operational mapping using AVIRIS or similar imaging spectrometer data sets without requiring a priori knowledge.

Differential expression of type X collagen in a mechanically active 3-D chondrocyte culture system: a quantitative study

PubMed Central

Yang, Xu; Vezeridis, Peter S; Nicholas, Brian; Crisco, Joseph J; Moore, Douglas C; Chen, Qian

2006-01-01

Objective Mechanical loading of cartilage influences chondrocyte metabolism and gene expression. The gene encoding type X collagen is expressed specifically by hypertrophic chondrocytes and up regulated during osteoarthritis. In this study we tested the hypothesis that the mechanical microenvironment resulting from higher levels of local strain in a three dimensional cell culture construct would lead to an increase in the expression of type X collagen mRNA by chondrocytes in those areas. Methods Hypertrophic chondrocytes were isolated from embryonic chick sterna and seeded onto rectangular Gelfoam sponges. Seeded sponges were subjected to various levels of cyclic uniaxial tensile strains at 1 Hz with the computer-controlled Bio-Stretch system. Strain distribution across the sponge was quantified by digital image analysis. After mechanical loading, sponges were cut and the end and center regions were separated according to construct strain distribution. Total RNA was extracted from the cells harvested from these regions, and real-time quantitative RT-PCR was performed to quantify mRNA levels for type X collagen and a housing-keeping gene 18S RNA. Results Chondrocytes distributed in high (9%) local strain areas produced more than two times type X collagen mRNA compared to the those under no load conditions, while chondrocytes located in low (2.5%) local strain areas had no appreciable difference in type X collagen mRNA production in comparison to non-loaded samples. Increasing local strains above 2.5%, either in the center or end regions of the sponge, resulted in increased expression of Col X mRNA by chondrocytes in that region. Conclusion These findings suggest that the threshold of chondrocyte sensitivity to inducing type X collagen mRNA production is more than 2.5% local strain, and that increased local strains above the threshold results in an increase of Col X mRNA expression. Such quantitative analysis has important implications for our understanding of mechanosensitivity of cartilage and mechanical regulation of chondrocyte gene expression. PMID:17150098

Advanced imaging techniques in brain tumors

PubMed Central

2009-01-01

Abstract Perfusion, permeability and magnetic resonance spectroscopy (MRS) are now widely used in the research and clinical settings. In the clinical setting, qualitative, semi-quantitative and quantitative approaches such as review of color-coded maps to region of interest analysis and analysis of signal intensity curves are being applied in practice. There are several pitfalls with all of these approaches. Some of these shortcomings are reviewed, such as the relative low sensitivity of metabolite ratios from MRS and the effect of leakage on the appearance of color-coded maps from dynamic susceptibility contrast (DSC) magnetic resonance (MR) perfusion imaging and what correction and normalization methods can be applied. Combining and applying these different imaging techniques in a multi-parametric algorithmic fashion in the clinical setting can be shown to increase diagnostic specificity and confidence. PMID:19965287

Frictional strength and heat flow of southern San Andreas Fault

NASA Astrophysics Data System (ADS)

Zhu, P. P.

2016-01-01

Frictional strength and heat flow of faults are two related subjects in geophysics and seismology. To date, the investigation on regional frictional strength and heat flow still stays at the stage of qualitative estimation. This paper is concentrated on the regional frictional strength and heat flow of the southern San Andreas Fault (SAF). Based on the in situ borehole measured stress data, using the method of 3D dynamic faulting analysis, we quantitatively determine the regional normal stress, shear stress, and friction coefficient at various seismogenic depths. These new data indicate that the southern SAF is a weak fault within the depth of 15 km. As depth increases, all the regional normal and shear stresses and friction coefficient increase. The former two increase faster than the latter. Regional shear stress increment per kilometer equals 5.75 ± 0.05 MPa/km for depth ≤15 km; regional normal stress increment per kilometer is equal to 25.3 ± 0.1 MPa/km for depth ≤15 km. As depth increases, regional friction coefficient increment per kilometer decreases rapidly from 0.08 to 0.01/km at depths less than ~3 km. As depth increases from ~3 to ~5 km, it is 0.01/km and then from ~5 to 15 km, and it is 0.002/km. Previously, frictional strength could be qualitatively determined by heat flow measurements. It is difficult to obtain the quantitative heat flow data for the SAF because the measured heat flow data exhibit large scatter. However, our quantitative results of frictional strength can be employed to investigate the heat flow in the southern SAF. We use a physical quantity P f to describe heat flow. It represents the dissipative friction heat power per unit area generated by the relative motion of two tectonic plates accommodated by off-fault deformation. P f is called "fault friction heat." On the basis of our determined frictional strength data, utilizing the method of 3D dynamic faulting analysis, we quantitatively determine the regional long-term fault friction heat at various seismogenic depths in the southern SAF. The new data show that as depth increases, regional friction stress increases within the depth of 15 km; its increment per kilometer equals 5.75 ± 0.05 MPa/km. As depth increases, regional long-term fault friction heat increases; its increment per kilometer is equal to 3.68 ± 0.03 mW/m2/km. The values of regional long-term fault friction heat provided by this study are always lower than those from heat flow measurements. The difference between them and the scatter existing in the measured heat flow data are mainly caused by the following processes: (i) heat convection, (ii) heat advection, (iii) stress accumulation, (iv) seismic bursts between short-term lull periods in a long-term period, and (v) influence of seismicity in short-term periods upon long-term slip rate and heat flow. Fault friction heat is a fundamental parameter in research on heat flow.

AUTOMATED ANALYSIS OF QUANTITATIVE IMAGE DATA USING ISOMORPHIC FUNCTIONAL MIXED MODELS, WITH APPLICATION TO PROTEOMICS DATA.

PubMed

Morris, Jeffrey S; Baladandayuthapani, Veerabhadran; Herrick, Richard C; Sanna, Pietro; Gutstein, Howard

2011-01-01

Image data are increasingly encountered and are of growing importance in many areas of science. Much of these data are quantitative image data, which are characterized by intensities that represent some measurement of interest in the scanned images. The data typically consist of multiple images on the same domain and the goal of the research is to combine the quantitative information across images to make inference about populations or interventions. In this paper, we present a unified analysis framework for the analysis of quantitative image data using a Bayesian functional mixed model approach. This framework is flexible enough to handle complex, irregular images with many local features, and can model the simultaneous effects of multiple factors on the image intensities and account for the correlation between images induced by the design. We introduce a general isomorphic modeling approach to fitting the functional mixed model, of which the wavelet-based functional mixed model is one special case. With suitable modeling choices, this approach leads to efficient calculations and can result in flexible modeling and adaptive smoothing of the salient features in the data. The proposed method has the following advantages: it can be run automatically, it produces inferential plots indicating which regions of the image are associated with each factor, it simultaneously considers the practical and statistical significance of findings, and it controls the false discovery rate. Although the method we present is general and can be applied to quantitative image data from any application, in this paper we focus on image-based proteomic data. We apply our method to an animal study investigating the effects of opiate addiction on the brain proteome. Our image-based functional mixed model approach finds results that are missed with conventional spot-based analysis approaches. In particular, we find that the significant regions of the image identified by the proposed method frequently correspond to subregions of visible spots that may represent post-translational modifications or co-migrating proteins that cannot be visually resolved from adjacent, more abundant proteins on the gel image. Thus, it is possible that this image-based approach may actually improve the realized resolution of the gel, revealing differentially expressed proteins that would not have even been detected as spots by modern spot-based analyses.

Isobaric Tags for Relative and Absolute Quantitation-Based Proteomic Analysis of Patent and Constricted Ductus Arteriosus Tissues Confirms the Systemic Regulation of Ductus Arteriosus Closure.

PubMed

Hong, Haifa; Ye, Lincai; Chen, Huiwen; Xia, Yu; Liu, Yue; Liu, Jinfen; Lu, Yanan; Zhang, Haibo

2015-08-01

We aimed to evaluate global changes in protein expression associated with patency by undertaking proteomic analysis of human constricted and patent ductus arteriosus (DA). Ten constricted and 10 patent human DAs were excised from infants with ductal-dependent heart disease during surgery. Using isobaric tags for relative and absolute quantitation-based quantitative proteomics, 132 differentially expressed proteins were identified. Of 132 proteins, voltage-gated sodium channel 1.3 (SCN3A), myosin 1d (Myo1d), Rho GTPase activating protein 26 (ARHGAP26), and retinitis pigmentosa 1 (RP1) were selected for validation by Western blot and quantitative real-time polymerase chain reaction analyses. Significant upregulation of SCN3A, Myo1d, and RP1 messenger RNA, and protein levels was observed in the patent DA group (all P ≤ 0.048). ARHGAP26 messenger RNA and protein levels were decreased in patent DA tissue (both P ≤ 0.018). Immunohistochemistry analysis revealed that Myo1d, ARHGAP26, and RP1 were specifically expressed in the subendothelial region of constricted DAs; however, diffuse expression of these proteins was noted in the patent group. Proteomic analysis revealed global changes in the expression of proteins that regulate oxygen sensing, ion channels, smooth muscle cell migration, nervous system, immune system, and metabolism, suggesting a basis for the systemic regulation of DA patency by diverse signaling pathways, which will be confirmed in further studies.

Quantitative Story Telling: Initial steps towards bridging perspectives and tools for a robust nexus assessment

NASA Astrophysics Data System (ADS)

Cabello, Violeta

2017-04-01

This communication will present the advancement of an innovative analytical framework for the analysis of Water-Energy-Food-Climate Nexus termed Quantitative Story Telling (QST). The methodology is currently under development within the H2020 project MAGIC - Moving Towards Adaptive Governance in Complexity: Informing Nexus Security (www.magic-nexus.eu). The key innovation of QST is that it bridges qualitative and quantitative analytical tools into an iterative research process in which each step is built and validated in interaction with stakeholders. The qualitative analysis focusses on the identification of the narratives behind the development of relevant WEFC-Nexus policies and innovations. The quantitative engine is the Multi-Scale Analysis of Societal and Ecosystem Metabolism (MuSIASEM), a resource accounting toolkit capable of integrating multiple analytical dimensions at different scales through relational analysis. Although QST may not be labelled a data-driven but a story-driven approach, I will argue that improving models per se may not lead to an improved understanding of WEF-Nexus problems unless we are capable of generating more robust narratives to frame them. The communication will cover an introduction to MAGIC project, the basic concepts of QST and a case study focussed on agricultural production in a semi-arid region in Southern Spain. Data requirements for this case study and the limitations to find, access or estimate them will be presented alongside a reflection on the relation between analytical scales and data availability.

New methodologies for multi-scale time-variant reliability analysis of complex lifeline networks

NASA Astrophysics Data System (ADS)

Kurtz, Nolan Scot

The cost of maintaining existing civil infrastructure is enormous. Since the livelihood of the public depends on such infrastructure, its state must be managed appropriately using quantitative approaches. Practitioners must consider not only which components are most fragile to hazard, e.g. seismicity, storm surge, hurricane winds, etc., but also how they participate on a network level using network analysis. Focusing on particularly damaged components does not necessarily increase network functionality, which is most important to the people that depend on such infrastructure. Several network analyses, e.g. S-RDA, LP-bounds, and crude-MCS, and performance metrics, e.g. disconnection bounds and component importance, are available for such purposes. Since these networks are existing, the time state is also important. If networks are close to chloride sources, deterioration may be a major issue. Information from field inspections may also have large impacts on quantitative models. To address such issues, hazard risk analysis methodologies for deteriorating networks subjected to seismicity, i.e. earthquakes, have been created from analytics. A bridge component model has been constructed for these methodologies. The bridge fragilities, which were constructed from data, required a deeper level of analysis as these were relevant for specific structures. Furthermore, chloride-induced deterioration network effects were investigated. Depending on how mathematical models incorporate new information, many approaches are available, such as Bayesian model updating. To make such procedures more flexible, an adaptive importance sampling scheme was created for structural reliability problems. Additionally, such a method handles many kinds of system and component problems with singular or multiple important regions of the limit state function. These and previously developed analysis methodologies were found to be strongly sensitive to the network size. Special network topologies may be more or less computationally difficult, while the resolution of the network also has large affects. To take advantage of some types of topologies, network hierarchical structures with super-link representation have been used in the literature to increase the computational efficiency by analyzing smaller, densely connected networks; however, such structures were based on user input and subjective at times. To address this, algorithms must be automated and reliable. These hierarchical structures may indicate the structure of the network itself. This risk analysis methodology has been expanded to larger networks using such automated hierarchical structures. Component importance is the most important objective from such network analysis; however, this may only provide the information of which bridges to inspect/repair earliest and little else. High correlations influence such component importance measures in a negative manner. Additionally, a regional approach is not appropriately modelled. To investigate a more regional view, group importance measures based on hierarchical structures have been created. Such structures may also be used to create regional inspection/repair approaches. Using these analytical, quantitative risk approaches, the next generation of decision makers may make both component and regional-based optimal decisions using information from both network function and further effects of infrastructure deterioration.

A note on the efficiencies of sampling strategies in two-stage Bayesian regional fine mapping of a quantitative trait.

PubMed

Chen, Zhijian; Craiu, Radu V; Bull, Shelley B

2014-11-01

In focused studies designed to follow up associations detected in a genome-wide association study (GWAS), investigators can proceed to fine-map a genomic region by targeted sequencing or dense genotyping of all variants in the region, aiming to identify a functional sequence variant. For the analysis of a quantitative trait, we consider a Bayesian approach to fine-mapping study design that incorporates stratification according to a promising GWAS tag SNP in the same region. Improved cost-efficiency can be achieved when the fine-mapping phase incorporates a two-stage design, with identification of a smaller set of more promising variants in a subsample taken in stage 1, followed by their evaluation in an independent stage 2 subsample. To avoid the potential negative impact of genetic model misspecification on inference we incorporate genetic model selection based on posterior probabilities for each competing model. Our simulation study shows that, compared to simple random sampling that ignores genetic information from GWAS, tag-SNP-based stratified sample allocation methods reduce the number of variants continuing to stage 2 and are more likely to promote the functional sequence variant into confirmation studies. © 2014 WILEY PERIODICALS, INC.

Feasibility of high-resolution quantitative perfusion analysis in patients with heart failure.

PubMed

Sammut, Eva; Zarinabad, Niloufar; Wesolowski, Roman; Morton, Geraint; Chen, Zhong; Sohal, Manav; Carr-White, Gerry; Razavi, Reza; Chiribiri, Amedeo

2015-02-12

Cardiac magnetic resonance (CMR) is playing an expanding role in the assessment of patients with heart failure (HF). The assessment of myocardial perfusion status in HF can be challenging due to left ventricular (LV) remodelling and wall thinning, coexistent scar and respiratory artefacts. The aim of this study was to assess the feasibility of quantitative CMR myocardial perfusion analysis in patients with HF. A group of 58 patients with heart failure (HF; left ventricular ejection fraction, LVEF ≤ 50%) and 33 patients with normal LVEF (LVEF >50%), referred for suspected coronary artery disease, were studied. All subjects underwent quantitative first-pass stress perfusion imaging using adenosine according to standard acquisition protocols. The feasibility of quantitative perfusion analysis was then assessed using high-resolution, 3 T kt perfusion and voxel-wise Fermi deconvolution. 30/58 (52%) subjects in the HF group had underlying ischaemic aetiology. Perfusion abnormalities were seen amongst patients with ischaemic HF and patients with normal LV function. No regional perfusion defect was observed in the non-ischaemic HF group. Good agreement was found between visual and quantitative analysis across all groups. Absolute stress perfusion rate, myocardial perfusion reserve (MPR) and endocardial-epicardial MPR ratio identified areas with abnormal perfusion in the ischaemic HF group (p = 0.02; p = 0.04; p = 0.02, respectively). In the Normal LV group, MPR and endocardial-epicardial MPR ratio were able to distinguish between normal and abnormal segments (p = 0.04; p = 0.02 respectively). No significant differences of absolute stress perfusion rate or MPR were observed comparing visually normal segments amongst groups. Our results demonstrate the feasibility of high-resolution voxel-wise perfusion assessment in patients with HF.

Structural Brain Anomalies and Chronic Pain: A Quantitative Meta-Analysis of Gray Matter Volume

PubMed Central

Smallwood, Rachel F.; Laird, Angela R.; Ramage, Amy E.; Parkinson, Amy L.; Lewis, Jeffrey; Clauw, Daniel J.; Williams, David A.; Schmidt-Wilcke, Tobias; Farrell, Michael J.; Eickhoff, Simon B.; Robin, Donald A.

2016-01-01

The diversity of chronic pain syndromes and the methods employed to study them make integrating experimental findings challenging. This study performed coordinate-based meta-analyses using voxel-based morphometry imaging results to examine gray matter volume (GMV) differences between chronic pain patients and healthy controls. There were 12 clusters where GMV was decreased in patients compared with controls, including many regions thought to be part of the “pain matrix” of regions involved in pain perception, but also including many other regions that are not commonly regarded as pain-processing areas. The right hippocampus and parahippocampal gyrus were the only regions noted to have increased GMV in patients. Functional characterizations were implemented using the BrainMap database to determine which behavioral domains were significantly represented in these regions. The most common behavioral domains associated with these regions were cognitive, affective, and perceptual domains. Because many of these regions are not classically connected with pain and because there was such significance in functionality outside of perception, it is proposed that many of these regions are related to the constellation of comorbidities of chronic pain, such as fatigue and cognitive and emotional impairments. Further research into the mechanisms of GMV changes could provide a perspective on these findings. Perspective Quantitative meta-analyses revealed structural differences between brains of individuals with chronic pain and healthy controls. These differences may be related to comorbidities of chronic pain. PMID:23685185

Time-dynamics of the two-color emission from vertical-external-cavity surface-emitting lasers

NASA Astrophysics Data System (ADS)

Chernikov, A.; Wichmann, M.; Shakfa, M. K.; Scheller, M.; Moloney, J. V.; Koch, S. W.; Koch, M.

2012-01-01

The temporal stability of a two-color vertical-external-cavity surface-emitting laser is studied using single-shot streak-camera measurements. The collected data is evaluated via quantitative statistical analysis schemes. Dynamically stable and unstable regions for the two-color operation are identified and the dependence on the pump conditions is analyzed.

Mapping of QTL associated with seed amino acids content in MD96-5722 by "Spencer" RIL population of soybean using SNP markers

USDA-ARS?s Scientific Manuscript database

Soybean seeds are major sources of essential amino acids, protein, and fatty acids. Limited information is available on the genetic analysis of amino acid composition in soybean. Therefore, the objective of this study was to identify genomic regions containing quantitative trait loci (QTL) controlli...

Guided Wave Delamination Detection and Quantification With Wavefield Data Analysis

NASA Technical Reports Server (NTRS)

Tian, Zhenhua; Campbell Leckey, Cara A.; Seebo, Jeffrey P.; Yu, Lingyu

2014-01-01

Unexpected damage can occur in aerospace composites due to impact events or material stress during off-nominal loading events. In particular, laminated composites are susceptible to delamination damage due to weak transverse tensile and inter-laminar shear strengths. Developments of reliable and quantitative techniques to detect delamination damage in laminated composites are imperative for safe and functional optimally-designed next-generation composite structures. In this paper, we investigate guided wave interactions with delamination damage and develop quantification algorithms by using wavefield data analysis. The trapped guided waves in the delamination region are observed from the wavefield data and further quantitatively interpreted by using different wavenumber analysis methods. The frequency-wavenumber representation of the wavefield shows that new wavenumbers are present and correlate to trapped waves in the damage region. These new wavenumbers are used to detect and quantify the delamination damage through the wavenumber analysis, which can show how the wavenumber changes as a function of wave propagation distance. The location and spatial duration of the new wavenumbers can be identified, providing a useful means not only for detecting the presence of delamination damage but also allowing for estimation of the delamination size. Our method has been applied to detect and quantify real delamination damage with complex geometry (grown using a quasi-static indentation technique). The detection and quantification results show the location, size, and shape of the delamination damage.

Ratio of sequential chromatograms for quantitative analysis and peak deconvolution: Application to standard addition method and process monitoring

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

Synovec, R.E.; Johnson, E.L.; Bahowick, T.J.

1990-08-01

This paper describes a new technique for data analysis in chromatography, based on taking the point-by-point ratio of sequential chromatograms that have been base line corrected. This ratio chromatogram provides a robust means for the identification and the quantitation of analytes. In addition, the appearance of an interferent is made highly visible, even when it coelutes with desired analytes. For quantitative analysis, the region of the ratio chromatogram corresponding to the pure elution of an analyte is identified and is used to calculate a ratio value equal to the ratio of concentrations of the analyte in sequential injections. For themore » ratio value calculation, a variance-weighted average is used, which compensates for the varying signal-to-noise ratio. This ratio value, or equivalently the percent change in concentration, is the basis of a chromatographic standard addition method and an algorithm to monitor analyte concentration in a process stream. In the case of overlapped peaks, a spiking procedure is used to calculate both the original concentration of an analyte and its signal contribution to the original chromatogram. Thus, quantitation and curve resolution may be performed simultaneously, without peak modeling or curve fitting. These concepts are demonstrated by using data from ion chromatography, but the technique should be applicable to all chromatographic techniques.« less

Sugar and acid content of Citrus prediction modeling using FT-IR fingerprinting in combination with multivariate statistical analysis.

PubMed

Song, Seung Yeob; Lee, Young Koung; Kim, In-Jung

2016-01-01

A high-throughput screening system for Citrus lines were established with higher sugar and acid contents using Fourier transform infrared (FT-IR) spectroscopy in combination with multivariate analysis. FT-IR spectra confirmed typical spectral differences between the frequency regions of 950-1100 cm(-1), 1300-1500 cm(-1), and 1500-1700 cm(-1). Principal component analysis (PCA) and subsequent partial least square-discriminant analysis (PLS-DA) were able to discriminate five Citrus lines into three separate clusters corresponding to their taxonomic relationships. The quantitative predictive modeling of sugar and acid contents from Citrus fruits was established using partial least square regression algorithms from FT-IR spectra. The regression coefficients (R(2)) between predicted values and estimated sugar and acid content values were 0.99. These results demonstrate that by using FT-IR spectra and applying quantitative prediction modeling to Citrus sugar and acid contents, excellent Citrus lines can be early detected with greater accuracy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparison of linkage analysis methods for genome-wide scanning of extended pedigrees, with application to the TG/HDL-C ratio in the Framingham Heart Study

PubMed Central

Horne, Benjamin D; Malhotra, Alka; Camp, Nicola J

2003-01-01

Background High triglycerides (TG) and low high-density lipoprotein cholesterol (HDL-C) jointly increase coronary disease risk. We performed linkage analysis for TG/HDL-C ratio in the Framingham Heart Study data as a quantitative trait, using methods implemented in LINKAGE, GENEHUNTER (GH), MCLINK, and SOLAR. Results were compared to each other and to those from a previous evaluation using SOLAR for TG/HDL-C ratio on this sample. We also investigated linked pedigrees in each region using by-pedigree analysis. Results Fourteen regions with at least suggestive linkage evidence were identified, including some that may increase and some that may decrease coronary risk. Ten of the 14 regions were identified by more than one analysis, and several of these regions were not previously detected. The best regions identified for each method were on chromosomes 2 (LOD = 2.29, MCLINK), 5 (LOD = 2.65, GH), 7 (LOD = 2.67, SOLAR), and 22 (LOD = 3.37, LINKAGE). By-pedigree multi-point LOD values in MCLINK showed linked pedigrees for all five regions, ranging from 3 linked pedigrees (chromosome 5) to 14 linked pedigrees (chromosome 7), and suggested localizations of between 9 cM and 27 cM in size. Conclusion Reasonable concordance was found across analysis methods. No single method identified all regions, either by full sample LOD or with by-pedigree analysis. Concordance across methods appeared better at the pedigree level, with many regions showing by-pedigree support in MCLINK when no evidence was observed in the full sample. Thus, investigating by-pedigree linkage evidence may provide a useful tool for evaluating linkage regions. PMID:14975161

Comparison of linkage analysis methods for genome-wide scanning of extended pedigrees, with application to the TG/HDL-C ratio in the Framingham Heart Study.

PubMed

Horne, Benjamin D; Malhotra, Alka; Camp, Nicola J

2003-12-31

High triglycerides (TG) and low high-density lipoprotein cholesterol (HDL-C) jointly increase coronary disease risk. We performed linkage analysis for TG/HDL-C ratio in the Framingham Heart Study data as a quantitative trait, using methods implemented in LINKAGE, GENEHUNTER (GH), MCLINK, and SOLAR. Results were compared to each other and to those from a previous evaluation using SOLAR for TG/HDL-C ratio on this sample. We also investigated linked pedigrees in each region using by-pedigree analysis. Fourteen regions with at least suggestive linkage evidence were identified, including some that may increase and some that may decrease coronary risk. Ten of the 14 regions were identified by more than one analysis, and several of these regions were not previously detected. The best regions identified for each method were on chromosomes 2 (LOD = 2.29, MCLINK), 5 (LOD = 2.65, GH), 7 (LOD = 2.67, SOLAR), and 22 (LOD = 3.37, LINKAGE). By-pedigree multi-point LOD values in MCLINK showed linked pedigrees for all five regions, ranging from 3 linked pedigrees (chromosome 5) to 14 linked pedigrees (chromosome 7), and suggested localizations of between 9 cM and 27 cM in size. Reasonable concordance was found across analysis methods. No single method identified all regions, either by full sample LOD or with by-pedigree analysis. Concordance across methods appeared better at the pedigree level, with many regions showing by-pedigree support in MCLINK when no evidence was observed in the full sample. Thus, investigating by-pedigree linkage evidence may provide a useful tool for evaluating linkage regions.

Qualitative and quantitative comparison of geostatistical techniques of porosity prediction from the seismic and logging data: a case study from the Blackfoot Field, Alberta, Canada

NASA Astrophysics Data System (ADS)

Maurya, S. P.; Singh, K. H.; Singh, N. P.

2018-05-01

In present study, three recently developed geostatistical methods, single attribute analysis, multi-attribute analysis and probabilistic neural network algorithm have been used to predict porosity in inter well region for Blackfoot field, Alberta, Canada, an offshore oil field. These techniques make use of seismic attributes, generated by model based inversion and colored inversion techniques. The principle objective of the study is to find the suitable combination of seismic inversion and geostatistical techniques to predict porosity and identification of prospective zones in 3D seismic volume. The porosity estimated from these geostatistical approaches is corroborated with the well log porosity. The results suggest that all the three implemented geostatistical methods are efficient and reliable to predict the porosity but the multi-attribute and probabilistic neural network analysis provide more accurate and high resolution porosity sections. A low impedance (6000-8000 m/s g/cc) and high porosity (> 15%) zone is interpreted from inverted impedance and porosity sections respectively between 1060 and 1075 ms time interval and is characterized as reservoir. The qualitative and quantitative results demonstrate that of all the employed geostatistical methods, the probabilistic neural network along with model based inversion is the most efficient method for predicting porosity in inter well region.

Sucrose lyophiles: a semi-quantitative study of residual water content by total X-ray diffraction analysis.

PubMed

Bates, S; Jonaitis, D; Nail, S

2013-10-01

Total X-ray Powder Diffraction Analysis (TXRPD) using transmission geometry was able to observe significant variance in measured powder patterns for sucrose lyophilizates with differing residual water contents. Integrated diffraction intensity corresponding to the observed variances was found to be linearly correlated to residual water content as measured by an independent technique. The observed variance was concentrated in two distinct regions of the lyophilizate powder pattern, corresponding to the characteristic sucrose matrix double halo and the high angle diffuse region normally associated with free-water. Full pattern fitting of the lyophilizate powder patterns suggested that the high angle variance was better described by the characteristic diffraction profile of a concentrated sucrose/water system rather than by the free-water diffraction profile. This suggests that the residual water in the sucrose lyophilizates is intimately mixed at the molecular level with sucrose molecules forming a liquid/solid solution. The bound nature of the residual water and its impact on the sucrose matrix gives an enhanced diffraction response between 3.0 and 3.5 beyond that expected for free-water. The enhanced diffraction response allows semi-quantitative analysis of residual water contents within the studied sucrose lyophilizates to levels below 1% by weight. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative genetic analysis of brain copper and zinc in BXD recombinant inbred mice.

PubMed

Jones, Leslie C; McCarthy, Kristin A; Beard, John L; Keen, Carl L; Jones, Byron C

2006-01-01

Copper and zinc are trace nutrients essential for normal brain function, yet an excess of these elements can be toxic. It is important therefore that these metals be closely regulated. We recently conducted a quantitative trait loci (QTL) analysis to identify chromosomal regions in the mouse containing possible regulatory genes. The animals came from 15 strains of the BXD/Ty recombinant inbred (RI) strain panel and the brain regions analyzed were frontal cortex, caudate-putamen, nucleus accumbens and ventral midbrain. Several QTL were identified for copper and/or zinc, most notably on chromosomes 1, 8, 16 and 17. Genetic correlational analysis also revealed associations between these metals and dopamine, cocaine responses, saccharine preference, immune response and seizure susceptibility. Notably, the QTL on chromosome 17 is also associated with seizure susceptibility and contains the histocompatibility H2 complex. This work shows that regulation of zinc and copper is under polygenic influence and is intimately related to CNS function. Future work will reveal genes underlying the QTL and how they interact with other genes and the environment. More importantly, revelation of the genetic underpinnings of copper and zinc brain homeostasis will aid our understanding of neurological diseases that are related to copper and zinc imbalance.

Neural networks related to dysfunctional face processing in autism spectrum disorder

PubMed Central

Nickl-Jockschat, Thomas; Rottschy, Claudia; Thommes, Johanna; Schneider, Frank; Laird, Angela R.; Fox, Peter T.; Eickhoff, Simon B.

2016-01-01

One of the most consistent neuropsychological findings in autism spectrum disorders (ASD) is a reduced interest in and impaired processing of human faces. We conducted an activation likelihood estimation meta-analysis on 14 functional imaging studies on neural correlates of face processing enrolling a total of 164 ASD patients. Subsequently, normative whole-brain functional connectivity maps for the identified regions of significant convergence were computed for the task-independent (resting-state) and task-dependent (co-activations) state in healthy subjects. Quantitative functional decoding was performed by reference to the BrainMap database. Finally, we examined the overlap of the delineated network with the results of a previous meta-analysis on structural abnormalities in ASD as well as with brain regions involved in human action observation/imitation. We found a single cluster in the left fusiform gyrus showing significantly reduced activation during face processing in ASD across all studies. Both task-dependent and task-independent analyses indicated significant functional connectivity of this region with the temporo-occipital and lateral occipital cortex, the inferior frontal and parietal cortices, the thalamus and the amygdala. Quantitative reverse inference then indicated an association of these regions mainly with face processing, affective processing, and language-related tasks. Moreover, we found that the cortex in the region of right area V5 displaying structural changes in ASD patients showed consistent connectivity with the region showing aberrant responses in the context of face processing. Finally, this network was also implicated in the human action observation/imitation network. In summary, our findings thus suggest a functionally and structurally disturbed network of occipital regions related primarily to face (but potentially also language) processing, which interact with inferior frontal as well as limbic regions and may be the core of aberrant face processing and reduced interest in faces in ASD. PMID:24869925

Cerebral edema, mass effects, and regional blood volume in man.

PubMed

Penn, R D; Kurtz, D

1977-03-01

The authors conducted quantitative analysis of computerized tomography (CT) scans to measure tumor size, cerebral edema, and regional blood volume in man. Mass lesions without edema caused a local reduction in blood volume. Cerebral edema also reduced blood volume in proportion to its severity. Consideration of the electrolyte changes and water shifts in white-matter edema suggested that the decrease in absorption coefficient seen in CT scans was due to the increase in water content. Thus, in cerebral edema separation of blood vessels as well as increased interstitial pressure decrease blood volume, and the regional differences in turn reflect pressure gradients within the brain.

A genome-wide association study of seed protein and oil content in soybean

PubMed Central

2014-01-01

Background Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. In this study, a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTL) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of seed protein and oil content. Results A total of 55,159 single nucleotide polymorphisms (SNPs) were genotyped using various methods including Illumina Infinium and GoldenGate assays and 31,954 markers with minor allele frequency >0.10 were used to estimate linkage disequilibrium (LD) in heterochromatic and euchromatic regions. In euchromatic regions, the mean LD (r 2 ) rapidly declined to 0.2 within 360 Kbp, whereas the mean LD declined to 0.2 at 9,600 Kbp in heterochromatic regions. The GWAS results identified 40 SNPs in 17 different genomic regions significantly associated with seed protein. Of these, the five SNPs with the highest associations and seven adjacent SNPs were located in the 27.6-30.0 Mbp region of Gm20. A major seed protein QTL has been previously mapped to the same location and potential candidate genes have recently been identified in this region. The GWAS results also detected 25 SNPs in 13 different genomic regions associated with seed oil. Of these markers, seven SNPs had a significant association with both protein and oil. Conclusions This research indicated that GWAS not only identified most of the previously reported QTL controlling seed protein and oil, but also resulted in narrower genomic regions than the regions reported as containing these QTL. The narrower GWAS-defined genome regions will allow more precise marker-assisted allele selection and will expedite positional cloning of the causal gene(s). PMID:24382143

A genome-wide association study of seed protein and oil content in soybean.

PubMed

Hwang, Eun-Young; Song, Qijian; Jia, Gaofeng; Specht, James E; Hyten, David L; Costa, Jose; Cregan, Perry B

2014-01-02

Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. In this study, a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTL) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of seed protein and oil content. A total of 55,159 single nucleotide polymorphisms (SNPs) were genotyped using various methods including Illumina Infinium and GoldenGate assays and 31,954 markers with minor allele frequency >0.10 were used to estimate linkage disequilibrium (LD) in heterochromatic and euchromatic regions. In euchromatic regions, the mean LD (r2) rapidly declined to 0.2 within 360 Kbp, whereas the mean LD declined to 0.2 at 9,600 Kbp in heterochromatic regions. The GWAS results identified 40 SNPs in 17 different genomic regions significantly associated with seed protein. Of these, the five SNPs with the highest associations and seven adjacent SNPs were located in the 27.6-30.0 Mbp region of Gm20. A major seed protein QTL has been previously mapped to the same location and potential candidate genes have recently been identified in this region. The GWAS results also detected 25 SNPs in 13 different genomic regions associated with seed oil. Of these markers, seven SNPs had a significant association with both protein and oil. This research indicated that GWAS not only identified most of the previously reported QTL controlling seed protein and oil, but also resulted in narrower genomic regions than the regions reported as containing these QTL. The narrower GWAS-defined genome regions will allow more precise marker-assisted allele selection and will expedite positional cloning of the causal gene(s).

Forest Connectivity Regions of Canada Using Circuit Theory and Image Analysis

PubMed Central

Pelletier, David; Lapointe, Marc-Élie; Wulder, Michael A.; White, Joanne C.; Cardille, Jeffrey A.

2017-01-01

Ecological processes are increasingly well understood over smaller areas, yet information regarding interconnections and the hierarchical nature of ecosystems remains less studied and understood. Information on connectivity over large areas with high resolution source information provides for both local detail and regional context. The emerging capacity to apply circuit theory to create maps of omnidirectional connectivity provides an opportunity for improved and quantitative depictions of forest connectivity, supporting the formation and testing of hypotheses about the density of animal movement, ecosystem structure, and related links to natural and anthropogenic forces. In this research, our goal was to delineate regions where connectivity regimes are similar across the boreal region of Canada using new quantitative analyses for characterizing connectivity over large areas (e.g., millions of hectares). Utilizing the Earth Observation for Sustainable Development of forests (EOSD) circa 2000 Landsat-derived land-cover map, we created and analyzed a national-scale map of omnidirectional forest connectivity at 25m resolution over 10000 tiles of 625 km2 each, spanning the forested regions of Canada. Using image recognition software to detect corridors, pinch points, and barriers to movements at multiple spatial scales in each tile, we developed a simple measure of the structural complexity of connectivity patterns in omnidirectional connectivity maps. We then mapped the Circuitscape resistance distance measure and used it in conjunction with the complexity data to study connectivity characteristics in each forested ecozone. Ecozone boundaries masked substantial systematic patterns in connectivity characteristics that are uncovered using a new classification of connectivity patterns that revealed six clear groups of forest connectivity patterns found in Canada. The resulting maps allow exploration of omnidirectional forest connectivity patterns at full resolution while permitting quantitative analyses of connectivity over broad areas, informing modeling, planning and monitoring efforts. PMID:28146573

A synchrotron-based local computed tomography combined with data-constrained modelling approach for quantitative analysis of anthracite coal microstructure

PubMed Central

Chen, Wen Hao; Yang, Sam Y. S.; Xiao, Ti Qiao; Mayo, Sherry C.; Wang, Yu Dan; Wang, Hai Peng

2014-01-01

Quantifying three-dimensional spatial distributions of pores and material compositions in samples is a key materials characterization challenge, particularly in samples where compositions are distributed across a range of length scales, and where such compositions have similar X-ray absorption properties, such as in coal. Consequently, obtaining detailed information within sub-regions of a multi-length-scale sample by conventional approaches may not provide the resolution and level of detail one might desire. Herein, an approach for quantitative high-definition determination of material compositions from X-ray local computed tomography combined with a data-constrained modelling method is proposed. The approach is capable of dramatically improving the spatial resolution and enabling finer details within a region of interest of a sample larger than the field of view to be revealed than by using conventional techniques. A coal sample containing distributions of porosity and several mineral compositions is employed to demonstrate the approach. The optimal experimental parameters are pre-analyzed. The quantitative results demonstrated that the approach can reveal significantly finer details of compositional distributions in the sample region of interest. The elevated spatial resolution is crucial for coal-bed methane reservoir evaluation and understanding the transformation of the minerals during coal processing. The method is generic and can be applied for three-dimensional compositional characterization of other materials. PMID:24763649

Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

NASA Astrophysics Data System (ADS)

Cao, Binghua; Fan, Mengbao

2010-10-01

Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

Genome-wide QTL analysis for anxiety trait in bipolar disorder type I.

PubMed

Contreras, J; Hare, E; Chavarría-Soley, G; Raventós, H

2018-07-01

Genetic studies have been consistent that bipolar disorder type I (BPI) runs in families and that this familial aggregation is strongly influenced by genes. In a preliminary study, we proved that anxiety trait meets endophenotype criteria for BPI. We assessed 619 individuals from the Central Valley of Costa Rica (CVCR) who have received evaluation for anxiety following the same methodological procedure used for the initial pilot study. Our goal was to conduct a multipoint quantitative trait linkage analysis to identify quantitative trait loci (QTLs) related to anxiety trait in subjects with BPI. We conducted the statistical analyses using Quantitative Trait Loci method (Variance-components models), implemented in Sequential Oligogenic Linkage Analysis Routines (SOLAR), using 5606 single nucleotide polymorphism (SNPs). We identified a suggestive linkage signal with a LOD score of 2.01 at chromosome 2 (2q13-q14). Since confounding factors such as substance abuse, medical illness and medication history were not assessed in our study, these conclusions should be taken as preliminary. We conclude that region 2q13-q14 may harbor a candidate gene(s) with an important role in the pathophysiology of BPI and anxiety. Published by Elsevier B.V.

Prediction of Coronal Mass Ejections from Vector Magnetograms: Quantitative Measures as Predictors

NASA Astrophysics Data System (ADS)

Falconer, D. A.; Moore, R. L.; Gary, G. A.

2001-05-01

In a pilot study of 4 active regions (Falconer, D.A. 2001, JGR, in press), we derived two quantitative measures of an active region's global nonpotentiality from the region's vector magnetogram, 1) the net current (IN), and 2) the length of the strong-shear, strong-field main neutral line (LSS), and used these two measures of the CME productivity of the active regions. We compared the global nonpotentiality measures to the active regions' CME productivity determined from GOES and Yohkoh/SXT observations. We found that two of the active regions were highly globally nonpotential and were CME productive, while the other two active regions had little global nonpotentiality and produced no CMEs. At the Fall 2000 AGU (Falconer, Moore, & Gary, 2000, EOS 81, 48 F998), we reported on an expanded study (12 active regions and 17 magnetograms) in which we evaluated four quantitative global measures of an active region's magnetic field and compared these measures with the CME productivity. The four global measures (all derived from MSFC vector magnetograms) included our two previous measures (IN and LSS) as well as two new ones, the total magnetic flux (Φ ) (a measure of an active region's size), and the normalized twist (α =μ IN/Φ ). We found that the three measures of global nonpotentiality (IN, LSS, α ) were all well correlated (>99% confidence level) with an active region's CME productivity within (2 days of the day of the magnetogram. We will now report on our findings of how good our quantitative measures are as predictors of active-region CME productivity, using only CMEs that occurred after the magnetogram. We report the preliminary skill test of these quantitative measures as predictors. We compare the CME prediction success of our quantitative measures to the CME prediction success based on an active region's past CME productivity. We examine the cases of the handful of false positive and false negatives to look for improvements to our predictors. This work is funded by NSF through the Space Weather Program and by NASA through the Solar Physics Supporting Research and Technology Program.

Analytical analysis and implementation of a low-speed high-torque permanent magnet vernier in-wheel motor for electric vehicle

NASA Astrophysics Data System (ADS)

Li, Jiangui; Wang, Junhua; Zhigang, Zhao; Yan, Weili

2012-04-01

In this paper, analytical analysis of the permanent magnet vernier (PMV) is presented. The key is to analytically solve the governing Laplacian/quasi-Poissonian field equations in the motor regions. By using the time-stepping finite element method, the analytical method is verified. Hence, the performances of the PMV machine are quantitatively compared with that of the analytical results. The analytical results agree well with the finite element method results. Finally, the experimental results are given to further show the validity of the analysis.

Quantitative Trait Locus Analysis of SIX1-SIX6 with Retinal Nerve Fiber Layer Thickness in Individuals of European Descent

PubMed Central

Kuo, Jane Z.; Zangwill, Linda M.; Medeiros, Felipe A.; Liebmann, Jeffery M.; Girkin, Christopher A.; Hammel, Na’ama; Rotter, Jerome I.; Weinreb, Robert N.

2015-01-01

Purpose To perform a quantitative trait locus (QTL) analysis and evaluate whether a locus between SIX1 and SIX6 is associated with retinal nerve fiber layer (RNFL) thickness in individuals of European descent. Design Observational, multi-center, cross-sectional study. Methods 231 participants were recruited from the Diagnostic Innovations in Glaucoma Study and the African Descent and Glaucoma Evaluation Study. Association of rs10483727 in SIX1-SIX6 with global and sectoral RNFL thickness was performed. Quantitative trait analysis with the additive model of inheritance was analyzed using linear regression. Trend analysis was performed to evaluate the mean global and sectoral RNFL thickness with 3 genotypes of interest (T/T, C/T, C/C). All models were adjusted for age and gender. Results Direction of association between T allele and RNFL thickness was consistent in the global and different sectoral RNFL regions. Each copy of the T risk allele in rs10483727 was associated with −0.16 μm thinner global RNFL thickness (β=−0.16, 95% CI: −0.28 to −0.03; P=0.01). Similar patterns were found for the sectoral regions, including inferior (P=0.03), inferior-nasal (P=0.017), superior-nasal (P=0.0025), superior (P=0.002) and superior-temporal (P=0.008). The greatest differences were observed in the superior and inferior quadrants, supporting clinical observations for RNFL thinning in glaucoma. Thinner global RNFL was found in subjects with T/T genotypes compared to subjects with C/T and C/C genotypes (P=0.044). Conclusions Each copy of the T risk allele has an additive effect and was associated with thinner global and sectoral RNFL. Findings from this QTL analysis further support a genetic contribution to glaucoma pathophysiology. PMID:25849520

Titan Polar Landscape Evolution

NASA Technical Reports Server (NTRS)

Moore, Jeffrey M.

2016-01-01

With the ongoing Cassini-era observations and studies of Titan it is clear that the intensity and distribution of surface processes (particularly fluvial erosion by methane and Aeolian transport) has changed through time. Currently however, alternate hypotheses substantially differ among specific scenarios with respect to the effects of atmospheric evolution, seasonal changes, and endogenic processes. We have studied the evolution of Titan's polar region through a combination of analysis of imaging, elevation data, and geomorphic mapping, spatially explicit simulations of landform evolution, and quantitative comparison of the simulated landscapes with corresponding Titan morphology. We have quantitatively evaluated alternate scenarios for the landform evolution of Titan's polar terrain. The investigations have been guided by recent geomorphic mapping and topographic characterization of the polar regions that are used to frame hypotheses of process interactions, which have been evaluated using simulation modeling. Topographic information about Titan's polar region is be based on SAR-Topography and altimetry archived on PDS, SAR-based stereo radar-grammetry, radar-sounding lake depth measurements, and superposition relationships between geomorphologic map units, which we will use to create a generalized topographic map.

Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

PubMed

Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

2013-11-15

The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray matter structures measured by Hallgren and Sourander (1958) allowed interpolation of the average iron concentration of several deep gray matter regions delineated in the EvePM. Copyright © 2013 Elsevier Inc. All rights reserved.

Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures

PubMed Central

Lim, Issel Anne L.; Faria, Andreia V.; Li, Xu; Hsu, Johnny T.C.; Airan, Raag D.; Mori, Susumu; van Zijl, Peter C. M.

2013-01-01

The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a “deep gray matter parcellation map” (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established “white matter parcellation map” (WMPM) from the same subject’s T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the “Everything Parcellation Map in Eve Space,” also known as the “EvePM.” It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting “almost perfect” agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray matter structures measured by Hallgren and Sourander (1958) allowed interpolation of the average iron concentration of several deep gray matter regions delineated in the EvePM. PMID:23769915

Quantitative systematic review of the associations between short-term exposure to nitrogen dioxide and mortality and hospital admissions.

PubMed

Mills, I C; Atkinson, R W; Kang, S; Walton, H; Anderson, H R

2015-05-11

Short-term exposure to NO₂ has been associated with adverse health effects and there is increasing concern that NO₂ is causally related to health effects, not merely a marker of traffic-generated pollution. No comprehensive meta-analysis of the time-series evidence on NO₂ has been published since 2007. To quantitatively assess the evidence from epidemiological time-series studies published worldwide to determine whether and to what extent short-term exposure to NO₂ is associated with increased numbers of daily deaths and hospital admissions. We conducted a quantitative systematic review of 204 time-series studies of NO₂ and daily mortality and hospital admissions for several diagnoses and ages, which were indexed in three bibliographic databases up to May 2011. We calculated random-effects estimates by different geographic regions and globally, and also tested for heterogeneity and small study bias. Sufficient estimates for meta-analysis were available for 43 cause-specific and age-specific combinations of mortality or hospital admissions (25 for 24 h NO₂ and 18 of the same combinations for 1 h measures). For the all-age group, a 10 µg/m(3) increase in 24 h NO₂ was associated with increases in all-cause, cardiovascular and respiratory mortality (0.71% (95% CI 0.43% to 1.00%), 0.88% (0.63% to 1.13%) and 1.09% (0.75% to 1.42%), respectively), and with hospital admissions for respiratory (0.57% (0.33% to 0.82%)) and cardiovascular (0.66% (0.32% to 1.01%)) diseases. Evidence of heterogeneity between geographical region-specific estimates was identified in more than half of the combinations analysed. Our review provides clear evidence of health effects associated with short-term exposure to NO₂ although further work is required to understand reasons for the regional heterogeneity observed. The growing literature, incorporating large multicentre studies and new evidence from less well-studied regions of the world, supports further quantitative review to assess the independence of NO₂ health effects from other air pollutants. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Quantitative estimation of time-variable earthquake hazard by using fuzzy set theory

NASA Astrophysics Data System (ADS)

Deyi, Feng; Ichikawa, M.

1989-11-01

In this paper, the various methods of fuzzy set theory, called fuzzy mathematics, have been applied to the quantitative estimation of the time-variable earthquake hazard. The results obtained consist of the following. (1) Quantitative estimation of the earthquake hazard on the basis of seismicity data. By using some methods of fuzzy mathematics, seismicity patterns before large earthquakes can be studied more clearly and more quantitatively, highly active periods in a given region and quiet periods of seismic activity before large earthquakes can be recognized, similarities in temporal variation of seismic activity and seismic gaps can be examined and, on the other hand, the time-variable earthquake hazard can be assessed directly on the basis of a series of statistical indices of seismicity. Two methods of fuzzy clustering analysis, the method of fuzzy similarity, and the direct method of fuzzy pattern recognition, have been studied is particular. One method of fuzzy clustering analysis is based on fuzzy netting, and another is based on the fuzzy equivalent relation. (2) Quantitative estimation of the earthquake hazard on the basis of observational data for different precursors. The direct method of fuzzy pattern recognition has been applied to research on earthquake precursors of different kinds. On the basis of the temporal and spatial characteristics of recognized precursors, earthquake hazards in different terms can be estimated. This paper mainly deals with medium-short-term precursors observed in Japan and China.

Characterization of potassium dichromate solutions for spectrophotometercalibration

NASA Astrophysics Data System (ADS)

Conceição, F. C.; Silva, E. M.; Gomes, J. F. S.; Borges, P. P.

2018-03-01

Spectrophotometric analysis in the ultraviolet (UV) region is used in the determination of several quantitative and qualitative parameters. For ensuring reliability of the analyses performed on the spectrophotometers, verification / calibration of the equipment must be performed periodically using certified reference materials (CRMs). This work presents the characterization stage needed for producing this CRM. The property value characterized was the absorbance for the wavelengths in the UV spectral regions. This CRM will contribute to guarantee the accuracy and linearity of the absorbance scale to the spectrophotometers, through which analytical measurement results will be provided with metrological traceability.

Bioimpedance Harmonic Analysis as a Diagnostic Tool to Assess Regional Circulation and Neural Activity

NASA Astrophysics Data System (ADS)

Mudraya, I. S.; Revenko, S. V.; Khodyreva, L. A.; Markosyan, T. G.; Dudareva, A. A.; Ibragimov, A. R.; Romich, V. V.; Kirpatovsky, V. I.

2013-04-01

The novel technique based on harmonic analysis of bioimpedance microvariations with original hard- and software complex incorporating a high-resolution impedance converter was used to assess the neural activity and circulation in human urinary bladder and penis in patients with pelvic pain, erectile dysfunction, and overactive bladder. The therapeutic effects of shock wave therapy and Botulinum toxin detrusor injections were evaluated quantitatively according to the spectral peaks at low 0.1 Hz frequency (M for Mayer wave), respiratory (R) and cardiac (C) rhythms with their harmonics. Enhanced baseline regional neural activity identified according to M and R peaks was found to be presumably sympathetic in pelvic pain patients, and parasympathetic - in patients with overactive bladder. Total pulsatile activity and pulsatile resonances found in the bladder as well as in the penile spectrum characterised regional circulation and vascular tone. The abnormal spectral parameters characteristic of the patients with genitourinary diseases shifted to the norm in the cases of efficient therapy. Bioimpedance harmonic analysis seems to be a potent tool to assess regional peculiarities of circulatory and autonomic nervous activity in the course of patient treatment.

Candidate Loci for Yield-Related Traits in Maize Revealed by a Combination of MetaQTL Analysis and Regional Association Mapping

PubMed Central

Chen, Lin; An, Yixin; Li, Yong-xiang; Li, Chunhui; Shi, Yunsu; Song, Yanchun; Zhang, Dengfeng; Wang, Tianyu; Li, Yu

2017-01-01

Maize grain yield and related traits are complex and are controlled by a large number of genes of small effect or quantitative trait loci (QTL). Over the years, a large number of yield-related QTLs have been identified in maize and deposited in public databases. However, integrating and re-analyzing these data and mining candidate loci for yield-related traits has become a major issue in maize. In this study, we collected information on QTLs conferring maize yield-related traits from 33 published studies. Then, 999 of these QTLs were iteratively projected and subjected to meta-analysis to obtain metaQTLs (MQTLs). A total of 76 MQTLs were found across the maize genome. Based on a comparative genomics strategy, several maize orthologs of rice yield-related genes were identified in these MQTL regions. Furthermore, three potential candidate genes (Gene ID: GRMZM2G359974, GRMZM2G301884, and GRMZM2G083894) associated with kernel size and weight within three MQTL regions were identified using regional association mapping, based on the results of the meta-analysis. This strategy, combining MQTL analysis and regional association mapping, is helpful for functional marker development and rapid identification of candidate genes or loci. PMID:29312420

Genetic, physiological and comparative genomic studies of hypertension and insulin resistance in the spontaneously hypertensive rat.

PubMed

Coan, Philip M; Hummel, Oliver; Garcia Diaz, Ana; Barrier, Marjorie; Alfazema, Neza; Norsworthy, Penny J; Pravenec, Michal; Petretto, Enrico; Hübner, Norbert; Aitman, Timothy J

2017-03-01

We previously mapped hypertension-related insulin resistance quantitative trait loci (QTLs) to rat chromosomes 4, 12 and 16 using adipocytes from F2 crosses between spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats, and subsequently identified Cd36 as the gene underlying the chromosome 4 locus. The identity of the chromosome 12 and 16 genes remains unknown. To identify whole-body phenotypes associated with the chromosome 12 and 16 linkage regions, we generated and characterised new congenic strains, with WKY donor segments introgressed onto an SHR genetic background, for the chromosome 12 and 16 linkage regions. We found a >50% increase in insulin sensitivity in both the chromosome 12 and 16 strains. Blood pressure and left ventricular mass were reduced in the two congenic strains consistent with the congenic segments harbouring SHR genes for insulin resistance, hypertension and cardiac hypertrophy. Integrated genomic analysis, using physiological and whole-genome sequence data across 42 rat strains, identified variants within the congenic regions in Upk3bl , RGD1565131 and AABR06087018.1 that were associated with blood pressure, cardiac mass and insulin sensitivity. Quantitative trait transcript analysis across 29 recombinant inbred strains showed correlation between expression of Hspb1 , Zkscan5 and Pdgfrl with adipocyte volume, systolic blood pressure and cardiac mass, respectively. Comparative genome analysis showed a marked enrichment of orthologues for human GWAS-associated genes for insulin resistance within the syntenic regions of both the chromosome 12 and 16 congenic intervals. Our study defines whole-body phenotypes associated with the SHR chromosome 12 and 16 insulin-resistance QTLs, identifies candidate genes for these SHR QTLs and finds human orthologues of rat genes in these regions that associate with related human traits. Further study of these genes in the congenic strains will lead to robust identification of the underlying genes and cellular mechanisms. © 2017. Published by The Company of Biologists Ltd.

Genetic, physiological and comparative genomic studies of hypertension and insulin resistance in the spontaneously hypertensive rat

PubMed Central

Hummel, Oliver; Garcia Diaz, Ana; Barrier, Marjorie; Alfazema, Neza; Norsworthy, Penny J.; Pravenec, Michal; Petretto, Enrico; Hübner, Norbert

2017-01-01

ABSTRACT We previously mapped hypertension-related insulin resistance quantitative trait loci (QTLs) to rat chromosomes 4, 12 and 16 using adipocytes from F2 crosses between spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats, and subsequently identified Cd36 as the gene underlying the chromosome 4 locus. The identity of the chromosome 12 and 16 genes remains unknown. To identify whole-body phenotypes associated with the chromosome 12 and 16 linkage regions, we generated and characterised new congenic strains, with WKY donor segments introgressed onto an SHR genetic background, for the chromosome 12 and 16 linkage regions. We found a >50% increase in insulin sensitivity in both the chromosome 12 and 16 strains. Blood pressure and left ventricular mass were reduced in the two congenic strains consistent with the congenic segments harbouring SHR genes for insulin resistance, hypertension and cardiac hypertrophy. Integrated genomic analysis, using physiological and whole-genome sequence data across 42 rat strains, identified variants within the congenic regions in Upk3bl, RGD1565131 and AABR06087018.1 that were associated with blood pressure, cardiac mass and insulin sensitivity. Quantitative trait transcript analysis across 29 recombinant inbred strains showed correlation between expression of Hspb1, Zkscan5 and Pdgfrl with adipocyte volume, systolic blood pressure and cardiac mass, respectively. Comparative genome analysis showed a marked enrichment of orthologues for human GWAS-associated genes for insulin resistance within the syntenic regions of both the chromosome 12 and 16 congenic intervals. Our study defines whole-body phenotypes associated with the SHR chromosome 12 and 16 insulin-resistance QTLs, identifies candidate genes for these SHR QTLs and finds human orthologues of rat genes in these regions that associate with related human traits. Further study of these genes in the congenic strains will lead to robust identification of the underlying genes and cellular mechanisms. PMID:28130354

Application of high-frequency Granger causality to analysis of epileptic seizures and surgical decision making.

PubMed

Epstein, Charles M; Adhikari, Bhim M; Gross, Robert; Willie, Jon; Dhamala, Mukesh

2014-12-01

In recent decades intracranial EEG (iEEG) recordings using increasing numbers of electrodes, higher sampling rates, and a variety of visual and quantitative analyses have indicated the presence of widespread, high frequency ictal and preictal oscillations (HFOs) associated with regions of seizure onset. Seizure freedom has been correlated with removal of brain regions generating pathologic HFOs. However, quantitative analysis of preictal HFOs has seldom been applied to the clinical problem of planning the surgical resection. We performed Granger causality (GC) analysis of iEEG recordings to analyze features of preictal seizure networks and to aid in surgical decision making. Ten retrospective and two prospective patients were chosen on the basis of individually stereotyped seizure patterns by visual criteria. Prospective patients were selected, additionally, for failure of those criteria to resolve apparent multilobar ictal onsets. iEEG was recorded at 500 or 1,000 Hz, using up to 128 surface and depth electrodes. Preictal and early ictal GC from individual electrodes was characterized by the strength of causal outflow, spatial distribution, and hierarchical causal relationships. In all patients we found significant, widespread preictal GC network activity at peak frequencies from 80 to 250 Hz, beginning 2-42 s before visible electrographic onset. In the two prospective patients, GC source/sink comparisons supported the exclusion of early ictal regions that were not the dominant causal sources, and contributed to planning of more limited surgical resections. Both patients have a class 1 outcome at 1 year. GC analysis of iEEG has the potential to increase understanding of preictal network activity, and to help improve surgical outcomes in cases of otherwise ambiguous iEEG onset. Wiley Periodicals, Inc. © 2014 International League Against Epilepsy.

Motion compensation using origin ensembles in awake small animal positron emission tomography

NASA Astrophysics Data System (ADS)

Gillam, John E.; Angelis, Georgios I.; Kyme, Andre Z.; Meikle, Steven R.

2017-02-01

In emission tomographic imaging, the stochastic origin ensembles algorithm provides unique information regarding the detected counts given the measured data. Precision in both voxel and region-wise parameters may be determined for a single data set based on the posterior distribution of the count density allowing uncertainty estimates to be allocated to quantitative measures. Uncertainty estimates are of particular importance in awake animal neurological and behavioral studies for which head motion, unique for each acquired data set, perturbs the measured data. Motion compensation can be conducted when rigid head pose is measured during the scan. However, errors in pose measurements used for compensation can degrade the data and hence quantitative outcomes. In this investigation motion compensation and detector resolution models were incorporated into the basic origin ensembles algorithm and an efficient approach to computation was developed. The approach was validated against maximum liklihood—expectation maximisation and tested using simulated data. The resultant algorithm was then used to analyse quantitative uncertainty in regional activity estimates arising from changes in pose measurement precision. Finally, the posterior covariance acquired from a single data set was used to describe correlations between regions of interest providing information about pose measurement precision that may be useful in system analysis and design. The investigation demonstrates the use of origin ensembles as a powerful framework for evaluating statistical uncertainty of voxel and regional estimates. While in this investigation rigid motion was considered in the context of awake animal PET, the extension to arbitrary motion may provide clinical utility where respiratory or cardiac motion perturb the measured data.

Multi-scale Quantitative Precipitation Forecasting Using ...

EPA Pesticide Factsheets

Global sea surface temperature (SST) anomalies can affect terrestrial precipitation via ocean-atmosphere interaction known as climate teleconnection. Non-stationary and non-linear characteristics of the ocean-atmosphere system make the identification of the teleconnection signals difficult to be detected at a local scale as it could cause large uncertainties when using linear correlation analysis only. This paper explores the relationship between global SST and terrestrial precipitation with respect to long-term non-stationary teleconnection signals during 1981-2010 over three regions in North America and one in Central America. Empirical mode decomposition as well as wavelet analysis is utilized to extract the intrinsic trend and the dominant oscillation of the SST and precipitation time series in sequence. After finding possible associations between the dominant oscillation of seasonal precipitation and global SST through lagged correlation analysis, the statistically significant SST regions are extracted based on the correlation coefficient. With these characterized associations, individual contribution of these SST forcing regions linked to the related precipitation responses are further quantified through nonlinear modeling with the aid of extreme learning machine. Results indicate that the non-leading SST regions also contribute a salient portion to the terrestrial precipitation variability compared to some known leading SST regions. In some cases, these

Simulation of realistic abnormal SPECT brain perfusion images: application in semi-quantitative analysis

NASA Astrophysics Data System (ADS)

Ward, T.; Fleming, J. S.; Hoffmann, S. M. A.; Kemp, P. M.

2005-11-01

Simulation is useful in the validation of functional image analysis methods, particularly when considering the number of analysis techniques currently available lacking thorough validation. Problems exist with current simulation methods due to long run times or unrealistic results making it problematic to generate complete datasets. A method is presented for simulating known abnormalities within normal brain SPECT images using a measured point spread function (PSF), and incorporating a stereotactic atlas of the brain for anatomical positioning. This allows for the simulation of realistic images through the use of prior information regarding disease progression. SPECT images of cerebral perfusion have been generated consisting of a control database and a group of simulated abnormal subjects that are to be used in a UK audit of analysis methods. The abnormality is defined in the stereotactic space, then transformed to the individual subject space, convolved with a measured PSF and removed from the normal subject image. The dataset was analysed using SPM99 (Wellcome Department of Imaging Neuroscience, University College, London) and the MarsBaR volume of interest (VOI) analysis toolbox. The results were evaluated by comparison with the known ground truth. The analysis showed improvement when using a smoothing kernel equal to system resolution over the slightly larger kernel used routinely. Significant correlation was found between effective volume of a simulated abnormality and the detected size using SPM99. Improvements in VOI analysis sensitivity were found when using the region median over the region mean. The method and dataset provide an efficient methodology for use in the comparison and cross validation of semi-quantitative analysis methods in brain SPECT, and allow the optimization of analysis parameters.

Four Linked Genes Participate in Controlling Sporulation Efficiency in Budding Yeast

PubMed Central

Ben-Ari, Giora; Zenvirth, Drora; Sherman, Amir; David, Lior; Klutstein, Michael; Lavi, Uri; Hillel, Jossi; Simchen, Giora

2006-01-01

Quantitative traits are conditioned by several genetic determinants. Since such genes influence many important complex traits in various organisms, the identification of quantitative trait loci (QTLs) is of major interest, but still encounters serious difficulties. We detected four linked genes within one QTL, which participate in controlling sporulation efficiency in Saccharomyces cerevisiae. Following the identification of single nucleotide polymorphisms by comparing the sequences of 145 genes between the parental strains SK1 and S288c, we analyzed the segregating progeny of the cross between them. Through reciprocal hemizygosity analysis, four genes, RAS2, PMS1, SWS2, and FKH2, located in a region of 60 kilobases on Chromosome 14, were found to be associated with sporulation efficiency. Three of the four “high” sporulation alleles are derived from the “low” sporulating strain. Two of these sporulation-related genes were verified through allele replacements. For RAS2, the causative variation was suggested to be a single nucleotide difference in the upstream region of the gene. This quantitative trait nucleotide accounts for sporulation variability among a set of ten closely related winery yeast strains. Our results provide a detailed view of genetic complexity in one “QTL region” that controls a quantitative trait and reports a single nucleotide polymorphism-trait association in wild strains. Moreover, these findings have implications on QTL identification in higher eukaryotes. PMID:17112318

Quantitative 3D breast magnetic resonance imaging fibroglandular tissue analysis and correlation with qualitative assessments: a feasibility study.

PubMed

Ha, Richard; Mema, Eralda; Guo, Xiaotao; Mango, Victoria; Desperito, Elise; Ha, Jason; Wynn, Ralph; Zhao, Binsheng

2016-04-01

The amount of fibroglandular tissue (FGT) has been linked to breast cancer risk based on mammographic density studies. Currently, the qualitative assessment of FGT on mammogram (MG) and magnetic resonance imaging (MRI) is prone to intra and inter-observer variability. The purpose of this study is to develop an objective quantitative FGT measurement tool for breast MRI that could provide significant clinical value. An IRB approved study was performed. Sixty breast MRI cases with qualitative assessment of mammographic breast density and MRI FGT were randomly selected for quantitative analysis from routine breast MRIs performed at our institution from 1/2013 to 12/2014. Blinded to the qualitative data, whole breast and FGT contours were delineated on T1-weighted pre contrast sagittal images using an in-house, proprietary segmentation algorithm which combines the region-based active contours and a level set approach. FGT (%) was calculated by: [segmented volume of FGT (mm(3))/(segmented volume of whole breast (mm(3))] ×100. Statistical correlation analysis was performed between quantified FGT (%) on MRI and qualitative assessments of mammographic breast density and MRI FGT. There was a significant positive correlation between quantitative MRI FGT assessment and qualitative MRI FGT (r=0.809, n=60, P<0.001) and mammographic density assessment (r=0.805, n=60, P<0.001). There was a significant correlation between qualitative MRI FGT assessment and mammographic density assessment (r=0.725, n=60, P<0.001). The four qualitative assessment categories of FGT correlated with the calculated mean quantitative FGT (%) of 4.61% (95% CI, 0-12.3%), 8.74% (7.3-10.2%), 18.1% (15.1-21.1%), 37.4% (29.5-45.3%). Quantitative measures of FGT (%) were computed with data derived from breast MRI and correlated significantly with conventional qualitative assessments. This quantitative technique may prove to be a valuable tool in clinical use by providing computer generated standardized measurements with limited intra or inter-observer variability.

Qualitative and quantitative assessment of collagen and elastin in annulus fibrosus of the physiologic and scoliotic intervertebral discs.

PubMed

Kobielarz, Magdalena; Szotek, Sylwia; Głowacki, Maciej; Dawidowicz, Joanna; Pezowicz, Celina

2016-09-01

The biophysical properties of the annulus fibrosus of the intervertebral disc are determined by collagen and elastin fibres. The progression of scoliosis is accompanied by a number of pathological changes concerning these structural proteins. This is a major cause of dysfunction of the intervertebral disc. The object of the study were annulus fibrosus samples excised from intervertebral discs of healthy subjects and patients treated surgically for scoliosis in the thoracolumbar or lumbar spine. The research material was subjected to structural analysis by light microscopy and quantitative analysis of the content of collagen types I, II, III and IV as well as elastin by immunoenzymatic test (ELISA). A statistical analysis was conducted to assess the impact of the sampling site (Mann-Whitney test, α=0.05) and scoliosis (Wilcoxon matched pairs test, α=0.05) on the obtained results. The microscopic studies conducted on scoliotic annulus fibrosus showed a significant architectural distortion of collagen and elastin fibres. Quantitative biochemical assays demonstrated region-dependent distribution of only collagen types I and II in the case of healthy intervertebral discs whereas in the case of scoliotic discs region-dependent distribution concerned all examined proteins of the extracellular matrix. Comparison of scoliotic and healthy annulus fibrosus revealed a significant decrease in the content of collagen type I and elastin as well as a slight increase in the proportion of collagen types III and IV. The content of collagen type II did not differ significantly between both groups. The observed anomalies are a manifestation of degenerative changes affecting annulus fibrosus of the intervertebral disc in patients suffering from scoliosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of Region of Interest Drawing for Quantitative Analysis: Differentiation Between Benign and Malignant Breast Lesions on Contrast-Enhanced Sonography.

PubMed

Nakata, Norio; Ohta, Tomoyuki; Nishioka, Makiko; Takeyama, Hiroshi; Toriumi, Yasuo; Kato, Kumiko; Nogi, Hiroko; Kamio, Makiko; Fukuda, Kunihiko

2015-11-01

This study was performed to evaluate the diagnostic utility of quantitative analysis of benign and malignant breast lesions using contrast-enhanced sonography. Contrast-enhanced sonography using the perflubutane-based contrast agent Sonazoid (Daiichi Sankyo, Tokyo, Japan) was performed in 94 pathologically proven palpable breast mass lesions, which could be depicted with B-mode sonography. Quantitative analyses using the time-intensity curve on contrast-enhanced sonography were performed in 5 region of interest (ROI) types (manually traced ROI and circular ROIs of 5, 10, 15, and 20 mm in diameter). The peak signal intensity, initial slope, time to peak, positive enhancement integral, and wash-out ratio were investigated in each ROI. There were significant differences between benign and malignant lesions in the time to peak (P < .05), initial slope (P < .001), and positive enhancement integral (P < .05) for the manual ROI. Significant differences were found between benign and malignant lesions in the time to peak (P < .05) for the 5-mm ROI; the time to peak (P < .05) and initial slope (P< .05) for the 10-mm ROI; absolute values of the peak signal intensity (P< .05), time to peak (P< .01), and initial slope (P< .005) for the 15-mm ROI; and the time to peak (P < .05) and initial slope (P < .05) for the 20-mm ROI. There were no statistically significant differences in any wash-out ratio values for the 5 ROI types. Kinetic analysis using contrast-enhanced sonography is useful for differentiation between benign and malignant breast lesions. © 2015 by the American Institute of Ultrasound in Medicine.

A new HPLC-DAD-MS/MS method for the simultaneous determination of major compounds in the crude extract of Lychnophora salicifolia Mart. (Brazilian arnicão) leaves: application to chemical variability evaluation.

PubMed

Gouvea, Dayana Rubio; Meloni, Fernando; Ribeiro, Arthur de Barros Bello; Lopes, João Luis Callegari; Lopes, Norberto Peporine

2012-10-20

Lychnophora salicifolia Mart., which occurs in the Brazilian Cerrado in the states of Bahia and Minas Gerais as well as in the southeast of the state of Goiás, is the most widely distributed and also the most polymorphic species of the genus. This plant is popularly known to have anti-inflammatory and analgesic activities. In this work, we have studied the variation in terms of polar metabolites of ninety-three Lychnophora salicifolia Mart. specimens collected from different regions of the Brazilian Cerrado. Identification of the constituents of this mixture was carried out by analysis of the UV spectra and MS data after chromatographic separation. Twenty substances were identified, including chlorogenic acid derivatives, a flavonoid C-glucoside, and other sesquiterpenes. The analytical method was validated, and the reliability and credibility of the results was ensured for the purposes of this study. The concentration range required for analysis of content variability within the analyzed group of specimens was covered with appropriate values of limits of detection and quantitation, as well as satisfactory precision and recovery. A quantitative variability was observed among specimens collected from the same location, but on average they were similar from a chemical viewpoint. In relation to the study involving specimens from different locations, there were both qualitative and quantitative differences among plants collected from different regions of Brazil. Statistical analysis revealed that there is a correlation between geographical localization and polar metabolites profile for specimens collected from different locations. This is evidence that the pattern of metabolites concentration depends on the geographical distribution of the specimens. Copyright © 2012 Elsevier B.V. All rights reserved.

A multi-element screening method to identify metal targets for blood biomonitoring in green sea turtles (Chelonia mydas).

PubMed

Villa, C A; Finlayson, S; Limpus, C; Gaus, C

2015-04-15

Biomonitoring of blood is commonly used to identify and quantify occupational or environmental exposure to chemical contaminants. Increasingly, this technique has been applied to wildlife contaminant monitoring, including for green turtles, allowing for the non-lethal evaluation of chemical exposure in their nearshore environment. The sources, composition, bioavailability and toxicity of metals in the marine environment are, however, often unknown and influenced by numerous biotic and abiotic factors. These factors can vary considerably across time and space making the selection of the most informative elements for biomonitoring challenging. This study aimed to validate an ICP-MS multi-element screening method for green turtle blood in order to identify and facilitate prioritisation of target metals for subsequent fully quantitative analysis. Multi-element screening provided semiquantitative results for 70 elements, 28 of which were also determined through fully quantitative analysis. Of the 28 comparable elements, 23 of the semiquantitative results had an accuracy between 67% and 112% relative to the fully quantified values. In lieu of any available turtle certified reference materials (CRMs), we evaluated the use of human blood CRMs as a matrix surrogate for quality control, and compared two commonly used sample preparation methods for matrix related effects. The results demonstrate that human blood provides an appropriate matrix for use as a quality control material in the fully quantitative analysis of metals in turtle blood. An example for the application of this screening method is provided by comparing screening results from blood of green turtles foraging in an urban and rural region in Queensland, Australia. Potential targets for future metal biomonitoring in these regions were identified by this approach. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative EEG After Brain Stimulation and Cognitive Training in Alzheimer Disease.

PubMed

Gandelman-Marton, Revital; Aichenbaum, Sergio; Dobronevsky, Evgenya; Khaigrekht, Michael; Rabey, Jose M

2017-01-01

Medications are the currently accepted symptomatic treatment of Alzheimer disease (AD), but their impact on delaying the progression of cognitive deficits and functional impairment is limited. The authors aimed to explore long-term electrophysiological effects of repetitive transcranial magnetic stimulation interlaced with cognitive training on quantitative electroencephalography (EEG) in patients with AD. Quantitative EEG was assessed on non-repetitive transcranial magnetic stimulation interlaced with cognitive training treatment days before treatment and after each treatment phase in seven patients with mild AD. After 4.5 months (54 sessions) of treatment, a significant increase of delta activity over the temporal region was found compared with pretreatment values. Nonsignificant increases of the log EEG power were found for alpha band over the frontal and temporal regions, beta band over the frontal region, theta band over the frontal, temporal, and parieto-occipital regions, and delta band over the frontal and parieto-occipital regions. Nonsignificant decreases were found for alpha over the parieto-occipital region, and for beta over the temporal and parieto-occipital regions. A positive correlation was found between log alpha power over the frontal and temporal regions at 6 weeks and Mini-Mental State Examination (MMSE) scores at 6 weeks and 4.5 months, and between log alpha power over the parieto-occipital regions and MMSE scores at 6 weeks. A negative correlation was found between log alpha power over the frontal and temporal regions at 6 weeks and baseline Alzheimer's Disease Assessment Scale-cognitive subscale scores. Repetitive transcranial magnetic stimulation interlaced with cognitive training has long-term effects on quantitative EEG in patients with mild AD. Further research on the quantitative EEG long-term effects of transcranial magnetic stimulation interlaced with cognitive training is required to confirm the authors' data.

Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity.

PubMed

Ochiai, K; Uemura, S; Shimizu, A; Okumoto, Y; Matoh, T

2008-06-01

Boron toxicity tolerance of rice plants was studied. Modern japonica subspecies such as Koshihikari, Nipponbare, and Sasanishiki were tolerant, whereas indica subspecies such as Kasalath and IR36 were intolerant to excessive application of boron (B), even though their shoot B contents under B toxicity were not significantly different. Recombinant inbred lines (RILs) of japonica Nekken-1 and indica IR36 were used for quantitative trait locus (QTL) analysis to identify the gene responsible for B toxicity tolerance. A major QTL that could explain 45% of the phenotypic variation was detected in chromosome 4. The QTL was confirmed using a population derived from a recombinant inbred line which is heterogenic at the QTL region. The QTL was also confirmed in other chromosome segment substitution lines (CSSLs).

Quantitative analysis and feature recognition in 3-D microstructural data sets

NASA Astrophysics Data System (ADS)

Lewis, A. C.; Suh, C.; Stukowski, M.; Geltmacher, A. B.; Spanos, G.; Rajan, K.

2006-12-01

A three-dimensional (3-D) reconstruction of an austenitic stainless-steel microstructure was used as input for an image-based finite-element model to simulate the anisotropic elastic mechanical response of the microstructure. The quantitative data-mining and data-warehousing techniques used to correlate regions of high stress with critical microstructural features are discussed. Initial analysis of elastic stresses near grain boundaries due to mechanical loading revealed low overall correlation with their location in the microstructure. However, the use of data-mining and feature-tracking techniques to identify high-stress outliers revealed that many of these high-stress points are generated near grain boundaries and grain edges (triple junctions). These techniques also allowed for the differentiation between high stresses due to boundary conditions of the finite volume reconstructed, and those due to 3-D microstructural features.

Disruption of the Putative Vascular Leak Peptide Sequence in the Stabilized Ricin Vaccine Candidate RTA1-33/44-198

DTIC Science & Technology

2013-01-29

Time- dependence of calculated LD50. The data shown in Panel A were submitted to probit analysis to determine the LD50 of ricin at every 0.5-day...degenerate neutrophils and necrotic debris evident; (C) Only a limited region of the epithelium lining a bronchus remains viable (arrowheads); the...quantitative analysis of the dose dependent protective effects of the immunizations. All vaccine doses (2.5, 10 or 40 μg immunogen) resulted in significant

Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis.

PubMed

Neilson, Julia W; Jordan, Fiona L; Maier, Raina M

2013-03-01

PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to document and analyze artifacts associated with multiband signatures and preferential template amplification and to highlight their impacts on the use of this technique for quantitative diversity analysis. Six bacterial species (three Betaproteobacteria, two Alphaproteobacteria, and one Firmicutes) were amplified individually and in combinations with primers targeting the V7/V8 region of the 16S rRNA gene. Two of the six isolates produced multiband profiles demonstrating that band number does not correlate directly with α-diversity. Analysis of the multiple bands from one of these isolates confirmed that both bands had identical sequences which lead to the hypothesis that the multiband pattern resulted from two distinct structural conformations of the same amplicon. In addition, consistent preferential amplification was demonstrated following pairwise amplifications of the six isolates. DGGE and real time PCR analysis identified primer mismatch and PCR inhibition due to 16S rDNA secondary structure as the most probable causes of preferential amplification patterns. Reproducible DGGE community profiles generated in this study confirm that PCR-DGGE provides an excellent high-throughput tool for comparative community structure analysis, but that method-specific artifacts preclude its use for accurate comparative diversity analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

A quantitative analysis to objectively appraise drought indicators and model drought impacts

NASA Astrophysics Data System (ADS)

Bachmair, S.; Svensson, C.; Hannaford, J.; Barker, L. J.; Stahl, K.

2016-07-01

Drought monitoring and early warning is an important measure to enhance resilience towards drought. While there are numerous operational systems using different drought indicators, there is no consensus on which indicator best represents drought impact occurrence for any given sector. Furthermore, thresholds are widely applied in these indicators but, to date, little empirical evidence exists as to which indicator thresholds trigger impacts on society, the economy, and ecosystems. The main obstacle for evaluating commonly used drought indicators is a lack of information on drought impacts. Our aim was therefore to exploit text-based data from the European Drought Impact report Inventory (EDII) to identify indicators that are meaningful for region-, sector-, and season-specific impact occurrence, and to empirically determine indicator thresholds. In addition, we tested the predictability of impact occurrence based on the best-performing indicators. To achieve these aims we applied a correlation analysis and an ensemble regression tree approach, using Germany and the UK (the most data-rich countries in the EDII) as test beds. As candidate indicators we chose two meteorological indicators (Standardized Precipitation Index, SPI, and Standardized Precipitation Evaporation Index, SPEI) and two hydrological indicators (streamflow and groundwater level percentiles). The analysis revealed that accumulation periods of SPI and SPEI best linked to impact occurrence are longer for the UK compared with Germany, but there is variability within each country, among impact categories and, to some degree, seasons. The median of regression tree splitting values, which we regard as estimates of thresholds of impact occurrence, was around -1 for SPI and SPEI in the UK; distinct differences between northern/northeastern vs. southern/central regions were found for Germany. Predictions with the ensemble regression tree approach yielded reasonable results for regions with good impact data coverage. The predictions also provided insights into the EDII, in particular highlighting drought events where missing impact reports may reflect a lack of recording rather than true absence of impacts. Overall, the presented quantitative framework proved to be a useful tool for evaluating drought indicators, and to model impact occurrence. In summary, this study demonstrates the information gain for drought monitoring and early warning through impact data collection and analysis. It highlights the important role that quantitative analysis with impact data can have in providing "ground truth" for drought indicators, alongside more traditional stakeholder-led approaches.

What Kind of International School Leaders Are in Demand around the World? A Test of Differences by Region and Stability over Time

ERIC Educational Resources Information Center

Roberts, Laura; Mancuso, Steven V.

2014-01-01

This mixed-methods study of 84 job advertisements for international school leaders on six continents from 2006 to 2012 entailed both qualitative and quantitative research methods. Job advertisements were obtained from the most active recruiting agency for school leaders worldwide. Conventional and summative content analysis procedures were used to…

A gas chromatography-mass spectrometry (GC-MS) method for the detection and quantitation of monofluoroacetate in plants toxic to livestock

USDA-ARS?s Scientific Manuscript database

Monofluoroacetate (MFA) is a potent toxin that occurs in over 50 plant species in Africa, Australia, and South America and is responsible for significant livestock deaths in these regions. A gas chromatography–mass spectrometry (GC-MS) method for the analysis of MFA in plants based on the derivatiza...

A gas chromatography-mass spectrometry (GC-MS) method for the detection and quantitation of monofluoroacetate in plants toxic to livestock

USDA-ARS?s Scientific Manuscript database

Monofluoroacetate (MFA) is a potent toxin that occurs in over 50 plant species in Africa, Australia, and South America and is responsible for significant livestock deaths in these regions. A gas chromatography–mass spectrometry (GC-MS) method for the analysis of MFA in plants based on the derivatiz...

User group attitudes toward forest management treatments on the Shawnee National Forest: application of a photo-evaluation technique

Treesearch

Jonathan M. Cohen; Jean C. Mangun; Mae A. Davenport; Andrew D. Carver

2008-01-01

Diverse public opinions, competing management goals, and polarized interest groups combine with problems of scale to create a complex management arena for managers in the Central Hardwood Forest region. A mixed-methods approach that incorporated quantitative analysis of data from a photo evaluation-attitude scale survey instrument was used to assess attitudes toward...

Long-wavelength Magnetic and Gravity Anomaly Correlations of Africa and Europe

NASA Technical Reports Server (NTRS)

Vonfrese, R. R. B.; Hinze, W. J. (Principal Investigator); Olivier, R.

1984-01-01

Preliminary MAGSAT scalar magnetic anomaly data were compiled for comparison with long-wavelength-pass filtered free-air gravity anomalies and regional heat-flow and tectonic data. To facilitate the correlation analysis at satellite elevations over a spherical-Earth, equivalent point source inversion was used to differentially reduce the magnetic satellite anomalies to the radial pole at 350 km elevation, and to upward continue the first radial derivative of the free-air gravity anomalies. Correlation patterns between these regional geopotential anomaly fields are quantitatively established by moving window linear regression based on Poisson's theorem. Prominent correlations include direct correspondences for the Baltic Shield, where both anomalies are negative, and the central Mediterranean and Zaire Basin where both anomalies are positive. Inverse relationships are generally common over the Precambrian Shield in northwest Africa, the Basins and Shields in southern Africa, and the Alpine Orogenic Belt. Inverse correlations also presist over the North Sea Rifts, the Benue Rift, and more generally over the East African Rifts. The results of this quantitative correlation analysis support the general inverse relationships of gravity and magnetic anomalies observed for North American continental terrain which may be broadly related to magnetic crustal thickness variations.

Long-wavelength magnetic and gravity anomaly correlations on Africa and Europe

NASA Technical Reports Server (NTRS)

Vonfrese, R. R. B.; Olivier, R.; Hinze, W. J.

1985-01-01

Preliminary MAGSAT scalar magnetic anomaly data were compiled for comparison with long-wavelength-pass filtered free-air gravity anomalies and regional heat-flow and tectonic data. To facilitate the correlation analysis at satellite elevations over a spherical-Earth, equivalent point source inversion was used to differentially reduce the magnetic satellite anomalies to the radial pole at 350 km elevation, and to upward continue the first radial derivative of the free-air gravity anomalies. Correlation patterns between these regional geopotential anomaly fields are quantitatively established by moving window linear regression based on Poisson's theorem. Prominent correlations include direct correspondences for the Baltic shield, where both anomalies are negative, and the central Mediterranean and Zaire Basin where both anomalies are positive. Inverse relationships are generally common over the Precambrian Shield in northwest Africa, the Basins and Shields in southern Africa, and the Alpine Orogenic Belt. Inverse correlations also presist over the North Sea Rifts, the Benue Rift, and more generally over the East African Rifts. The results of this quantitative correlation analysis support the general inverse relationships of gravity and magnetic anomalies observed for North American continental terrain which may be broadly related to magnetic crustal thickness variations.

Quantitative and Qualitative Changes in V-J α Rearrangements During Mouse Thymocytes Differentiation

PubMed Central

Pasqual, Nicolas; Gallagher, Maighréad; Aude-Garcia, Catherine; Loiodice, Mélanie; Thuderoz, Florence; Demongeot, Jacques; Ceredig, Rod; Marche, Patrice Noël; Jouvin-Marche, Evelyne

2002-01-01

Knowledge of the complete nucleotide sequence of the mouse TCRAD locus allows an accurate determination V-J rearrangement status. Using multiplex genomic PCR assays and real time PCR analysis, we report a comprehensive and systematic analysis of the V-J recombination of TCR α chain in normal mouse thymocytes during development. These respective qualitative and quantitative approaches give rise to four major points describing the control of gene rearrangements. (a) The V-J recombination pattern is not random during ontogeny and generates a limited TCR α repertoire; (b) V-J rearrangement control is intrinsic to the thymus; (c) each V gene rearranges to a set of contiguous J segments with a gaussian-like frequency; (d) there are more rearrangements involving V genes at the 3′ side than 5′ end of V region. Taken together, this reflects a preferential association of V and J gene segments according to their respective positions in the locus, indicating that accessibility of both V and J regions is coordinately regulated, but in different ways. These results provide a new insight into TCR α repertoire size and suggest a scenario for V usage during differentiation. PMID:12417627

Patient-specific assessment of left ventricular thrombogenesis risk after acute myocardial infarction: a pilot clinical study

NASA Astrophysics Data System (ADS)

Rossini, L.; Khan, A.; Del Alamo, J. C.; Martinez-Legazpi, P.; Pérez Del Villar, C.; Benito, Y.; Yotti, R.; Barrio, A.; Delgado-Montero, A.; Gonzalez-Mansilla, A.; Fernandez-Avilés, F.; Bermejo, J.

2016-11-01

Left ventricular thrombosis (LVT) is a major complication of acute myocardial infarction (AMI). In these patients, the benefits of chronic anticoagulation therapy need to be balanced with its pro-hemorrhagic effects. Blood stasis in the cardiac chambers, a risk factor for LVT, is not addressed in current clinical practice. We recently developed a method to quantitatively assess the blood residence time (RT) inside the left ventricle (LV) based on 2D color-Doppler velocimetry (echo-CDV). Using time-resolved blood velocity fields acquired non-invasively, we integrate a modified advection equation to map intraventricular stasis regions. Here, we present how this tool can be used to estimate the risk of LVT in patients with AMI. 73 patients with a first anterior-AMI were studied by echo-CDV and RT analysis within 72h from admission and at a 5-month follow-up. Patients who eventually develop LVT showed early abnormalities of intraventricular RT: the apical region with RT>2s was significantly larger, had a higher RT and a longer wall contact length. Thus, quantitative analysis of intraventricular flow based on echocardiography may provide subclinical markers of LV thrombosis risk to guide clinical decision making.

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.

Quantitative EEG analysis in minimally conscious state patients during postural changes.

PubMed

Greco, A; Carboncini, M C; Virgillito, A; Lanata, A; Valenza, G; Scilingo, E P

2013-01-01

Mobilization and postural changes of patients with cognitive impairment are standard clinical practices useful for both psychic and physical rehabilitation process. During this process, several physiological signals, such as Electroen-cephalogram (EEG), Electrocardiogram (ECG), Photopletysmography (PPG), Respiration activity (RESP), Electrodermal activity (EDA), are monitored and processed. In this paper we investigated how quantitative EEG (qEEG) changes with postural modifications in minimally conscious state patients. This study is quite novel and no similar experimental data can be found in the current literature, therefore, although results are very encouraging, a quantitative analysis of the cortical area activated in such postural changes still needs to be deeply investigated. More specifically, this paper shows EEG power spectra and brain symmetry index modifications during a verticalization procedure, from 0 to 60 degrees, of three patients in Minimally Consciousness State (MCS) with focused region of impairment. Experimental results show a significant increase of the power in β band (12 - 30 Hz), commonly associated to human alertness process, thus suggesting that mobilization and postural changes can have beneficial effects in MCS patients.

Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models.

PubMed

Fan, Ruzong; Wang, Yifan; Boehnke, Michael; Chen, Wei; Li, Yun; Ren, Haobo; Lobach, Iryna; Xiong, Momiao

2015-08-01

Meta-analysis of genetic data must account for differences among studies including study designs, markers genotyped, and covariates. The effects of genetic variants may differ from population to population, i.e., heterogeneity. Thus, meta-analysis of combining data of multiple studies is difficult. Novel statistical methods for meta-analysis are needed. In this article, functional linear models are developed for meta-analyses that connect genetic data to quantitative traits, adjusting for covariates. The models can be used to analyze rare variants, common variants, or a combination of the two. Both likelihood-ratio test (LRT) and F-distributed statistics are introduced to test association between quantitative traits and multiple variants in one genetic region. Extensive simulations are performed to evaluate empirical type I error rates and power performance of the proposed tests. The proposed LRT and F-distributed statistics control the type I error very well and have higher power than the existing methods of the meta-analysis sequence kernel association test (MetaSKAT). We analyze four blood lipid levels in data from a meta-analysis of eight European studies. The proposed methods detect more significant associations than MetaSKAT and the P-values of the proposed LRT and F-distributed statistics are usually much smaller than those of MetaSKAT. The functional linear models and related test statistics can be useful in whole-genome and whole-exome association studies. Copyright © 2015 by the Genetics Society of America.

Quantifying Low Energy Proton Damage in Multijunction Solar Cells

NASA Technical Reports Server (NTRS)

Messenger, Scott R.; Burke, Edward A.; Walters, Robert J.; Warner, Jeffrey H.; Summers, Geoffrey P.; Lorentzen, Justin R.; Morton, Thomas L.; Taylor, Steven J.

2007-01-01

An analysis of the effects of low energy proton irradiation on the electrical performance of triple junction (3J) InGaP2/GaAs/Ge solar cells is presented. The Monte Carlo ion transport code (SRIM) is used to simulate the damage profile induced in a 3J solar cell under the conditions of typical ground testing and that of the space environment. The results are used to present a quantitative analysis of the defect, and hence damage, distribution induced in the cell active region by the different radiation conditions. The modelling results show that, in the space environment, the solar cell will experience a uniform damage distribution through the active region of the cell. Through an application of the displacement damage dose analysis methodology, the implications of this result on mission performance predictions are investigated.

Differentiation of Glioblastoma from Brain Metastasis: Qualitative and Quantitative Analysis Using Arterial Spin Labeling MR Imaging.

PubMed

Sunwoo, Leonard; Yun, Tae Jin; You, Sung-Hye; Yoo, Roh-Eul; Kang, Koung Mi; Choi, Seung Hong; Kim, Ji-Hoon; Sohn, Chul-Ho; Park, Sun-Won; Jung, Cheolkyu; Park, Chul-Kee

2016-01-01

To evaluate the diagnostic performance of cerebral blood flow (CBF) by using arterial spin labeling (ASL) perfusion magnetic resonance (MR) imaging to differentiate glioblastoma (GBM) from brain metastasis. The institutional review board of our hospital approved this retrospective study. The study population consisted of 128 consecutive patients who underwent surgical resection and were diagnosed as either GBM (n = 89) or brain metastasis (n = 39). All participants underwent preoperative MR imaging including ASL. For qualitative analysis, the tumors were visually graded into five categories based on ASL-CBF maps by two blinded reviewers. For quantitative analysis, the reviewers drew regions of interest (ROIs) on ASL-CBF maps upon the most hyperperfused portion within the tumor and upon peritumoral T2 hyperintensity area. Signal intensities of intratumoral and peritumoral ROIs for each subject were normalized by dividing the values by those of contralateral normal gray matter (nCBFintratumoral and nCBFperitumoral, respectively). Visual grading scales and quantitative parameters between GBM and brain metastasis were compared. In addition, the area under the receiver-operating characteristic curve was used to evaluate the diagnostic performance of ASL-driven CBF to differentiate GBM from brain metastasis. For qualitative analysis, GBM group showed significantly higher grade compared to metastasis group (p = 0.001). For quantitative analysis, both nCBFintratumoral and nCBFperitumoral in GBM were significantly higher than those in metastasis (both p < 0.001). The areas under the curve were 0.677, 0.714, and 0.835 for visual grading, nCBFintratumoral, and nCBFperitumoral, respectively (all p < 0.001). ASL perfusion MR imaging can aid in the differentiation of GBM from brain metastasis.

Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production.

PubMed

Thurber, Carrie S; Ma, Justin M; Higgins, Race H; Brown, Patrick J

2013-06-26

Sorghum is a tropical C4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation. We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time. Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.

Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei.

PubMed

Bass, Hank W; Hoffman, Gregg G; Lee, Tae-Jin; Wear, Emily E; Joseph, Stacey R; Allen, George C; Hanley-Bowdoin, Linda; Thompson, William F

2015-11-01

Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.

Detection of propofol concentrations in blood by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Wróbel, M. S.; Gnyba, M.; UrniaŻ, R.; Myllylä, T. S.; Jedrzejewska-Szczerska, M.

2015-07-01

In this paper we present a proof-of-concept of a Raman spectroscopy-based approach for measuring the content of propofol, a common anesthesia drug, in whole human blood, and plasma, which is intended for use during clinical procedures. This method utilizes the Raman spectroscopy as a chemically-sensitive method for qualitative detection of the presence of a drug and a quantitative determination of its concentration. A number of samples from different patients with added various concentrations of propofol IV solution were measured. This is most equivalent to a real in-vivo situation. Subsequent analysis of a set of spectra was carried out to extract qualitative and quantitative information. We conclude, that the changes in the spectra of blood with propofol, overlap with the most prominent lines of the propofol solution, especially at spectral regions: 1450 cm-1, 1250- 1260 cm-1, 1050 cm-1, 875-910 cm-1, 640 cm-1. Later, we have introduced a quantitative analysis program based on correlation matrix closest fit, and a LOO cross-validation. We have achieved 36.67% and 60% model precision when considering full spectra, or specified bands, respectively. These results prove the possibility of using Raman spectroscopy for quantitative detection of propofol concentrations in whole human blood.

An analysis of dissolved organic matter from freshwater Karelian Lakes using reversed-phase high-performance liquid chromatography with online absorbance and fluorescence analysis

NASA Astrophysics Data System (ADS)

Khundzhua, D. A.; Patsaeva, S. V.; Trubetskoj, O. A.; Trubetskaya, O. E.

2017-01-01

The spectral and optical properties of the fractionated components of dissolved organic matter (DOM) of three freshwater lakes in Karelia were studied using reversed-phase high-performance liquid chromatography (RP-HPLC) with online detection of fluorescence and absorption spectra. It is shown that the DOM fractions are qualitatively similar, but differ quantitatively in the ratio of components and consist of at least three types of fluorophores: (1) hydrophilic "humic-like" fluorophore(s) with the emission maximum in the region of 420 nm and an absorption band at 260-270 nm; (2) hydrophobic "humic-like" fluorophore(s) with the emission maximum at approximately 450 nm that has no characteristic absorption maxima in the region from 220 to 400 nm; and (3) a "protein-like" fluorophore with the emission maximum in the region of 340-350 nm, which is typical of proteins and peptides containing tryptophan.

Quantitative evaluation method for differentiation of C2C12 myoblasts by ultrasonic microscopy

NASA Astrophysics Data System (ADS)

Takanashi, Kyoichi; Washiya, Mamoru; Ota, Kazuki; Yoshida, Sachiko; Hozumi, Naohiro; Kobayashi, Kazuto

2017-07-01

Cell differentiation was evaluated by ultrasonic microscopy. However, there were some regions that showed a lower acoustic impedance than the culture liquid. It was considered that, in such regions, the cells were not perfectly in contact with the film substrate. Hence, a waveform analysis was performed, and compensated acoustic impedances in such regions were in a reasonable range of values. By the same analysis, the displacements of partially floated cells were also successfully calculated. The elapsed day transitions of the compensated acoustic impedances and displacements were successfully evaluated. In the process of differentiation, actin fibers comprising the cytoskeleton are supposed to loosen in order to induce cellular fusion. In addition, the progress in cell differentiation accompanied by a change into a three-dimensional structure can partially be assessed by the displacement between a cell and a cultured film. Hence, we believe that cell differentiation can be evaluated using an ultrasonic microscope.

DISCRIMINATION OF GRANITOIDS AND MINERALIZED GRANITOIDS IN THE MIDYAN REGION, NORTHWESTERN ARABIAN SHIELD, SAUDI ARABIA, BY LANDSAT MSS DATA-ANALYSIS.

USGS Publications Warehouse

Davis, Philip A.; Grolier, Maurice J.

1984-01-01

Landsat multispectral scanner (MSS) band and band-ratio databases of two scenes covering the Midyan region of northwestern Saudi Arabia were examined quantitatively and qualitatively to determine which databases best discriminate the geologic units of this semi-arid and arid region. Unsupervised, linear-discriminant cluster-analysis was performed on these two band-ratio combinations and on the MSS bands for both scenes. The results for granitoid-rock discrimination indicated that the classification images using the MSS bands are superior to the band-ratio classification images for two reasons, discussed in the paper. Yet, the effects of topography and material type (including desert varnish) on the MSS-band data produced ambiguities in the MSS-band classification results. However, these ambiguities were clarified by using a simulated natural-color image in conjunction with the MSS-band classification image.

Detection of regional air pollution episodes utilizing satellite data in the visual range

NASA Technical Reports Server (NTRS)

Bowley, C. J.; Burke, H. K.; Barnes, J. C.

1981-01-01

A comparative analysis of satellite-observed haze patterns and ground-based aerosol measurements is carried out for July 20-23, 1978. During this period, a significant regional air pollution episode existed across the northeastern United States, accompanied by widespread haze, reduced surface visibility, and elevated sulfate levels measured by the Sulfate Regional Experiment (SURE) network. The results show that the satellite-observed haze patterns correlate closely with the area of reported low surface visibility (less than 4 mi) and high sulfate levels. Quantitative information on total aerosol loading derived from the satellite-digitized data, using an atmospheric radiative transfer model, agrees well with the results obtained from the ground-based measurements.

Brain Region-Specific Trafficking of the Dopamine Transporter

PubMed Central

Block, Ethan R.; Nuttle, Jacob; Balcita-Pedicino, Judith Joyce; Caltagarone, John; Watkins, Simon C.

2015-01-01

The dopamine (DA) transporter (DAT) controls dopaminergic neurotransmission by removing extracellular DA. Although DA reuptake is proposed to be regulated by DAT traffic to and from the cell surface, the membrane trafficking system involved in the endocytic cycling of DAT in the intact mammalian brain has not been characterized. Hence, we performed immunolabeling and quantitative analysis of the subcellular and regional distribution of DAT using the transgenic knock-in mouse expressing hemagglutinin (HA) epitope-tagged DAT (HA-DAT) and by using a combination of electron microscopy and a novel method for immunofluorescence labeling of HA-DAT in acute sagittal brain slices. Both approaches demonstrated that, in midbrain somatodendritic regions, HA-DAT was present in the plasma membrane, endoplasmic reticulum, and Golgi complex, with a small fraction in early and recycling endosomes and an even smaller fraction in late endosomes and lysosomes. In the striatum and in axonal tracts between the midbrain and striatum, HA-DAT was detected predominantly in the plasma membrane, and quantitative analysis revealed increased DAT density in striatal compared with midbrain plasma membranes. Endosomes were strikingly rare and lysosomes were absent in striatal axons, in which there was little intracellular HA-DAT. Acute administration of amphetamine in vivo (60 min) or to slices ex vivo (10–60 min) did not result in detectable changes in DAT distribution. Altogether, these data provide evidence for regional differences in DAT plasma membrane targeting and retention and suggest a surprisingly low level of endocytic trafficking of DAT in the striatum along with limited DAT endocytic activity in somatodendritic areas. SIGNIFICANCE STATEMENT The dopamine transporter (DAT) is the key regulator of the dopamine neurotransmission in the CNS. In the present study, we developed a new approach for studying DAT localization and dynamics in intact neurons in acute sagittal brain slices from the knock-in mouse expressing epitope-tagged DAT. For the first time, the fluorescence imaging analysis of DAT was combined with the immunogold labeling of DAT and quantitative electron microscopy. In contrast to numerous studies of DAT trafficking in heterologous expression systems and dissociated cultured neurons, studies in intact neurons revealed a surprisingly low amount of endocytic trafficking of DAT at steady state and after acute amphetamine treatment and suggested that non-vesicular transport could be the main mechanism establishing DAT distribution within the dopaminergic neuron. PMID:26377471

Quantitative trait loci at the 11q23.3 chromosomal region related to dyslipidemia in the population of Andhra Pradesh, India.

PubMed

Pranavchand, Rayabarapu; Reddy, Battini Mohan

2017-06-13

Given the characteristic atherogenic dyslipidemia of south Indian population and crucial role of APOA1, APOC3, APOA4 and APOA5 genes clustered in 11q23.3 chromosomal region in regulating lipoprotein metabolism and cholesterol homeostasis, a large number of recently identified variants are to be explored for their role in regulating the serum lipid parameters among south Indians. Using fluidigm SNP genotyping platform, a prioritized set of 96 SNPs of the 11q23.3 chromosomal region were genotyped on 516 individuals from Hyderabad, India, and its vicinity and aged >45 years. The linear regression analysis of the individual lipid traits viz., TC, LDLC, HDLC, VLDL and TG with each of the 78 SNPs that confirm to HWE and with minor allele frequency > 1%, suggests 23 of those to be significantly associated (p ≤ 0.05) with at least one of these quantitative traits. Most importantly, the variant rs632153 is involved in elevating TC, LDLC, TG and VLDLs and probably playing a crucial role in the manifestation of dyslipidemia. Additionally, another three SNPs rs633389, rs2187126 and rs1263163 are found risk conferring to dyslipidemia by elevating LDLC and TC levels in the present population. Further, the ROC (receiver operating curve) analysis for the risk scores and dyslipidemia status yielded a significant area under curve (AUC) = 0.675, suggesting high discriminative power of the risk variants towards the condition. The interaction analysis suggests rs10488699-rs2187126 pair of the BUD13 gene to confer significant risk (Interaction odds ratio = 14.38, P = 7.17 × 10 5 ) towards dyslipidemia by elevating the TC levels (β = 37.13, p = 6.614 × 10 5 ). On the other hand, the interaction between variants of APOA1 gene and BUD13 and/or ZPR1 regulatory genes at this region are associated with elevated TG and VLDL. The variants at 11q23.3 chromosomal region seem to determine the quantitative lipid traits and in turn dyslipidemia in the population of Hyderabad. Particularly, the variants rs632153, rs633389, rs2187126 and rs1263163 might be risk conferring to dyslipidemia by elevating LDLC and TC levels, while the variants of APOC3 and APOA1 genes might be the genetic determinants of elevated triglycerides in the present population.

Regionally variant collagen alignment correlates with viscoelastic properties of the disc of the human temporomandibular joint.

PubMed

Gutman, Shawn; Kim, Daniel; Tarafder, Solaiman; Velez, Sergio; Jeong, Julia; Lee, Chang H

2018-02-01

To determine the regionally variant quality of collagen alignment in human TMJ discs and its statistical correlation with viscoelastic properties. For quantitative analysis of the quality of collagen alignment, horizontal sections of human TMJ discs with Pricrosirius Red staining were imaged under circularly polarized microscopy. Mean angle and angular deviation of collagen fibers in each region were analyzed using a well-established automated image-processing for angular gradient. Instantaneous and relaxation moduli of each disc region were measured under stress-relaxation test both in tensile and compression. Then Spearman correlation analysis was performed between the angular deviation and the moduli. To understand the effect of glycosaminoglycans on the correlation, TMJ disc samples were treated by chondroitinase ABC (C-ABC). Our imaging processing analysis showed the region-variant direction of collagen alignment, consistently with previous findings. Interestingly, the quality of collagen alignment, not only the directions, was significantly different in between the regions. The angular deviation of fiber alignment in the anterior and intermediate regions were significantly smaller than the posterior region. Medial and lateral regions showed significantly bigger angular deviation than all the other regions. The regionally variant angular deviation values showed statistically significant correlation with the tensile instantaneous modulus and the relaxation modulus, partially dependent on C-ABC treatment. Our findings suggest the region-variant degree of collagen fiber alignment is likely attributed to the heterogeneous viscoelastic properties of TMJ disc that may have significant implications in development of regenerative therapy for TMJ disc. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Liebetreu, John; Moore, Michael S.; Price, Jeremy C.; Abbott, Ben

2005-01-01

This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

Modeling and Analysis of Space Based Transceivers

NASA Technical Reports Server (NTRS)

Moore, Michael S.; Price, Jeremy C.; Abbott, Ben; Liebetreu, John; Reinhart, Richard C.; Kacpura, Thomas J.

2007-01-01

This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

Analysis of dose heterogeneity using a subvolume-DVH

NASA Astrophysics Data System (ADS)

Said, M.; Nilsson, P.; Ceberg, C.

2017-11-01

The dose-volume histogram (DVH) is universally used in radiation therapy for its highly efficient way of summarizing three-dimensional dose distributions. An apparent limitation that is inherent to standard histograms is the loss of spatial information, e.g. it is no longer possible to tell where low- and high-dose regions are, and whether they are connected or disjoint. Two methods for overcoming the spatial fragmentation of low- and high-dose regions are presented, both based on the gray-level size zone matrix, which is a two-dimensional histogram describing the frequencies of connected regions of similar intensities. The first approach is a quantitative metric which can be likened to a homogeneity index. The large cold spot metric (LCS) is here defined to emphasize large contiguous regions receiving too low a dose; emphasis is put on both size, and deviation from the prescribed dose. In contrast, the subvolume-DVH (sDVH) is an extension to the standard DVH and allows for a qualitative evaluation of the degree of dose heterogeneity. The information retained from the two-dimensional histogram is overlaid on top of the DVH and the two are presented simultaneously. Both methods gauge the underlying heterogeneity in ways that the DVH alone cannot, and both have their own merits—the sDVH being more intuitive and the LCS being quantitative.

Utility of Gram stain for the microbiological analysis of burn wound surfaces.

PubMed

Elsayed, Sameer; Gregson, Daniel B; Lloyd, Tracie; Crichton, Marilyn; Church, Deirdre L

2003-11-01

Surface swab cultures have attracted attention as a potential alternative to biopsy histology or quantitative culture methods for microbiological burn wound monitoring. To our knowledge, the utility of adding a Gram-stained slide in this context has not been evaluated previously. To determine the degree of correlation of Gram stain with culture for the microbiological analysis of burn wound surfaces. Prospective laboratory analysis. Urban health region/centralized diagnostic microbiology laboratory. Burn patients hospitalized in any Calgary Health Region burn center from November 2000 to September 2001. Gram stain plus culture of burn wound surface swab specimens obtained during routine dressing changes or based on clinical signs of infection. Degree of correlation (complete, high, partial, none), including weighted kappa statistic (kappa(w)), of Gram stain with culture based on quantitative microscopy and degree of culture growth. A total of 375 specimens from 50 burn patients were evaluated. Of these, 239 were negative by culture and Gram stain, 7 were positive by Gram stain only, 89 were positive by culture only, and 40 were positive by both methods. The degree of complete, high, partial, and no correlation of Gram stain with culture was 70.9% (266/375), 1.1% (4/375), 2.4% (9/375), and 25.6% (96/375), respectively. The degree of correlation for all 375 specimens, as expressed by the weighted kappa statistic, was found to be fair (kappa(w) = 0.32).Conclusion.-The Gram stain is not suitable for the microbiological analysis of burn wound surfaces.

Use of FTA® classic cards for epigenetic analysis of sperm DNA.

PubMed

Serra, Olga; Frazzi, Raffaele; Perotti, Alessio; Barusi, Lorenzo; Buschini, Annamaria

2018-02-01

FTA® technologies provide the most reliable method for DNA extraction. Although FTA technologies have been widely used for genetic analysis, there is no literature on their use for epigenetic analysis yet. We present for the first time, a simple method for quantitative methylation assessment based on sperm cells stored on Whatman FTA classic cards. Specifically, elution of seminal DNA from FTA classic cards was successfully tested with an elution buffer and an incubation step in a thermocycler. The eluted DNA was bisulfite converted, amplified by PCR, and a region of interest was pyrosequenced.

Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping

NASA Technical Reports Server (NTRS)

Royce, Thomas E.; Rozowsky, Joel S.; Bertone, Paul; Samanta, Manoj; Stolc, Viktor; Weissman, Sherman; Snyder, Michael; Gerstein, Mark

2005-01-01

Traditional microarrays use probes complementary to known genes to quantitate the differential gene expression between two or more conditions. Genomic tiling microarray experiments differ in that probes that span a genomic region at regular intervals are used to detect the presence or absence of transcription. This difference means the same sets of biases and the methods for addressing them are unlikely to be relevant to both types of experiment. We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology.

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

PubMed

Chen, Li; Wang, Chi; Qin, Zhaohui S; Wu, Hao

2015-06-15

ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. 'peak detection'), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed. In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones. An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Impact of inflammation on iron stores in involved and non-involved psoriatic skin

NASA Astrophysics Data System (ADS)

Pinheiro, T.; Ynsa, M. D.; Alves, L. C.; Teixeira, P.; Ferreira, J.; Filipe, P.

2015-04-01

Accumulating evidence supports a role for cellular Fe in cell proliferation, inflammation, and disease tolerance. Psoriasis is a severe inflammatory and hyper proliferative condition of human skin whose aetiology remains poorly understood. Herein, we performed nuclear microscopy techniques to quantify with cellular resolution and high sensitivity the concentration of Fe in lesional (psoriatic plaques) and non-lesional adjacent skin of psoriatic patients. Fe contents were measured across skin depth and along epidermal strata either by quantitatively imaging Fe distribution in regions of interest, or by determining Fe profiles through analysis of sequential points along selected transepts. Both procedures require deconvolution of spectra to project quantitative elemental data through the application of different software codes. Using these approaches a detailed quantitative distribution of Fe was resolved. We show that in both lesional and non-lesional skin, the epidermal profiles of Fe contents showed a peak at the basal layer and that Fe concentration along the basal layer was not uniformly distributed. Typically, Fe levels were significantly higher in epidermal ridges relative to regions above dermal papillae. Lesional skin displayed excess Fe over extended regions above basal layer. In conclusion, we found significantly increased Fe deposits in the epidermis of psoriatic patients, particularly in areas of epidermal hyper proliferation. These findings suggest an important role for Fe in the pathogenesis of psoriasis. They also raise the possibility that manipulation of Fe levels in the skin may become relevant for the clinical management of psoriasis.

Quantifying the Intra-Regional Precipitation Variability in Northwestern China over the Past 1,400 Years

PubMed Central

Lee, Harry F.; Pei, Qing; Zhang, David D.; Choi, Kan P. K.

2015-01-01

There has been a surge of paleo-climatic/environmental studies of Northwestern China (NW China), a region characterized by a diverse assortment of hydro-climatic systems. Their common approach, however, focuses on “deducing regional resemblance” rather than “exploring regional variance.” To date, efforts to produce a quantitative assessment of long-term intra-regional precipitation variability (IRPV) in NW China has been inadequate. In the present study, we base on historical flood/drought records to compile a decadal IRPV index for NW China spanned AD580–1979 and to find its major determinants via wavelet analysis. Results show that our IRPV index captures the footprints of internal hydro-climatic disparity in NW China. In addition, we find distinct ~120–200 year periodicities in the IRPV index over the Little Ice Age, which are attributable to the change of hydro-climatic influence of ocean-atmospheric modes during the period. Also, we offer statistical evidence of El Niño Southern Oscillation (Indo-Pacific warm pool sea surface temperature and China-wide land surface temperature) as the prominent multi-decadal to centennial (centennial to multi-centennial) determinant of the IRPV in NW China. The present study contributes to the quantitative validation of the long-term IRPV in NW China and its driving forces, covering the periods with and without instrumental records. It may help to comprehend the complex hydro-climatic regimes in the region. PMID:26154711

Landsat analysis of tropical forest succession employing a terrain model

NASA Technical Reports Server (NTRS)

Barringer, T. H.; Robinson, V. B.; Coiner, J. C.; Bruce, R. C.

1980-01-01

Landsat multispectral scanner (MSS) data have yielded a dual classification of rain forest and shadow in an analysis of a semi-deciduous forest on Mindonoro Island, Philippines. Both a spatial terrain model, using a fifth side polynomial trend surface analysis for quantitatively estimating the general spatial variation in the data set, and a spectral terrain model, based on the MSS data, have been set up. A discriminant analysis, using both sets of data, has suggested that shadowing effects may be due primarily to local variations in the spectral regions and can therefore be compensated for through the decomposition of the spatial variation in both elevation and MSS data.

Novel quantitative analysis of autofluorescence images for oral cancer screening.

PubMed

Huang, Tze-Ta; Huang, Jehn-Shyun; Wang, Yen-Yun; Chen, Ken-Chung; Wong, Tung-Yiu; Chen, Yi-Chun; Wu, Che-Wei; Chan, Leong-Perng; Lin, Yi-Chu; Kao, Yu-Hsun; Nioka, Shoko; Yuan, Shyng-Shiou F; Chung, Pau-Choo

2017-05-01

VELscope® was developed to inspect oral mucosa autofluorescence. However, its accuracy is heavily dependent on the examining physician's experience. This study was aimed toward the development of a novel quantitative analysis of autofluorescence images for oral cancer screening. Patients with either oral cancer or precancerous lesions and a control group with normal oral mucosa were enrolled in this study. White light images and VELscope® autofluorescence images of the lesions were taken with a digital camera. The lesion in the image was chosen as the region of interest (ROI). The average intensity and heterogeneity of the ROI were calculated. A quadratic discriminant analysis (QDA) was utilized to compute boundaries based on sensitivity and specificity. 47 oral cancer lesions, 54 precancerous lesions, and 39 normal oral mucosae controls were analyzed. A boundary of specificity of 0.923 and a sensitivity of 0.979 between the oral cancer lesions and normal oral mucosae were validated. The oral cancer and precancerous lesions could also be differentiated from normal oral mucosae with a specificity of 0.923 and a sensitivity of 0.970. The novel quantitative analysis of the intensity and heterogeneity of VELscope® autofluorescence images used in this study in combination with a QDA classifier can be used to differentiate oral cancer and precancerous lesions from normal oral mucosae. Copyright © 2017 Elsevier Ltd. All rights reserved.

Middle School A/B Block and Traditional Scheduling: An Analysis of Math and Reading Performance by Race

ERIC Educational Resources Information Center

Gill, Willie Wallicia Allen

2011-01-01

The purpose of this quantitative study was to examine whether a difference existed in the percentage performance of students earning a pass/advanced score on the Standards of Learning (SOL) Test in math and reading in Virginia's Region IV for schools using an A/B block schedule and those using a traditional schedule. The research also examined if…

The Brain Network for Deductive Reasoning: A Quantitative Meta-analysis of 28 Neuroimaging Studies

PubMed Central

Prado, Jérôme; Chadha, Angad; Booth, James R.

2011-01-01

Over the course of the past decade, contradictory claims have been made regarding the neural bases of deductive reasoning. Researchers have been puzzled by apparent inconsistencies in the literature. Some have even questioned the effectiveness of the methodology used to study the neural bases of deductive reasoning. However, the idea that neuroimaging findings are inconsistent is not based on any quantitative evidence. Here, we report the results of a quantitative meta-analysis of 28 neuroimaging studies of deductive reasoning published between 1997 and 2010, combining 382 participants. Consistent areas of activations across studies were identified using the multilevel kernel density analysis method. We found that results from neuroimaging studies are more consistent than what has been previously assumed. Overall, studies consistently report activations in specific regions of a left fronto-parietal system, as well as in the left Basal Ganglia. This brain system can be decomposed into three subsystems that are specific to particular types of deductive arguments: relational, categorical, and propositional. These dissociations explain inconstancies in the literature. However, they are incompatible with the notion that deductive reasoning is supported by a single cognitive system relying either on visuospatial or rule-based mechanisms. Our findings provide critical insight into the cognitive organization of deductive reasoning and need to be accounted for by cognitive theories. PMID:21568632

A detailed pathway analysis of the chemical reaction system generating the Martian vertical ozone profile

NASA Astrophysics Data System (ADS)

Stock, Joachim W.; Blaszczak-Boxe, Christopher S.; Lehmann, Ralph; Grenfell, J. Lee; Patzer, A. Beate C.; Rauer, Heike; Yung, Yuk L.

2017-07-01

Atmospheric chemical composition is crucial in determining a planet's atmospheric structure, stability, and evolution. Attaining a quantitative understanding of the essential chemical mechanisms governing atmospheric composition is nontrivial due to complex interactions between chemical species. Trace species, for example, can participate in catalytic cycles - affecting the abundance of major and other trace gas species. Specifically, for Mars, such cycles dictate the abundance of its primary atmospheric constituent, carbon dioxide (CO2), but also for one of its trace gases, ozone (O3). The identification of chemical pathways/cycles by hand is extremely demanding; hence, the application of numerical methods, such as the Pathway Analysis Program (PAP), is crucial to analyze and quantitatively exemplify chemical reaction networks. Here, we carry out the first automated quantitative chemical pathway analysis of Mars' atmosphere with respect to O3. PAP was applied to JPL/Caltech's 1-D updated photochemical Mars model's output data. We determine all significant chemical pathways and their contribution to O3 production and consumption (up to 80 km) in order to investigate the mechanisms causing the characteristic shape of the O3 volume mixing ratio profile, i.e. a ground layer maximum and an ozone layer at ∼50 km. These pathways explain why an O3 layer is present, why it is located at that particular altitude and what the different processes forming the near-surface and middle atmosphere O3 maxima are. Furthermore, we show that the Martian atmosphere can be divided into two chemically distinct regions according to the O(3P):O3 ratio. In the lower region (below approximately 24 km altitude) O3 is the most abundant Ox (= O3 + O(3P)) species. In the upper region (above approximately 24 km altitude), where the O3 layer is located, O(3P) is the most abundant Ox species. Earlier results concerning the formation of O3 on Mars can now be explained with the help of chemical pathways leading to a better understanding of the vertical O3 profile.

Research Review: Neural response to threat in children, adolescents, and adults after child maltreatment - a quantitative meta-analysis.

PubMed

Hein, Tyler C; Monk, Christopher S

2017-03-01

Child maltreatment is common and has long-term consequences for affective function. Investigations of neural consequences of maltreatment have focused on the amygdala. However, developmental neuroscience indicates that other brain regions are also likely to be affected by child maltreatment, particularly in the social information processing network (SIPN). We conducted a quantitative meta-analysis to: confirm that maltreatment is related to greater bilateral amygdala activation in a large sample that was pooled across studies; investigate other SIPN structures that are likely candidates for altered function; and conduct a data-driven examination to identify additional regions that show altered activation in maltreated children, teens, and adults. We conducted an activation likelihood estimation analysis with 1,733 participants across 20 studies of emotion processing in maltreated individuals. Maltreatment is associated with increased bilateral amygdala activation to emotional faces. One SIPN structure is altered: superior temporal gyrus, of the detection node, is hyperactive in maltreated individuals. The results of the whole-brain corrected analysis also show hyperactivation of the parahippocampal gyrus and insula in maltreated individuals. The meta-analysis confirms that maltreatment is related to increased bilateral amygdala reactivity and also shows that maltreatment affects multiple additional structures in the brain that have received little attention in the literature. Thus, although the majority of studies examining maltreatment and brain function have focused on the amygdala, these findings indicate that the neural consequences of child maltreatment involve a broader network of structures. © 2016 Association for Child and Adolescent Mental Health.

Modern Material Analysis Instruments Add a New Dimension to Materials Characterization and Failure Analysis

NASA Technical Reports Server (NTRS)

Panda, Binayak

2009-01-01

Modern analytical tools can yield invaluable results during materials characterization and failure analysis. Scanning electron microscopes (SEMs) provide significant analytical capabilities, including angstrom-level resolution. These systems can be equipped with a silicon drift detector (SDD) for very fast yet precise analytical mapping of phases, as well as electron back-scattered diffraction (EBSD) units to map grain orientations, chambers that admit large samples, variable pressure for wet samples, and quantitative analysis software to examine phases. Advanced solid-state electronics have also improved surface and bulk analysis instruments: Secondary ion mass spectroscopy (SIMS) can quantitatively determine and map light elements such as hydrogen, lithium, and boron - with their isotopes. Its high sensitivity detects impurities at parts per billion (ppb) levels. X-ray photo-electron spectroscopy (XPS) can determine oxidation states of elements, as well as identifying polymers and measuring film thicknesses on coated composites. This technique is also known as electron spectroscopy for chemical analysis (ESCA). Scanning Auger electron spectroscopy (SAM) combines surface sensitivity, spatial lateral resolution (10 nm), and depth profiling capabilities to describe elemental compositions of near and below surface regions down to the chemical state of an atom.

Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck.

PubMed

Alam, Imranul; Sun, Qiwei; Liu, Lixiang; Koller, Daniel L; Liu, Yunlong; Edenberg, Howard J; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

2008-10-08

Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Several studies in humans and animal models identified chromosomal regions linked to hip size and bone mass. Previously, we identified that the region of 4q21-q41 on rat chromosome (Chr) 4 harbors multiple femoral neck quantitative trait loci (QTLs) in inbred Fischer 344 (F344) and Lewis (LEW) rats. The purpose of this study is to identify the candidate genes for femoral neck structure and density by correlating gene expression in the proximal femur with the femoral neck phenotypes linked to the QTLs on Chr 4. RNA was extracted from proximal femora of 4-wk-old rats from F344 and LEW strains, and two other strains, Copenhagen 2331 and Dark Agouti, were used as a negative control. Microarray analysis was performed using Affymetrix Rat Genome 230 2.0 arrays. A total of 99 genes in the 4q21-q41 region were differentially expressed (P < 0.05) among all strains of rats with a false discovery rate <10%. These 99 genes were then ranked based on the strength of correlation between femoral neck phenotypes measured in F2 animals, homozygous for a particular strain's allele at the Chr 4 QTL and the expression level of the gene in that strain. A total of 18 candidate genes were strongly correlated (r(2) > 0.50) with femoral neck width and prioritized for further analysis. Quantitative PCR analysis confirmed 14 of 18 of the candidate genes. Ingenuity pathway analysis revealed several direct or indirect relationships among the candidate genes related to angiogenesis (VEGF), bone growth (FGF2), bone formation (IGF2 and IGF2BP3), and resorption (TNF). This study provides a shortened list of genetic determinants of skeletal traits at the hip and may lead to novel approaches for prevention and treatment of hip fracture.

Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck

PubMed Central

Alam, Imranul; Sun, Qiwei; Liu, Lixiang; Koller, Daniel L.; Liu, Yunlong; Edenberg, Howard J.; Econs, Michael J.; Foroud, Tatiana; Turner, Charles H.

2008-01-01

Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Several studies in humans and animal models identified chromosomal regions linked to hip size and bone mass. Previously, we identified that the region of 4q21-q41 on rat chromosome (Chr) 4 harbors multiple femoral neck quantitative trait loci (QTLs) in inbred Fischer 344 (F344) and Lewis (LEW) rats. The purpose of this study is to identify the candidate genes for femoral neck structure and density by correlating gene expression in the proximal femur with the femoral neck phenotypes linked to the QTLs on Chr 4. RNA was extracted from proximal femora of 4-wk-old rats from F344 and LEW strains, and two other strains, Copenhagen 2331 and Dark Agouti, were used as a negative control. Microarray analysis was performed using Affymetrix Rat Genome 230 2.0 arrays. A total of 99 genes in the 4q21-q41 region were differentially expressed (P < 0.05) among all strains of rats with a false discovery rate <10%. These 99 genes were then ranked based on the strength of correlation between femoral neck phenotypes measured in F2 animals, homozygous for a particular strain's allele at the Chr 4 QTL and the expression level of the gene in that strain. A total of 18 candidate genes were strongly correlated (r2 > 0.50) with femoral neck width and prioritized for further analysis. Quantitative PCR analysis confirmed 14 of 18 of the candidate genes. Ingenuity pathway analysis revealed several direct or indirect relationships among the candidate genes related to angiogenesis (VEGF), bone growth (FGF2), bone formation (IGF2 and IGF2BP3), and resorption (TNF). This study provides a shortened list of genetic determinants of skeletal traits at the hip and may lead to novel approaches for prevention and treatment of hip fracture. PMID:18728226

Quantitative Trait Loci Controlling Vegetative Growth Rate in the Edible Basidiomycete Pleurotus ostreatus

PubMed Central

Larraya, Luis M.; Idareta, Eneko; Arana, Dani; Ritter, Enrique; Pisabarro, Antonio G.; Ramírez, Lucia

2002-01-01

Mycelium growth rate is a quantitative characteristic that exhibits continuous variation. This trait has applied interest, as growth rate is correlated with production yield and increased advantage against competitors. In this work, we studied growth rate variation in the edible basidiomycete Pleurotus ostreatus growing as monokaryotic or dikaryotic mycelium on Eger medium or on wheat straw. Our analysis resulted in identification of several genomic regions (quantitative trait loci [QTLs]) involved in the control of growth rate that can be mapped on the genetic linkage map of this fungus. In some cases monokaryotic and dikaryotic QTLs clustered at the same map position, indicating that there are principal genomic areas responsible for growth rate control. The availability of this linkage map of growth rate QTLs can help in the design of rational strain breeding programs based on genomic information. PMID:11872457

Mild hypothermia for treatment of diffuse axonal injury: a quantitative analysis of diffusion tensor imaging

PubMed Central

Jing, Guojie; Yao, Xiaoteng; Li, Yiyi; Xie, Yituan; Li, Wang#x2019;an; Liu, Kejun; Jing, Yingchao; Li, Baisheng; Lv, Yifan; Ma, Baoxin

2014-01-01

Fractional anisotropy values in diffusion tensor imaging can quantitatively reflect the consistency of nerve fibers after brain damage, where higher values generally indicate less damage to nerve fibers. Therefore, we hypothesized that diffusion tensor imaging could be used to evaluate the effect of mild hypothermia on diffuse axonal injury. A total of 102 patients with diffuse axonal injury were randomly divided into two groups: normothermic and mild hypothermic treatment groups. Patient's modified Rankin scale scores 2 months after mild hypothermia were significantly lower than those for the normothermia group. The difference in average fractional anisotropy value for each region of interest before and after mild hypothermia was 1.32-1.36 times higher than the value in the normothermia group. Quantitative assessment of diffusion tensor imaging indicates that mild hypothermia therapy may be beneficial for patients with diffuse axonal injury. PMID:25206800

Determining conduction patterns on a sparse electrode grid: Implications for the analysis of clinical arrhythmias

NASA Astrophysics Data System (ADS)

Vidmar, David; Narayan, Sanjiv M.; Krummen, David E.; Rappel, Wouter-Jan

2016-11-01

We present a general method of utilizing bioelectric recordings from a spatially sparse electrode grid to compute a dynamic vector field describing the underlying propagation of electrical activity. This vector field, termed the wave-front flow field, permits quantitative analysis of the magnitude of rotational activity (vorticity) and focal activity (divergence) at each spatial point. We apply this method to signals recorded during arrhythmias in human atria and ventricles using a multipolar contact catheter and show that the flow fields correlate with corresponding activation maps. Further, regions of elevated vorticity and divergence correspond to sites identified as clinically significant rotors and focal sources where therapeutic intervention can be effective. These flow fields can provide quantitative insights into the dynamics of normal and abnormal conduction in humans and could potentially be used to enhance therapies for cardiac arrhythmias.

Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

PubMed

Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

2014-02-01

Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications.

Quantitative analysis of spatial variability of geotechnical parameters

NASA Astrophysics Data System (ADS)

Fang, Xing

2018-04-01

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

Quantitative fluorescence-polymerase chain reaction assay for the detection of the duplication of the Charcot Marie Tooth disease type 1A critical region.

PubMed

De Toffol, Simona; Bellone, Emilia; Dulcetti, Francesca; Ruggeri, Anna Maria; Maggio, Pietro Paolo; Pulimeno, Maria Rosaria; Mandich, Paola; Maggi, Federico; Simoni, Giuseppe; Grati, Francesca Romana

2010-04-01

Charcot Marie Tooth (CMT) syndrome is the most common hereditary peripheral neuropathy, with an incidence of about 1 in 2500. The subtype 1A (CMT1A) is caused by a tandem duplication of a 1.5-Mb region encompassing the PMP22 gene. Conventional short tandem repeat (STR) analysis can reveal this imbalance if a triallelic pattern, defining with certainty the presence of duplication, is present. In case of duplication with a biallelic pattern, it can only indicate a semiquantitative dosage of the fluorescence intensity ratio of the two fragments. In this study we developed a quantitative fluorescence-PCR using seven highly informative STRs within the CMT1A critical region that successfully disclosed or excluded the presence of the pathogenic imbalance in a cohort of 60 samples including 40 DNAs from samples with the CMT1A duplication previously characterized with two different molecular approaches, and 20 diagnostic samples from 10 members of a five-generation pedigree segregating CMT1A, 8 unrelated cases and 2 prenatal samples. The application of the quantitative fluorescence-PCR using STRs located in the critical region could be a reliable method to evaluate the presence of the PMP22 duplication for the diagnosis and classification of hereditary neuropathies in asymptomatic subjects with a family history of inherited neuropathy, in prenatal samples in cases with one affected parent, and in unrelated patients with a sporadic demyelinating neuropathy with clinical features resembling CMT (i.e., pes cavus with hammer toes) or with conduction velocities in the range of CMT1A.

EQUIFAT: A novel scoring system for the semi-quantitative evaluation of regional adipose tissues in Equidae.

PubMed

Morrison, Philippa K; Harris, Patricia A; Maltin, Charlotte A; Grove-White, Dai; Argo, Caroline McG

2017-01-01

Anatomically distinct adipose tissues represent variable risks to metabolic health in man and some other mammals. Quantitative-imaging of internal adipose depots is problematic in large animals and associations between regional adiposity and health are poorly understood. This study aimed to develop and test a semi-quantitative system (EQUIFAT) which could be applied to regional adipose tissues. Anatomically-defined, photographic images of adipose depots (omental, mesenteric, epicardial, rump) were collected from 38 animals immediately post-mortem. Images were ranked and depot-specific descriptors were developed (1 = no fat visible; 5 = excessive fat present). Nuchal-crest and ventro-abdominal-retroperitoneal adipose depot depths (cm) were transformed to categorical 5 point scores. The repeatability and reliability of EQUIFAT was independently tested by 24 observers. When half scores were permitted, inter-observer agreement was substantial (average κw: mesenteric, 0.79; omental, 0.79; rump 0.61) or moderate (average κw; epicardial, 0.60). Intra-observer repeatability was tested by 8 observers on 2 occasions. Kappa analysis indicated perfect (omental and mesenteric) and substantial agreement (epicardial and rump) between attempts. A further 207 animals were evaluated ante-mortem (age, height, breed-type, gender, body condition score [BCS]) and again immediately post-mortem (EQUIFAT scores, carcass weight). Multivariable, random effect linear regression models were fitted (breed as random effect; BCS as outcome variable). Only height, carcass weight, omental and retroperitoneal EQUIFAT scores remained as explanatory variables in the final model. The EQUIFAT scores developed here demonstrate clear functional differences between regional adipose depots and future studies could be directed towards describing associations between adiposity and disease risk in surgical and post-mortem situations.

Interspecies synteny mapping identifies a quantitative trait locus for bone mineral density on human chromosome Xp22.

PubMed

Parsons, Claire A; Mroczkowski, H Joel; McGuigan, Fiona E A; Albagha, Omar M E; Manolagas, Stavros; Reid, David M; Ralston, Stuart H; Shmookler Reis, Robert J

2005-11-01

Bone mineral density (BMD) is a complex trait with a strong genetic component and an important predictor of osteoporotic fracture risk. Here we report the use of a cross-species strategy to identify genes that regulate BMD, proceeding from quantitative trait mapping in mice to association mapping of the syntenic region in the human genome. We identified a quantitative trait locus (QTL) on the mouse X-chromosome for post-maturity change in spine BMD in a cross of SAMP6 and AKR/J mice and conducted association mapping of the syntenic region on human chromosome Xp22. We studied 76 single nucleotide polymorphisms (SNP) from the human region in two sets of DNA pools prepared from individuals with lumbar spine-BMD (LS-BMD) values falling into the top and bottom 13th percentiles of a population-based study of 3100 post-menopausal women. This procedure identified a region of significant association for two adjacent SNP (rs234494 and rs234495) within the Xp22 locus (P<0.001). Individual genotyping for rs234494 in the BMD pools confirmed the presence of an association for alleles (P=0.018) and genotypes (P=0.008). Analysis of rs234494 and rs234495 in 1053 women derived from the same population who were not selected for BMD values showed an association with LS-BMD for rs234495 (P=0.01) and for haplotypes defined by both SNP (P=0.002). Our study illustrates that interspecies synteny can be used to identify and refine QTL for complex traits and represents the first example where a human QTL for BMD regulation has been mapped using this approach.

EQUIFAT: A novel scoring system for the semi-quantitative evaluation of regional adipose tissues in Equidae

PubMed Central

Morrison, Philippa K.; Harris, Patricia A.; Maltin, Charlotte A.; Grove-White, Dai; Argo, Caroline McG.

2017-01-01

Anatomically distinct adipose tissues represent variable risks to metabolic health in man and some other mammals. Quantitative-imaging of internal adipose depots is problematic in large animals and associations between regional adiposity and health are poorly understood. This study aimed to develop and test a semi-quantitative system (EQUIFAT) which could be applied to regional adipose tissues. Anatomically-defined, photographic images of adipose depots (omental, mesenteric, epicardial, rump) were collected from 38 animals immediately post-mortem. Images were ranked and depot-specific descriptors were developed (1 = no fat visible; 5 = excessive fat present). Nuchal-crest and ventro-abdominal-retroperitoneal adipose depot depths (cm) were transformed to categorical 5 point scores. The repeatability and reliability of EQUIFAT was independently tested by 24 observers. When half scores were permitted, inter-observer agreement was substantial (average κw: mesenteric, 0.79; omental, 0.79; rump 0.61) or moderate (average κw; epicardial, 0.60). Intra-observer repeatability was tested by 8 observers on 2 occasions. Kappa analysis indicated perfect (omental and mesenteric) and substantial agreement (epicardial and rump) between attempts. A further 207 animals were evaluated ante-mortem (age, height, breed-type, gender, body condition score [BCS]) and again immediately post-mortem (EQUIFAT scores, carcass weight). Multivariable, random effect linear regression models were fitted (breed as random effect; BCS as outcome variable). Only height, carcass weight, omental and retroperitoneal EQUIFAT scores remained as explanatory variables in the final model. The EQUIFAT scores developed here demonstrate clear functional differences between regional adipose depots and future studies could be directed towards describing associations between adiposity and disease risk in surgical and post-mortem situations. PMID:28296956

dCLIP: a computational approach for comparative CLIP-seq analyses

PubMed Central

2014-01-01

Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/. PMID:24398258

Application of high-resolution melting analysis for authenticity testing of valuable Dendrobium commercial products.

PubMed

Dong, Xiaoman; Jiang, Chao; Yuan, Yuan; Peng, Daiyin; Luo, Yuqin; Zhao, Yuyang; Huang, Luqi

2018-01-01

The accurate identification of botanical origin in commercial products is important to ensure food authenticity and safety for consumers. The Dendrobium species have long been commercialised as functional food supplements and herbal medicines in Asia. Three valuable Dendrobium species, namely Dendrobium officinale, D. huoshanense and D. moniliforme, are often mutually adulterated in trade products in pursuit of higher profit. In this paper, a rapid and reliable semi-quantitative method for identifying the botanical origin of Dendrobium products in terminal markets was developed using high-resolution melting (HRM) analysis with specific primer pairs to target the trnL-F region. The HRM analysis method detected amounts of D. moniliforme adulterants as low as 1% in D. huoshanense or D. officinale products. The results have demonstrated that HRM analysis is a fast and effective tool for the differentiation of these Dendrobium species both for their authenticity as well as for the semi-quantitative determination of the purity of their processed products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Two-phase designs for joint quantitative-trait-dependent and genotype-dependent sampling in post-GWAS regional sequencing.

PubMed

Espin-Garcia, Osvaldo; Craiu, Radu V; Bull, Shelley B

2018-02-01

We evaluate two-phase designs to follow-up findings from genome-wide association study (GWAS) when the cost of regional sequencing in the entire cohort is prohibitive. We develop novel expectation-maximization-based inference under a semiparametric maximum likelihood formulation tailored for post-GWAS inference. A GWAS-SNP (where SNP is single nucleotide polymorphism) serves as a surrogate covariate in inferring association between a sequence variant and a normally distributed quantitative trait (QT). We assess test validity and quantify efficiency and power of joint QT-SNP-dependent sampling and analysis under alternative sample allocations by simulations. Joint allocation balanced on SNP genotype and extreme-QT strata yields significant power improvements compared to marginal QT- or SNP-based allocations. We illustrate the proposed method and evaluate the sensitivity of sample allocation to sampling variation using data from a sequencing study of systolic blood pressure. © 2017 The Authors. Genetic Epidemiology Published by Wiley Periodicals, Inc.

Importance of Multimodal MRI in Characterizing Brain Tissue and Its Potential Application for Individual Age Prediction.

PubMed

Cherubini, Andrea; Caligiuri, Maria Eugenia; Peran, Patrice; Sabatini, Umberto; Cosentino, Carlo; Amato, Francesco

2016-09-01

This study presents a voxel-based multiple regression analysis of different magnetic resonance image modalities, including anatomical T1-weighted, T2(*) relaxometry, and diffusion tensor imaging. Quantitative parameters sensitive to complementary brain tissue alterations, including morphometric atrophy, mineralization, microstructural damage, and anisotropy loss, were compared in a linear physiological aging model in 140 healthy subjects (range 20-74 years). The performance of different predictors and the identification of the best biomarker of age-induced structural variation were compared without a priori anatomical knowledge. The best quantitative predictors in several brain regions were iron deposition and microstructural damage, rather than macroscopic tissue atrophy. Age variations were best resolved with a combination of markers, suggesting that multiple predictors better capture age-induced tissue alterations. The results of the linear model were used to predict apparent age in different regions of individual brain. This approach pointed to a number of novel applications that could potentially help highlighting areas particularly vulnerable to disease.

Relationship of the Interaction Between Two Quantitative Trait Loci with γ-Globin Expression in β-Thalassemia Intermedia Patients.

PubMed

NickAria, Shiva; Haghpanah, Sezaneh; Ramzi, Mani; Karimi, Mehran

2018-05-10

Globin switching is a significant factor on blood hemoglobin (Hb) level but its molecular mechanisms have not yet been identified, however, several quantitative trait loci (QTL) and polymorphisms involved regions on chromosomes 2p, 6q, 8q and X account for variation in the γ-globin expression level. We studied the effect of interaction between a region on intron six of the TOX gene, chromosome 8q (chr8q) and XmnI locus on the γ-globin promoter, chr11p on γ-globin expression in 150 β-thalassemia intermedia (β-TI) patients, evaluated by statistical interaction analysis. Our results showed a significant interaction between one QTL on intron six of the TOX gene (rs9693712) and XmnI locus that effect γ-globin expression. Interchromosomal interaction mediates through transcriptional machanisms to preserve true genome architectural features, chromosomes localization and DNA bending. This interaction can be a part of the unknown molecular mechanism of globin switching and regulation of gene expression.

Regional Attribution of Ozone Production and Associated Radiative Forcing: a Step to Crediting NOx Emission Reductions

NASA Astrophysics Data System (ADS)

Naik, V.; Mauzerall, D. L.; Horowitz, L.; Schwarzkopf, D.; Ramaswamy, V.; Oppenheimer, M.

2004-12-01

The global distribution of tropospheric ozone (O3) depends on the location of emissions of its precursors in addition to chemical and dynamical factors. The global picture of O3 forcing is, therefore, a sum of regional forcings arising from emissions of precursors from different sources. The Kyoto Protocol does not include ozone as a greenhouse gas, and emission reductions of ozone precursors made under Kyoto or any similar agreement would presently receive no credit. In this study, we quantitatively estimate the contribution of emissions of nitrogen oxides (NOx), the primary limiting O3 precursor in the non-urban atmosphere, from specific countries and regions of the world to global O3 concentration distributions. We then estimate radiative forcing resulting from the regional perturbations of NOx emissions. This analysis is intended as an early step towards incorporating O3 into the Kyoto Protocol or any successor agreement. Under such a system countries could obtain credit for improvements in local air quality that result in reductions of O3 concentrations because of the associated reductions in radiative forcing. We use the global chemistry transport model, MOZART-2, to simulate the global O3 distribution for base year 1990 and perturbations to this distribution caused by a 10% percent reduction in the base emissions of NOx from the United States, Europe, East Asia, India, South America, and Africa. We calculate the radiative forcing for the simulated base and perturbed O3 distributions using the GFDL radiative transfer model. The difference between the radiative forcing from O3 for the base and perturbed distributions provides an estimate of the marginal radiative forcing from a region's emissions of NOx. We will present a quantitative analysis of the magnitude, spatial, and temporal distribution of radiative forcing resulting from marginal changes in the NOx emissions from each region.

STATISTICAL GROWTH MODELING OF LONGITUDINAL DT-MRI FOR REGIONAL CHARACTERIZATION OF EARLY BRAIN DEVELOPMENT.

PubMed

Sadeghi, Neda; Prastawa, Marcel; Fletcher, P Thomas; Gilmore, John H; Lin, Weili; Gerig, Guido

2012-01-01

A population growth model that represents the growth trajectories of individual subjects is critical to study and understand neurodevelopment. This paper presents a framework for jointly estimating and modeling individual and population growth trajectories, and determining significant regional differences in growth pattern characteristics applied to longitudinal neuroimaging data. We use non-linear mixed effect modeling where temporal change is modeled by the Gompertz function. The Gompertz function uses intuitive parameters related to delay, rate of change, and expected asymptotic value; all descriptive measures which can answer clinical questions related to growth. Our proposed framework combines nonlinear modeling of individual trajectories, population analysis, and testing for regional differences. We apply this framework to the study of early maturation in white matter regions as measured with diffusion tensor imaging (DTI). Regional differences between anatomical regions of interest that are known to mature differently are analyzed and quantified. Experiments with image data from a large ongoing clinical study show that our framework provides descriptive, quantitative information on growth trajectories that can be directly interpreted by clinicians. To our knowledge, this is the first longitudinal analysis of growth functions to explain the trajectory of early brain maturation as it is represented in DTI.

Quantified acoustic-optical speech signal incongruity identifies cortical sites of audiovisual speech processing

PubMed Central

Bernstein, Lynne E.; Lu, Zhong-Lin; Jiang, Jintao

2008-01-01

A fundamental question about human perception is how the speech perceiving brain combines auditory and visual phonetic stimulus information. We assumed that perceivers learn the normal relationship between acoustic and optical signals. We hypothesized that when the normal relationship is perturbed by mismatching the acoustic and optical signals, cortical areas responsible for audiovisual stimulus integration respond as a function of the magnitude of the mismatch. To test this hypothesis, in a previous study, we developed quantitative measures of acoustic-optical speech stimulus incongruity that correlate with perceptual measures. In the current study, we presented low incongruity (LI, matched), medium incongruity (MI, moderately mismatched), and high incongruity (HI, highly mismatched) audiovisual nonsense syllable stimuli during fMRI scanning. Perceptual responses differed as a function of the incongruity level, and BOLD measures were found to vary regionally and quantitatively with perceptual and quantitative incongruity levels. Each increase in level of incongruity resulted in an increase in overall levels of cortical activity and in additional activations. However, the only cortical region that demonstrated differential sensitivity to the three stimulus incongruity levels (HI > MI > LI) was a subarea of the left supramarginal gyrus (SMG). The left SMG might support a fine-grained analysis of the relationship between audiovisual phonetic input in comparison with stored knowledge, as hypothesized here. The methods here show that quantitative manipulation of stimulus incongruity is a new and powerful tool for disclosing the system that processes audiovisual speech stimuli. PMID:18495091

A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

PubMed Central

Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

2009-01-01

We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

Validation of voxel-based morphometry (VBM) based on MRI

NASA Astrophysics Data System (ADS)

Yang, Xueyu; Chen, Kewei; Guo, Xiaojuan; Yao, Li

2007-03-01

Voxel-based morphometry (VBM) is an automated and objective image analysis technique for detecting differences in regional concentration or volume of brain tissue composition based on structural magnetic resonance (MR) images. VBM has been used widely to evaluate brain morphometric differences between different populations, but there isn't an evaluation system for its validation until now. In this study, a quantitative and objective evaluation system was established in order to assess VBM performance. We recruited twenty normal volunteers (10 males and 10 females, age range 20-26 years, mean age 22.6 years). Firstly, several focal lesions (hippocampus, frontal lobe, anterior cingulate, back of hippocampus, back of anterior cingulate) were simulated in selected brain regions using real MRI data. Secondly, optimized VBM was performed to detect structural differences between groups. Thirdly, one-way ANOVA and post-hoc test were used to assess the accuracy and sensitivity of VBM analysis. The results revealed that VBM was a good detective tool in majority of brain regions, even in controversial brain region such as hippocampus in VBM study. Generally speaking, much more severity of focal lesion was, better VBM performance was. However size of focal lesion had little effects on VBM analysis.

Attenuation correction with region growing method used in the positron emission mammography imaging system

NASA Astrophysics Data System (ADS)

Gu, Xiao-Yue; Li, Lin; Yin, Peng-Fei; Yun, Ming-Kai; Chai, Pei; Huang, Xian-Chao; Sun, Xiao-Li; Wei, Long

2015-10-01

The Positron Emission Mammography imaging system (PEMi) provides a novel nuclear diagnosis method dedicated for breast imaging. With a better resolution than whole body PET, PEMi can detect millimeter-sized breast tumors. To address the requirement of semi-quantitative analysis with a radiotracer concentration map of the breast, a new attenuation correction method based on a three-dimensional seeded region growing image segmentation (3DSRG-AC) method has been developed. The method gives a 3D connected region as the segmentation result instead of image slices. The continuity property of the segmentation result makes this new method free of activity variation of breast tissues. The threshold value chosen is the key process for the segmentation method. The first valley in the grey level histogram of the reconstruction image is set as the lower threshold, which works well in clinical application. Results show that attenuation correction for PEMi improves the image quality and the quantitative accuracy of radioactivity distribution determination. Attenuation correction also improves the probability of detecting small and early breast tumors. Supported by Knowledge Innovation Project of The Chinese Academy of Sciences (KJCX2-EW-N06)

Neural network of cognitive emotion regulation — An ALE meta-analysis and MACM analysis

PubMed Central

Kohn, N.; Eickhoff, S.B.; Scheller, M.; Laird, A.R.; Fox, P.T.; Habel, U.

2016-01-01

Cognitive regulation of emotions is a fundamental prerequisite for intact social functioning which impacts on both well being and psychopathology. The neural underpinnings of this process have been studied intensively in recent years, without, however, a general consensus. We here quantitatively summarize the published literature on cognitive emotion regulation using activation likelihood estimation in fMRI and PET (23 studies/479 subjects). In addition, we assessed the particular functional contribution of identified regions and their interactions using quantitative functional inference and meta-analytic connectivity modeling, respectively. In doing so, we developed a model for the core brain network involved in emotion regulation of emotional reactivity. According to this, the superior temporal gyrus, angular gyrus and (pre) supplementary motor area should be involved in execution of regulation initiated by frontal areas. The dorsolateral prefrontal cortex may be related to regulation of cognitive processes such as attention, while the ventrolateral prefrontal cortex may not necessarily reflect the regulatory process per se, but signals salience and therefore the need to regulate. We also identified a cluster in the anterior middle cingulate cortex as a region, which is anatomically and functionally in an ideal position to influence behavior and subcortical structures related to affect generation. Hence this area may play a central, integrative role in emotion regulation. By focusing on regions commonly active across multiple studies, this proposed model should provide important a priori information for the assessment of dysregulated emotion regulation in psychiatric disorders. PMID:24220041

Magnetoencephalographic Mapping of Epileptic Spike Population Using Distributed Source Analysis: Comparison With Intracranial Electroencephalographic Spikes.

PubMed

Tanaka, Naoaki; Papadelis, Christos; Tamilia, Eleonora; Madsen, Joseph R; Pearl, Phillip L; Stufflebeam, Steven M

2018-04-27

This study evaluates magnetoencephalographic (MEG) spike population as compared with intracranial electroencephalographic (IEEG) spikes using a quantitative method based on distributed source analysis. We retrospectively studied eight patients with medically intractable epilepsy who had an MEG and subsequent IEEG monitoring. Fifty MEG spikes were analyzed in each patient using minimum norm estimate. For individual spikes, each vertex in the source space was considered activated when its source amplitude at the peak latency was higher than a threshold, which was set at 50% of the maximum amplitude over all vertices. We mapped the total count of activation at each vertex. We also analyzed 50 IEEG spikes in the same manner over the intracranial electrodes and created the activation count map. The location of the electrodes was obtained in the MEG source space by coregistering postimplantation computed tomography to MRI. We estimated the MEG- and IEEG-active regions associated with the spike populations using the vertices/electrodes with a count over 25. The activation count maps of MEG spikes demonstrated the localization associated with the spike population by variable count values at each vertex. The MEG-active region overlapped with 65 to 85% of the IEEG-active region in our patient group. Mapping the MEG spike population is valid for demonstrating the trend of spikes clustering in patients with epilepsy. In addition, comparison of MEG and IEEG spikes quantitatively may be informative for understanding their relationship.

Analyzing the Impact of Ambient Temperature Indicators on Transformer Life in Different Regions of Chinese Mainland

PubMed Central

Bai, Cui-fen; Gao, Wen-Sheng; Liu, Tong

2013-01-01

Regression analysis is applied to quantitatively analyze the impact of different ambient temperature characteristics on the transformer life at different locations of Chinese mainland. 200 typical locations in Chinese mainland are selected for the study. They are specially divided into six regions so that the subsequent analysis can be done in a regional context. For each region, the local historical ambient temperature and load data are provided as inputs variables of the life consumption model in IEEE Std. C57.91-1995 to estimate the transformer life at every location. Five ambient temperature indicators related to the transformer life are involved into the partial least squares regression to describe their impact on the transformer life. According to a contribution measurement criterion of partial least squares regression, three indicators are conclusively found to be the most important factors influencing the transformer life, and an explicit expression is provided to describe the relationship between the indicators and the transformer life for every region. The analysis result is applicable to the area where the temperature characteristics are similar to Chinese mainland, and the expressions obtained can be applied to the other locations that are not included in this paper if these three indicators are known. PMID:23843729

Analyzing the impact of ambient temperature indicators on transformer life in different regions of Chinese mainland.

PubMed

Bai, Cui-fen; Gao, Wen-Sheng; Liu, Tong

2013-01-01

Regression analysis is applied to quantitatively analyze the impact of different ambient temperature characteristics on the transformer life at different locations of Chinese mainland. 200 typical locations in Chinese mainland are selected for the study. They are specially divided into six regions so that the subsequent analysis can be done in a regional context. For each region, the local historical ambient temperature and load data are provided as inputs variables of the life consumption model in IEEE Std. C57.91-1995 to estimate the transformer life at every location. Five ambient temperature indicators related to the transformer life are involved into the partial least squares regression to describe their impact on the transformer life. According to a contribution measurement criterion of partial least squares regression, three indicators are conclusively found to be the most important factors influencing the transformer life, and an explicit expression is provided to describe the relationship between the indicators and the transformer life for every region. The analysis result is applicable to the area where the temperature characteristics are similar to Chinese mainland, and the expressions obtained can be applied to the other locations that are not included in this paper if these three indicators are known.

Comparative performance analysis of cervix ROI extraction and specular reflection removal algorithms for uterine cervix image analysis

NASA Astrophysics Data System (ADS)

Xue, Zhiyun; Antani, Sameer; Long, L. Rodney; Jeronimo, Jose; Thoma, George R.

2007-03-01

Cervicography is a technique for visual screening of uterine cervix images for cervical cancer. One of our research goals is the automated detection in these images of acetowhite (AW) lesions, which are sometimes correlated with cervical cancer. These lesions are characterized by the whitening of regions along the squamocolumnar junction on the cervix when treated with 5% acetic acid. Image preprocessing is required prior to invoking AW detection algorithms on cervicographic images for two reasons: (1) to remove Specular Reflections (SR) caused by camera flash, and (2) to isolate the cervix region-of-interest (ROI) from image regions that are irrelevant to the analysis. These image regions may contain medical instruments, film markup, or other non-cervix anatomy or regions, such as vaginal walls. We have qualitatively and quantitatively evaluated the performance of alternative preprocessing algorithms on a test set of 120 images. For cervix ROI detection, all approaches use a common feature set, but with varying combinations of feature weights, normalization, and clustering methods. For SR detection, while one approach uses a Gaussian Mixture Model on an intensity/saturation feature set, a second approach uses Otsu thresholding on a top-hat transformed input image. Empirical results are analyzed to derive conclusions on the performance of each approach.

Movement Correction Method for Human Brain PET Images: Application to Quantitative Analysis of Dynamic [18F]-FDDNP Scans

PubMed Central

Wardak, Mirwais; Wong, Koon-Pong; Shao, Weber; Dahlbom, Magnus; Kepe, Vladimir; Satyamurthy, Nagichettiar; Small, Gary W.; Barrio, Jorge R.; Huang, Sung-Cheng

2010-01-01

Head movement during a PET scan (especially, dynamic scan) can affect both the qualitative and quantitative aspects of an image, making it difficult to accurately interpret the results. The primary objective of this study was to develop a retrospective image-based movement correction (MC) method and evaluate its implementation on dynamic [18F]-FDDNP PET images of cognitively intact controls and patients with Alzheimer’s disease (AD). Methods Dynamic [18F]-FDDNP PET images, used for in vivo imaging of beta-amyloid plaques and neurofibrillary tangles, were obtained from 12 AD and 9 age-matched controls. For each study, a transmission scan was first acquired for attenuation correction. An accurate retrospective MC method that corrected for transmission-emission misalignment as well as emission-emission misalignment was applied to all studies. No restriction was assumed for zero movement between the transmission scan and first emission scan. Logan analysis with cerebellum as the reference region was used to estimate various regional distribution volume ratio (DVR) values in the brain before and after MC. Discriminant analysis was used to build a predictive model for group membership, using data with and without MC. Results MC improved the image quality and quantitative values in [18F]-FDDNP PET images. In this subject population, medial temporal (MTL) did not show a significant difference between controls and AD before MC. However, after MC, significant differences in DVR values were seen in frontal, parietal, posterior cingulate (PCG), MTL, lateral temporal (LTL), and global between the two groups (P < 0.05). In controls and AD, the variability of regional DVR values (as measured by the coefficient of variation) decreased on average by >18% after MC. Mean DVR separation between controls and ADs was higher in frontal, MTL, LTL and global after MC. Group classification by discriminant analysis based on [18F]-FDDNP DVR values was markedly improved after MC. Conclusion The streamlined and easy to use MC method presented in this work significantly improves the image quality and the measured tracer kinetics of [18F]-FDDNP PET images. The proposed MC method has the potential to be applied to PET studies on patients having other disorders (e.g., Down syndrome and Parkinson’s disease) and to brain PET scans with other molecular imaging probes. PMID:20080894

Correlation between Parameters of Calcaneal Quantitative Ultrasound and Hip Structural Analysis in Osteoporotic Fracture Patients

PubMed Central

Zheng, Hailiang; Li, Ming; Yin, Pengbin; Peng, Ye; Gao, Yuan; Zhang, Lihai; Tang, Peifu

2015-01-01

Background Calcaneal quantitative ultrasound (QUS), which is used in the evaluation of osteoporosis, is believed to be intimately associated with the characteristics of the proximal femur. However, the specific associations of calcaneal QUS with characteristics of the hip sub-regions remain unclear. Design A cross-sectional assessment of 53 osteoporotic patients was performed for the skeletal status of the heel and hip. Methods We prospectively enrolled 53 female osteoporotic patients with femoral fractures. Calcaneal QUS, dual energy X-ray absorptiometry (DXA), and hip structural analysis (HSA) were performed for each patient. Femoral heads were obtained during the surgery, and principal compressive trabeculae (PCT) were extracted by a three-dimensional printing technique-assisted method. Pearson’s correlation between QUS measurement with DXA, HSA-derived parameters and Young’s modulus were calculated in order to evaluate the specific association of QUS with the parameters for the hip sub-regions, including the femoral neck, trochanteric and Ward’s areas, and the femoral shaft, respectively. Results Significant correlations were found between estimated BMD (Est.BMD) and BMD of different sub-regions of proximal femur. However, the correlation coefficient of trochanteric area (r = 0.356, p = 0.009) was higher than that of the neck area (r = 0.297, p = 0.031) and total proximal femur (r = 0.291, p = 0.034). Furthermore, the quantitative ultrasound index (QUI) was significantly correlated with the HSA-derived parameters of the trochanteric area (r value: 0.315–0.356, all p<0.05) as well as with the Young’s modulus of PCT from the femoral head (r = 0.589, p<0.001). Conclusion The calcaneal bone had an intimate association with the trochanteric cancellous bone. To a certain extent, the parameters of the calcaneal QUS can reflect the characteristics of the trochanteric area of the proximal hip, although not specifically reflective of those of the femoral neck or shaft. PMID:26710123

Predicting Future Morphological Changes of Lesions from Radiotracer Uptake in 18F-FDG-PET Images

PubMed Central

Bagci, Ulas; Yao, Jianhua; Miller-Jaster, Kirsten; Chen, Xinjian; Mollura, Daniel J.

2013-01-01

We introduce a novel computational framework to enable automated identification of texture and shape features of lesions on 18F-FDG-PET images through a graph-based image segmentation method. The proposed framework predicts future morphological changes of lesions with high accuracy. The presented methodology has several benefits over conventional qualitative and semi-quantitative methods, due to its fully quantitative nature and high accuracy in each step of (i) detection, (ii) segmentation, and (iii) feature extraction. To evaluate our proposed computational framework, thirty patients received 2 18F-FDG-PET scans (60 scans total), at two different time points. Metastatic papillary renal cell carcinoma, cerebellar hemongioblastoma, non-small cell lung cancer, neurofibroma, lymphomatoid granulomatosis, lung neoplasm, neuroendocrine tumor, soft tissue thoracic mass, nonnecrotizing granulomatous inflammation, renal cell carcinoma with papillary and cystic features, diffuse large B-cell lymphoma, metastatic alveolar soft part sarcoma, and small cell lung cancer were included in this analysis. The radiotracer accumulation in patients' scans was automatically detected and segmented by the proposed segmentation algorithm. Delineated regions were used to extract shape and textural features, with the proposed adaptive feature extraction framework, as well as standardized uptake values (SUV) of uptake regions, to conduct a broad quantitative analysis. Evaluation of segmentation results indicates that our proposed segmentation algorithm has a mean dice similarity coefficient of 85.75±1.75%. We found that 28 of 68 extracted imaging features were correlated well with SUVmax (p<0.05), and some of the textural features (such as entropy and maximum probability) were superior in predicting morphological changes of radiotracer uptake regions longitudinally, compared to single intensity feature such as SUVmax. We also found that integrating textural features with SUV measurements significantly improves the prediction accuracy of morphological changes (Spearman correlation coefficient = 0.8715, p<2e-16). PMID:23431398

Brain Responses to Dynamic Facial Expressions: A Normative Meta-Analysis.

PubMed

Zinchenko, Oksana; Yaple, Zachary A; Arsalidou, Marie

2018-01-01

Identifying facial expressions is crucial for social interactions. Functional neuroimaging studies show that a set of brain areas, such as the fusiform gyrus and amygdala, become active when viewing emotional facial expressions. The majority of functional magnetic resonance imaging (fMRI) studies investigating face perception typically employ static images of faces. However, studies that use dynamic facial expressions (e.g., videos) are accumulating and suggest that a dynamic presentation may be more sensitive and ecologically valid for investigating faces. By using quantitative fMRI meta-analysis the present study examined concordance of brain regions associated with viewing dynamic facial expressions. We analyzed data from 216 participants that participated in 14 studies, which reported coordinates for 28 experiments. Our analysis revealed bilateral fusiform and middle temporal gyri, left amygdala, left declive of the cerebellum and the right inferior frontal gyrus. These regions are discussed in terms of their relation to models of face processing.

Paradoxes of the comparative analysis of ground-based and satellite geodetic measurements in recent geodynamics

NASA Astrophysics Data System (ADS)

Kuzmin, Yu. O.

2017-11-01

The comparative analysis of the Earth's surface deformations measured by ground-based and satellite geodetic methods on the regional and zonal measurement scales is carried out. The displacement velocities and strain rates are compared in the active regions such as Turkmenian-Iranian zone of interaction of the Arabian and Eurasian lithospheric plates and the Kamchatka segment of the subduction of the Pacific Plate beneath the Okotsk Plate. The comparison yields a paradoxical result. With the qualitatively identical kinematics of the motion, the quantitative characteristics of the displacement velocities and rates of strain revealed by the observations using the global navigational satellite system (GNSS) are by 1-2 orders of magnitude higher than those estimated by the more accurate methods of ground-based geodesy. For resolving the revealed paradoxes, it is required to set up special studies on the joint analysis of ground-based and satellite geodetic data from the combined observation sites.

Spatial analysis on future housing markets: economic development and housing implications.

PubMed

Liu, Xin; Wang, Lizhe

2014-01-01

A coupled projection method combining formal modelling and other statistical techniques was developed to delineate the relationship between economic and social drivers for net new housing allocations. Using the example of employment growth in Tyne and Wear, UK, until 2016, the empirical analysis yields housing projections at the macro- and microspatial levels (e.g., region to subregion to elected ward levels). The results have important implications for the strategic planning of locations for housing and employment, demonstrating both intuitively and quantitatively how local economic developments affect housing demand.

Utility of correlation techniques in gravity and magnetic interpretation

NASA Technical Reports Server (NTRS)

Chandler, V. W.; Koski, J. S.; Braile, L. W.; Hinze, W. J.

1977-01-01

Two methods of quantitative combined analysis, internal correspondence and clustering, are presented. Model studies are used to illustrate implementation and interpretation procedures of these methods, particularly internal correspondence. Analysis of the results of applying these methods to data from the midcontinent and a transcontinental profile show they can be useful in identifying crustal provinces, providing information on horizontal and vertical variations of physical properties over province size zones, validating long wave-length anomalies, and isolating geomagnetic field removal problems. Thus, these techniques are useful in considering regional data acquired by satellites.

Interdisciplinary study of atmospheric processes and constituents of the mid-Atlantic coastal region.. [air pollution control studies in Virginia

NASA Technical Reports Server (NTRS)

Kindle, E. C.; Bandy, E. C.; Copeland, G.; Blais, R.; Levy, G.; Sonenshine, D.

1975-01-01

Past research projects for the year 1974-1975 are listed along with future research programs in the area of air pollution control, remote sensor analysis of smoke plumes, the biosphere component, and field experiments. A detailed budget analysis is presented. Attachments are included on the following topics: mapping forest vegetation with ERTS-1 MSS data and automatic data processing techniques, and use of LARS system for the quantitative determination of smoke plume lateral diffusion coefficients from ERTS images of Virginia.

Spatial Analysis on Future Housing Markets: Economic Development and Housing Implications

PubMed Central

Liu, Xin; Wang, Lizhe

2014-01-01

A coupled projection method combining formal modelling and other statistical techniques was developed to delineate the relationship between economic and social drivers for net new housing allocations. Using the example of employment growth in Tyne and Wear, UK, until 2016, the empirical analysis yields housing projections at the macro- and microspatial levels (e.g., region to subregion to elected ward levels). The results have important implications for the strategic planning of locations for housing and employment, demonstrating both intuitively and quantitatively how local economic developments affect housing demand. PMID:24892097

The superiority of indium ratio over blood pool subtraction in analysis of indium-111 platelet deposition on thoraco-abdominal prosthetic grafts

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

Ripley, S.; Wakefield, T.; Spaulding, S.

1985-05-01

In this investigation platelet deposition in polytetrafluroethylene (PTFE) thoracoabdominal grafts (TAC's) was evaluated using two different semi-quantitative techniques. Ten PTFE TAG's 6 mm in diameter and 30 cm in length were inserted into 10 mongrel dogs. One, 4 and 6 weeks after graft implantation the animals were injected with autologous In-111 platelets labelled by a modified Thakur technique. Platelet imaging in grafts was performed 48 hrs after injection. Blood pool was determined by Tc99m labelled RBC's (in vivo/in vitro technique). Semi-quantitative analysis was performed by subdividing the imaged graft into three major regions and selecting a reference region from eithermore » the native aorta or common iliac artery. Excess platelet deposition was determined by two methods: 1) the ratio of In-111 counts in the graft ROI''s to the reference region and 2) the percent In-111 excess using the Tc99m blood pool subtraction technique (TBPST). Animals were sacrificed 7 weeks after implantation and radioactivity in the excised grafts was determined using a well counter. A positive correlation was found to exist between the In-111 ratio percent analysis (IRPA) and the direct gamma counting (DCC) for all three segments of the prosthetic graft. Correlation coefficients for the thorax, midsegment and abdominal segments were 0.80, 0.73 and 0.48 respectivly. There was no correlation between TBPST and DGC. Using the IRPA technique the thrombogenicity of TAG's can be routinely assessed and is clinically applicable for patient use. TBPST should probably be limited to the extremities to avoid error due to free Tc99m counts from kidneys and ureters.« less

Comparison of Grid Nudging and Spectral Nudging Techniques for Dynamical Climate Downscaling within the WRF Model

NASA Astrophysics Data System (ADS)

Fan, X.; Chen, L.; Ma, Z.

2010-12-01

Climate downscaling has been an active research and application area in the past several decades focusing on regional climate studies. Dynamical downscaling, in addition to statistical methods, has been widely used in downscaling as the advanced modern numerical weather and regional climate models emerge. The utilization of numerical models enables that a full set of climate variables are generated in the process of downscaling, which are dynamically consistent due to the constraints of physical laws. While we are generating high resolution regional climate, the large scale climate patterns should be retained. To serve this purpose, nudging techniques, including grid analysis nudging and spectral nudging, have been used in different models. There are studies demonstrating the benefit and advantages of each nudging technique; however, the results are sensitive to many factors such as nudging coefficients and the amount of information to nudge to, and thus the conclusions are controversy. While in a companion work of developing approaches for quantitative assessment of the downscaled climate, in this study, the two nudging techniques are under extensive experiments in the Weather Research and Forecasting (WRF) model. Using the same model provides fair comparability. Applying the quantitative assessments provides objectiveness of comparison. Three types of downscaling experiments were performed for one month of choice. The first type is serving as a base whereas the large scale information is communicated through lateral boundary conditions only; the second is using the grid analysis nudging; and the third is using spectral nudging. Emphases are given to the experiments of different nudging coefficients and nudging to different variables in the grid analysis nudging; while in spectral nudging, we focus on testing the nudging coefficients, different wave numbers on different model levels to nudge.

Regional Distribution of Pulmonary Blood Volume with Dual-Energy Computed Tomography: Results in 42 Subjects.

PubMed

Felloni, Paul; Duhamel, Alain; Faivre, Jean-Baptiste; Giordano, Jessica; Khung, Suonita; Deken, Valérie; Remy, Jacques; Remy-Jardin, Martine

2017-11-01

The noninvasive approach of lung perfusion generated from dual-energy computed tomography acquisitions has entered clinical practice. The purpose of this study was to analyze the regional distribution of iodine within distal portions of the pulmonary arterial bed on dual-source, dual-energy computed tomography examinations in a cohort of subjects without cardiopulmonary pathologies. The study population included 42 patients without cardiorespiratory disease, enabling quantitative and qualitative analysis of pulmonary blood volume after administration of a 40% contrast agent. Qualitative analysis was based on visual assessment. Quantitative analysis was obtained after semiautomatic division of each lung into 18 areas. The iodine concentration did not significantly differ between the right (R) and left (L) lungs (P = .49), with a mean attenuation of 41.35 Hounsfield units (HU) and 41.14 HU, respectively. Three regional gradients of attenuation were observed between: (a) lung bases and apices (P < .001), linked to the conditions of examination (mean Δ: 6.23 in the R lung; 5.96 in the L lung); (b) posterior and anterior parts of the lung (P < .001) due to gravity (mean Δ: 11.92 in the R lung ; 15.93 in the L lung); and (c) medullary and cortical lung zones (P < .001) (mean Δ: 9.35 in the R lung ; 8.37 in the L lung). The intensity of dependent-nondependent (r = 0.42; P < .001) and corticomedullary (r = 0.58; P < .0001) gradients was correlated to the overall iodine concentration. Distribution of pulmonary blood volume is influenced by physiological gradients and scanning conditions. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Usefulness of myocardial parametric imaging to evaluate myocardial viability in experimental and in clinical studies.

PubMed

Korosoglou, G; Hansen, A; Bekeredjian, R; Filusch, A; Hardt, S; Wolf, D; Schellberg, D; Katus, H A; Kuecherer, H

2006-03-01

To evaluate whether myocardial parametric imaging (MPI) is superior to visual assessment for the evaluation of myocardial viability. Myocardial contrast echocardiography (MCE) was assessed in 11 pigs before, during, and after left anterior descending coronary artery occlusion and in 32 patients with ischaemic heart disease by using intravenous SonoVue administration. In experimental studies perfusion defect area assessment by MPI was compared with visually guided perfusion defect planimetry. Histological assessment of necrotic tissue was the standard reference. In clinical studies viability was assessed on a segmental level by (1) visual analysis of myocardial opacification; (2) quantitative estimation of myocardial blood flow in regions of interest; and (3) MPI. Functional recovery between three and six months after revascularisation was the standard reference. In experimental studies, compared with visually guided perfusion defect planimetry, planimetric assessment of infarct size by MPI correlated more significantly with histology (r2 = 0.92 versus r2 = 0.56) and had a lower intraobserver variability (4% v 15%, p < 0.05). In clinical studies, MPI had higher specificity (66% v 43%, p < 0.05) than visual MCE and good accuracy (81%) for viability detection. It was less time consuming (3.4 (1.6) v 9.2 (2.4) minutes per image, p < 0.05) than quantitative blood flow estimation by regions of interest and increased the agreement between observers interpreting myocardial perfusion (kappa = 0.87 v kappa = 0.75, p < 0.05). MPI is useful for the evaluation of myocardial viability both in animals and in patients. It is less time consuming than quantification analysis by regions of interest and less observer dependent than visual analysis. Thus, strategies incorporating this technique may be valuable for the evaluation of myocardial viability in clinical routine.

4D MEMRI atlas of neonatal FVB/N mouse brain development.

PubMed

Szulc, Kamila U; Lerch, Jason P; Nieman, Brian J; Bartelle, Benjamin B; Friedel, Miriam; Suero-Abreu, Giselle A; Watson, Charles; Joyner, Alexandra L; Turnbull, Daniel H

2015-09-01

The widespread use of the mouse as a model system to study brain development has created the need for noninvasive neuroimaging methods that can be applied to early postnatal mice. The goal of this study was to optimize in vivo three- (3D) and four-dimensional (4D) manganese (Mn)-enhanced MRI (MEMRI) approaches for acquiring and analyzing data from the developing mouse brain. The combination of custom, stage-dependent holders and self-gated (motion-correcting) 3D MRI sequences enabled the acquisition of high-resolution (100-μm isotropic), motion artifact-free brain images with a high level of contrast due to Mn-enhancement of numerous brain regions and nuclei. We acquired high-quality longitudinal brain images from two groups of FVB/N strain mice, six mice per group, each mouse imaged on alternate odd or even days (6 3D MEMRI images at each day) covering the developmental stages between postnatal days 1 to 11. The effects of Mn-exposure, anesthesia and MRI were assessed, showing small but significant transient effects on body weight and brain volume, which recovered with time and did not result in significant morphological differences when compared to controls. Metrics derived from deformation-based morphometry (DBM) were used for quantitative analysis of changes in volume and position of a number of brain regions. The cerebellum, a brain region undergoing significant changes in size and patterning at early postnatal stages, was analyzed in detail to demonstrate the spatiotemporal characterization made possible by this new atlas of mouse brain development. These results show that MEMRI is a powerful tool for quantitative analysis of mouse brain development, with great potential for in vivo phenotype analysis in mouse models of neurodevelopmental diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

Determination of Paleoseismic Ground Motions from Inversion of Block Failures in Masonry Structures

NASA Astrophysics Data System (ADS)

Yagoda-Biran, G.; Hatzor, Y. H.

2010-12-01

Accurate estimation of ground motion parameters such as expected peak ground acceleration (PGA), predominant frequency and duration of motion in seismically active regions, is crucial for hazard preparedness and sound engineering design. The best way to estimate quantitatively these parameters would be to investigate long term recorded data of past strong earthquakes in a studied region. In some regions of the world however recorded data are scarce due to lack of seismic network infrastructure, and in all regions the availability of recorded data is restricted to the late 19th century and onwards. Therefore, existing instrumental data are hardly representative of the true seismicity of a region. When recorded data are scarce or not available, alternative methods may be applied, for example adopting a quantitative paleoseismic approach. In this research we suggest the use of seismically damaged masonry structures as paleoseismic indicators. Visitors to archeological sites all over the world are often struck by structural failure features which seem to be "seismically driven", particularly when inspecting old masonry structures. While it is widely accepted that no other loading mechanism can explain the preserved damage, the actual driving mechanism remains enigmatic even now. In this research we wish to explore how such failures may be triggered by earthquake induced ground motions and use observed block displacements to determine the characteristic parameters of the paleoseismic earthquake motion, namely duration, frequency, and amplitude. This is performed utilizing a 3D, fully dynamic, numerical analysis performed with the Discontinuous Deformation Analysis (DDA) method. Several case studies are selected for 3D numerical analysis. First we study a simple structure in the old city of L'Aquila, Italy. L'Aquila was hit by an earthquake on April 6th, 2009, with over 300 casualties and many of its medieval buildings damaged. This case study is an excellent opportunity to validate our method, since in the case of L'Aquila, both the damaged structure and the ground motions are recorded. The 3D modeling of the structure is rather complicated, and is performed by first modeling the structure with CAD software and later "translating" the model to the numerical code used. In the future, several more case studies will be analyzed, such as Kedesh and Avdat in Israel, and in collaboration with Hugh and Bilham the Temple of Shiva at Pandrethan, Kashmir. Establishing a numerical 3D dynamic analysis for back analysis of stone displacement in masonry structures as a paleoseismic tool can provide much needed data on ground motion parameters in regions where instrumental data are scarce, or are completely absent.

Automatic Detection of Decadal Shoreline Change on Northern Coastal of Gresik, East Java - Indonesia

NASA Astrophysics Data System (ADS)

Fuad, M. A. Z.; A, M. Fais D.

2017-12-01

The Coastal zone is a dynamic region that has high environmental and economic values. This present research focuses on the analyzing the rate of shoreline change using multi-temporal Landsat Imagery and Digital Shoreline Analysis Systems (DSAS) along the northern part of Gresik coastal area, East Java Indonesia. Five village were selected for analysis; Campurejo, Dalegan, Prupuh, Ngemboh, and Banyuurip. Erosion and Accretion were observed and detected on Multi-temporal satellite Images along the area of interest from 1972 - 2016. Landsat Images were radiometrically and geometrically corrected before using for analysis. Coastline delineation for each Landsat image was performed by MNDWI method before digitized for quantitative shoreline change analysis. DSAS was performed for quantitative analysis of Net Shoreline Movement (NSM) and End Point Rate (EPR). The results indicate that in the study area accretion and abrasion was occurred, but overall abrasion was dominated than accretion. The remarkable shoreline changes were observed in the entire region. The highest abrasion area was occurred in Ngemboh village. From 1972 to 2016, coastline was retreat 242.56 meter to the land and the rate of movement was -5.54m/yr. In contrast, Campurejo area was relatively stable due to the introduction of manmade structure, i.e. Jetty and Groin. The Shoreline movement and the rate of movement in this area were -6.11m and -0.12 m/yr respectively. The research represents an important step in understanding the dynamics of coastal area in this area. By identification and analysis of coastline evolution, the stake holder could perform a scenario for reducing the risk of coastal erosion and minimize the social and economic lost.

Spatio-temporal patterns of foot-and-mouth disease transmission in cattle between 2007 and 2015 and quantitative assessment of the economic impact of the disease in Niger.

PubMed

Souley Kouato, B; Thys, E; Renault, V; Abatih, E; Marichatou, H; Issa, S; Saegerman, C

2018-03-05

Foot-and-mouth disease (FMD) is endemic in Niger, with outbreaks occurring every year. Recently, there was an increasing interest from veterinary authorities to implement preventive and control measures against FMD. However, for an efficient control, improving the current knowledge on the disease dynamics and factors related to FMD occurrence is a prerequisite. The objective of this study was therefore to obtain insights into the incidence and the spatio-temporal patterns of transmission of FMD outbreaks in Niger based on the retrospective analysis of 9-year outbreak data. A regression tree analysis model was used to identify statistically significant predictors associated with FMD incidence, including the period (year and month), the location (region), the animal-contact density and the animal-contact frequency. This study provided also a first report on economic losses associated with FMD. From 2007 to 2015, 791 clinical FMD outbreaks were reported from the eight regions of Niger, with the number of outbreaks per region ranging from 5 to 309. The statistical analysis revealed that three regions (Dosso, Tillabery and Zinder), the months (September, corresponding to the end of rainy season, to December and January, i.e., during the dry and cold season), the years (2007 and 2015) and the density of contact were the main predictors of FMD occurrence. The quantitative assessment of the economic impacts showed that the average total cost of FMD at outbreak level was 499 euros, while the average price for FMD vaccination of one outbreak was estimated to be more than 314 euros. Despite some limitations of the clinical data used, this study will guide further research into the epidemiology of FMD in Niger and will promote a better understanding of the disease as well as an efficient control and prevention of FMD. © 2018 Blackwell Verlag GmbH.

Characterizing the anthropogenic signature in the LCLU dynamics in the Central Asia region

NASA Astrophysics Data System (ADS)

Tatarskii, V.; Sokolik, I. N.; de Beurs, K.; Shiklomanov, A. I.

2017-12-01

Humans have been changing the LCLU dynamics over time through the world. In the Central Asia region, these changes have been especially pronounced due to the political and economic transformation. We present a detailed analysis, focusing on identifying and quantifying the anthropogenic signature in the water and land use across the region. We have characterized the anthropogenic dust emission by combining the modeling and observations. The model is a fully coupled model called WRF-Chem-DuMo that takes explicitly into account the vegetation treatment in modeling the dust emission. We have reconstructed the anthropogenic dust sources in the region, such as the retreat of the Aral Sea, changes in agricultural fields, etc. In addition, we characterize the anthropogenic water use dynamics, including the changes in the water use for the agricultural production. Furthermore, we perform an analysis to identify the anthropogenic signature in the NDVI pattern. The NDVI were analyzed in conjunction with the meteorological fields that were simulated at the high special resolution using the WRF model. Meteorological fields of precipitation and temperature were used for the correlation analysis to separate the natural vs. anthropogenic changes. In this manner, we were able to identify the regions that have been affected by human activities. We will present the quantitative assessment of the anthropogenic changes. The diverse consequences for the economy of the region, as well as, the environment will be addressed.

Modelling irrigated maize with a combination of coupled-model simulation and uncertainty analysis, in the northwest of China

NASA Astrophysics Data System (ADS)

Li, Y.; Kinzelbach, W.; Zhou, J.; Cheng, G. D.; Li, X.

2012-05-01

The hydrologic model HYDRUS-1-D and the crop growth model WOFOST are coupled to efficiently manage water resources in agriculture and improve the prediction of crop production. The results of the coupled model are validated by experimental studies of irrigated-maize done in the middle reaches of northwest China's Heihe River, a semi-arid to arid region. Good agreement is achieved between the simulated evapotranspiration, soil moisture and crop production and their respective field measurements made under current maize irrigation and fertilization. Based on the calibrated model, the scenario analysis reveals that the most optimal amount of irrigation is 500-600 mm in this region. However, for regions without detailed observation, the results of the numerical simulation can be unreliable for irrigation decision making owing to the shortage of calibrated model boundary conditions and parameters. So, we develop a method of combining model ensemble simulations and uncertainty/sensitivity analysis to speculate the probability of crop production. In our studies, the uncertainty analysis is used to reveal the risk of facing a loss of crop production as irrigation decreases. The global sensitivity analysis is used to test the coupled model and further quantitatively analyse the impact of the uncertainty of coupled model parameters and environmental scenarios on crop production. This method can be used for estimation in regions with no or reduced data availability.

Myelination progression in language-correlated regions in brain of normal children determined by quantitative MRI assessment.

PubMed

Su, Peijen; Kuan, Chen-Chieh; Kaga, Kimitaka; Sano, Masaki; Mima, Kazuo

2008-12-01

To investigate the myelination progression course in language-correlated regions of children with normal brain development by quantitative magnetic resonance imaging (MRI) analysis compared with histological studies. The subjects were 241 neurologically intact neonates, infants and young children (128 boys and 113 girls) who underwent MRI between 2001 and 2007 at the University of Tokyo Hospital, ranging in age from 0 to 429 weeks corrected by postnatal age. To compare their data with adult values, 25 adolescents and adults (14 men and 11 women, aged from 14 to 83 years) were examined as controls. Axial T2-weighted images were obtained using spin-echo sequences at 1.5 T. Subjects with a history of prematurity, birth asphyxia, low Apgar score, seizures, active systemic disease, congenital anomaly, delayed development, infarcts, hemorrhages, brain lesions, or central nervous system malformation were excluded from the analysis. Seven regions of interest in language-correlated areas, namely Broca's area, Wernicke's area, the arcuate fasciculus, and the angular gyrus, as well as their right hemisphere homologous regions, and the auditory cortex, the motor cortex, and the visual cortex were examined. Signal intensity obtained by a region-of-interest methodology progresses from hyper- to hypointensity during myelination. We chose the inferior cerebellar peduncle as the internal standard of maturation. Myelination in all these seven language-correlated regions examined in this study shared the same curve pattern: no myelination was observed at birth, it reached maturation at about 1.5 years of age, and it continued to progress slowly thereafter into adult life. On the basis of scatter plot results, we put these areas into three groups: Group A, which included the motor cortex, the auditory cortex, and the visual cortex, myelinated faster than Group B, which included Broca's area, Wernicke's area, and the angular gyrus before 1.5 years old; Group C, consisting of the arcuate fasciculus, has similar degree of myelination as Group B before 1.5 years but then myelinated more slowly after 3 years of age. No gender or left-right differences between homologous regions were found. In this study, we determined the sequence of myelination of language-correlated regions in infants and children by quantitative MRI assessment. The higher cortical areas matured later than the primary cortical areas, and the arcuate fasciculus matured last. The observation that myelination reaches maturity after 18 months suggests that myelination may be a reason for the acceleration in vocabulary acquisition observed in children from that age. The slow pace of myelination also suggested the possibility of language development's continuation into early adult life. Myelination assessed by MRI was at least 1 month behind that assessed by histological staining. No gender or left-right hemisphere differences in myelination were noted.

How does landscape structure influence catchment transit time across different geomorphic provinces?

USGS Publications Warehouse

Tetzlaff, D.; Seibert, J.; McGuire, K.J.; Laudon, H.; Burns, Douglas A.; Dunn, S.M.; Soulsby, C.

2009-01-01

Despite an increasing number of empirical investigations of catchment transit times (TTs), virtually all are based on individual catchments and there are few attempts to synthesize understanding across different geographical regions. Uniquely, this paper examines data from 55 catchments in five geomorphic provinces in northern temperate regions (Scotland, United States of America and Sweden). The objective is to understand how the role of catchment topography as a control on the TTs differs in contrasting geographical settings. Catchment inverse transit time proxies (ITTPs) were inferred by a simple metric of isotopic tracer damping, using the ratio of standard deviation of ??18O in streamwater to the standard deviation of ??18O in precipitation. Quantitative landscape analysis was undertaken to characterize the catchments according to hydrologically relevant topographic indices that could be readily determined from a digital terrain model (DTM). The nature of topographic controls on transit times varied markedly in different geomorphic regions. In steeper montane regions, there are stronger gravitational influences on hydraulic gradients and TTs tend to be lower in the steepest catchments. In provinces where terrain is more subdued, direct topographic control weakened; in particular, where flatter areas with less permeable soils give rise to overland flow and lower TTs. The steeper slopes within this flatter terrain appear to have a greater coverage of freely draining soils, which increase sub-surface flow, therefore increasing TTs. Quantitative landscape analysis proved a useful tool for intercatchment comparison. However, the critical influence of sub-surface permeability and connectivity may limit the transferability of predictive tools of hydrological function based on topographic parameters alone. Copyright ?? 2009 John Wiley & Sons, Ltd.

How a Country-Wide Seismological Network Can Improve Understanding of Seismicity and Seismic Hazard -- The Example of Bhutan

NASA Astrophysics Data System (ADS)

Hetényi, G.; Diehl, T.; Singer, J.; Kissling, E. H.; Clinton, J. F.; Wiemer, S.

2015-12-01

The Eastern Himalayas are home to a seemingly complex seismo-tectonic evolution. The rate of instrumental seismicity is lower than the average along the orogen, there is no record of large historical events, but both paleoseismology and GPS studies point to potentially large (M>8) earthquakes. Due to the lack of a permanent seismic monitoring system in the area, our current level of understanding is inappropriate to create a reliable quantitative seismic hazard model for the region. Existing maps are based on questionable hypotheses and show major inconsistencies when compared to each other. Here we present results on national and regional scales from a 38-station broadband seismological network we operated for almost 2 years in the Kingdom of Bhutan. A thorough, state-of-the-art analysis of local and regional earthquakes builds a comprehensive catalogue that reveals significantly (2-to-3 orders of magnitude) more events than detected from global networks. The seismotectonic analysis reveals new patterns of seismic activity as well as striking differences over relatively short distances within the Himalayas, only partly explained by surface observations such as geology. We compare a priori and a posteriori (BMC) magnitude of completeness maps and show that our network was able to detect all felt events during its operation. Some of these events could be felt at surprisingly large distances. Based on our experiment and experience, we draft the pillars on which a permanent seismological observatory for Bhutan could be constructed. Such a continuous monitoring system of seismic activity could then lead to a reliable quantitative seismic hazard model for Bhutan and surrounding regions, and serve as a base to improve building codes and general preparedness.

Geohydrologic systems in Kansas; physical framework of the confining unit in the Western Interior Plains aquifer system

USGS Publications Warehouse

Hansen, C.V.; Wolf, R.J.; Spinazola, J.M.

1992-01-01

The purpose of this Hydrologic Investigations Atlas is to provide a description of the geohydrologic systems in Upper Cambrian through Lower Cretaceous rocks in Kansas. This investigation was made as part of the Central Midwest Regional Aquifer-System Analysis (CMRASA). The CMRASA is one of several major investigations by the U.S. Geological Survey of regional aquifer systems in the United States. These regional investigations are designed to increase knowledge of the flow regime and hydrologic properties of major aquifer systems and to provide quantitative information for the assessment, development, and management of water supplies. The CMRASA study area includes all or parts of 10 Central Midwestern States (Jorgensen and Signor, 1981), as shown on the envelope cover.

Geohydrologic systems in Kansas physical framework of the western interior plains confining system

USGS Publications Warehouse

Wolf, R.J.; McGovern, Harold E.; Spinazola, Joseph M.

1992-01-01

The purpose of this Hydrologic Investigations Atlas is to provide a description of the principal geohydrologic systems in the Upper Cambrian through Lower Cretaceous rocks in Kansas.  This investigation was made as part of the Central Midwest Regional Aquifer-System Analysis (CMRASA). The CMRASA is one of several major investigations by the U.S. Geological Survey of regional aquifer systems in the United States. These regional investigations are designed to increase knowledge of the flow regime and hydrologic properties of major aquifer systems and to provide quantitative information for assessing, developing, and managing water supplies.  The CMRASA study area includes all or parts of 10 Central Midwestern States (Jorgensen and Signor, 1981) as shown on the envelope cover.

Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle

PubMed Central

2012-01-01

Background Significant quantitative trait loci (QTL) for carcass weight were previously mapped on several chromosomes in Japanese Black half-sib families. Two QTL, CW-1 and CW-2, were narrowed down to 1.1-Mb and 591-kb regions, respectively. Recent advances in genomic tools allowed us to perform a genome-wide association study (GWAS) in cattle to detect associations in a general population and estimate their effect size. Here, we performed a GWAS for carcass weight using 1156 Japanese Black steers. Results Bonferroni-corrected genome-wide significant associations were detected in three chromosomal regions on bovine chromosomes (BTA) 6, 8, and 14. The associated single nucleotide polymorphisms (SNP) on BTA 6 were in linkage disequilibrium with the SNP encoding NCAPG Ile442Met, which was previously identified as a candidate quantitative trait nucleotide for CW-2. In contrast, the most highly associated SNP on BTA 14 was located 2.3-Mb centromeric from the previously identified CW-1 region. Linkage disequilibrium mapping led to a revision of the CW-1 region within a 0.9-Mb interval around the associated SNP, and targeted resequencing followed by association analysis highlighted the quantitative trait nucleotides for bovine stature in the PLAG1-CHCHD7 intergenic region. The association on BTA 8 was accounted for by two SNP on the BovineSNP50 BeadChip and corresponded to CW-3, which was simultaneously detected by linkage analyses using half-sib families. The allele substitution effects of CW-1, CW-2, and CW-3 were 28.4, 35.3, and 35.0 kg per allele, respectively. Conclusion The GWAS revealed the genetic architecture underlying carcass weight variation in Japanese Black cattle in which three major QTL accounted for approximately one-third of the genetic variance. PMID:22607022

Quantitative analysis of cardiovascular MR images.

PubMed

van der Geest, R J; de Roos, A; van der Wall, E E; Reiber, J H

1997-06-01

The diagnosis of cardiovascular disease requires the precise assessment of both morphology and function. Nearly all aspects of cardiovascular function and flow can be quantified nowadays with fast magnetic resonance (MR) imaging techniques. Conventional and breath-hold cine MR imaging allow the precise and highly reproducible assessment of global and regional left ventricular function. During the same examination, velocity encoded cine (VEC) MR imaging provides measurements of blood flow in the heart and great vessels. Quantitative image analysis often still relies on manual tracing of contours in the images. Reliable automated or semi-automated image analysis software would be very helpful to overcome the limitations associated with the manual and tedious processing of the images. Recent progress in MR imaging of the coronary arteries and myocardial perfusion imaging with contrast media, along with the further development of faster imaging sequences, suggest that MR imaging could evolve into a single technique ('one stop shop') for the evaluation of many aspects of heart disease. As a result, it is very likely that the need for automated image segmentation and analysis software algorithms will further increase. In this paper the developments directed towards the automated image analysis and semi-automated contour detection for cardiovascular MR imaging are presented.

Geospatial Analysis of Grey Wolf Movement Patterns

NASA Astrophysics Data System (ADS)

Sur, D.

2017-12-01

The grey wolf is a top predator that lives across a diverse habitat, ranging from Europe to North America. They often hunt in packs, preferring caribou, deer and elk as prey. Currently, many gray wolves live in Denali National Park and Preserve. In this study, several wolf packs were studied in three distinct regions of Denali. The purpose of my research was to investigate the links between wolf habitat, movement patterns, and prey thresholds. These are needed for projecting future population, growth and distribution of wolves in the studied region. I also investigated the effect wolves have on the ecological structure of the communities they inhabit. In the study I carried out a quantitative analysis of wolf population trends and daily distance movement by utilizing an analysis of variance (ANOVA) in the program JmpPro12 (SAS Institute, Crary, NC) to assess regional differences in pack size, wolf density, average daily distance moved. I found a clear link between the wolf habitat and prey thresholds; the habitat directly influences the types of prey available. However there was no link between the daily distance movement, the wolf habitat and prey density.

A qualitative and quantitative analysis of risk perception and treatment options as related to wildfires in the USDA FS Region 3 National Forests

Treesearch

Ingrid M. Martin; Wade E. Martin; Carol B. Raish

2011-01-01

As the incidence of devastating fires rises, managing the risk posed by these fires has become critical. This report provides important information to examine the ways that different groups or disaster subcultures develop the mentalities or perceived realities that affect their views and responses concerning risk and disaster preparedness. Fire risk beliefs and...

Isolation and Identification of Lactic Acid Bacteria from Traditional Dairy Products in Baotou and Bayannur of Midwestern Inner Mongolia and q-PCR Analysis of Predominant Species

PubMed Central

2016-01-01

In this study, traditional culture method and 16S rRNA gene analysis were applied to reveal the composition and diversity of lactic acid bacteria (LAB) of fermented cow milk, huruud and urum from Baotou and Bayannur of midwestern Inner Mongolia. Also, the quantitative results of dominant LAB species in three different types of dairy products from Baotou and Bayannur were gained by quantitative polymerase chain reaction (q-PCR) technology. Two hundred and two LAB strains isolated from sixty-six samples were identified and classified into four genera, namely Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, and twenty-one species and subspecies. From these isolates, Lactococcus lactis subsp. lactis (32.18%), Lactobacillus plantarum (12.38%) and Leuconosto mesenteroides (11.39%) were considered as the dominated LAB species under the condition of cultivating in MRS and M17 medium. And the q-PCR results revealed that the number of dominant species varied from samples to samples and from region to region. This study clearly shows the composition and diversity of LAB existing in fermented cow milk, huruud and urum, which could be considered as valuable resources for LAB isolation and further probiotic selection. PMID:27621691

Improving efficacy of metastatic tumor segmentation to facilitate early prediction of ovarian cancer patients' response to chemotherapy

NASA Astrophysics Data System (ADS)

Danala, Gopichandh; Wang, Yunzhi; Thai, Theresa; Gunderson, Camille C.; Moxley, Katherine M.; Moore, Kathleen; Mannel, Robert S.; Cheng, Samuel; Liu, Hong; Zheng, Bin; Qiu, Yuchen

2017-02-01

Accurate tumor segmentation is a critical step in the development of the computer-aided detection (CAD) based quantitative image analysis scheme for early stage prognostic evaluation of ovarian cancer patients. The purpose of this investigation is to assess the efficacy of several different methods to segment the metastatic tumors occurred in different organs of ovarian cancer patients. In this study, we developed a segmentation scheme consisting of eight different algorithms, which can be divided into three groups: 1) Region growth based methods; 2) Canny operator based methods; and 3) Partial differential equation (PDE) based methods. A number of 138 tumors acquired from 30 ovarian cancer patients were used to test the performance of these eight segmentation algorithms. The results demonstrate each of the tested tumors can be successfully segmented by at least one of the eight algorithms without the manual boundary correction. Furthermore, modified region growth, classical Canny detector, and fast marching, and threshold level set algorithms are suggested in the future development of the ovarian cancer related CAD schemes. This study may provide meaningful reference for developing novel quantitative image feature analysis scheme to more accurately predict the response of ovarian cancer patients to the chemotherapy at early stage.

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription.

PubMed

Lee, Jinwoo; Foong, Yee Hoon; Musaitif, Ibrahim; Tong, Tiegang; Jefcoate, Colin

2016-07-05

The steroidogenic acute regulatory protein (StAR) has been proposed to serve as the switch that can turn on/off steroidogenesis. We investigated the events that facilitate dynamic StAR transcription in response to cAMP stimulation in MA-10 Leydig cells, focusing on splicing anomalies at StAR gene loci. We used 3' reverse primers in a single reaction to respectively quantify StAR primary (p-RNA), spliced (sp-RNA/mRNA), and extended 3' untranslated region (UTR) transcripts, which were quantitatively imaged by high-resolution fluorescence in situ hybridization (FISH). This approach delivers spatio-temporal resolution of initiation and splicing at single StAR loci, and transfers individual mRNA molecules to cytoplasmic sites. Gene expression was biphasic, initially showing slow splicing, transitioning to concerted splicing. The alternative 3.5-kb mRNAs were distinguished through the use of extended 3'UTR probes, which exhibited distinctive mitochondrial distribution. Combining quantitative PCR and FISH enables imaging of localization of RNA expression and analysis of RNA processing rates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

In Vivo Characterization of Traumatic Brain Injury Neuropathology with Structural and Functional Neuroimaging

PubMed Central

LEVINE, BRIAN; FUJIWARA, ESTHER; O’CONNOR, CHARLENE; RICHARD, NADINE; KOVACEVIC, NATASA; MANDIC, MARINA; RESTAGNO, ADRIANA; EASDON, CRAIG; ROBERTSON, IAN H.; GRAHAM, SIMON J.; CHEUNG, GORDON; GAO, FUQIANG; SCHWARTZ, MICHAEL L.; BLACK, SANDRA E.

2007-01-01

Quantitative neuroimaging is increasingly used to study the effects of traumatic brain injury (TBI) on brain structure and function. This paper reviews quantitative structural and functional neuroimaging studies of patients with TBI, with an emphasis on the effects of diffuse axonal injury (DAI), the primary neuropathology in TBI. Quantitative structural neuroimaging has evolved from simple planometric measurements through targeted region-of-interest analyses to whole-brain analysis of quantified tissue compartments. Recent studies converge to indicate widespread volume loss of both gray and white matter in patients with moderate-to-severe TBI. These changes can be documented even when patients with focal lesions are excluded. Broadly speaking, performance on standard neuropsychological tests of speeded information processing are related to these changes, but demonstration of specific brain-behavior relationships requires more refined experimental behavioral measures. The functional consequences of these structural changes can be imaged with activation functional neuroimaging. Although this line of research is at an early stage, results indicate that TBI causes a more widely dispersed activation in frontal and posterior cortices. Further progress in analysis of the consequences of TBI on neural structure and function will require control of variability in neuropathology and behavior. PMID:17020478

99mTc-sestamibi scintigraphy used to evaluate tumor response to neoadjuvant chemotherapy in locally advanced breast cancer: A quantitative analysis

PubMed Central

KOGA, KATIA HIROMOTO; MORIGUCHI, SONIA MARTA; NETO, JORGE NAHÁS; PERES, STELA VERZINHASSE; SILVA, EDUARDO TINÓIS DA; SARRI, ALMIR JOSÉ; MICHELIN, ODAIR CARLITO; MARQUES, MARIANGELA ESTHER ALENCAR; GRIVA, BEATRIZ LOTUFO

2010-01-01

To evaluate the tumor response to neoadjuvant chemotherapy, 99mTc-sestamibi breast scintigraphy was proposed as a quantitative method. Fifty-five patients with ductal carcinoma were studied. They underwent breast scintigraphy before and after neoadjuvant chemotherapy, along with clinical assessment and surgical specimen analysis. The regions of interest on the lesion and contralateral breast were identified, and the pixel counts were used to evaluate lesion uptake in relation to background radiation. The ratio of these counts before to after neoadjuvant chemotherapy was assessed. The decrease in uptake rate due to chemotherapy characterized the scintigraphy tumor response. The Kruskal-Wallis test was used to compare the mean scintigraphic tumor response and histological type. Dunn’s multiple comparison test was used to detect differences between histological types. The Mann-Whitney test was used to compare means between quantitative and qualitative variables: scintigraphic tumor response vs. clinical response and uptake before chemotherapy vs. scintigraphic tumor response. The Spearman’s test was used to correlate the quantitative variables of clinical reduction in tumor size and scintigraphic tumor response. All of the variables compared presented significant differences. The change in 99mTc-sestamibi uptake noted on breast scintigraphy, before to after neoadjuvant chemotherapy, may be used as an effective method for evaluating the response to neoadjuvant chemotherapy, since this quantification reflects the biological behavior of the tumor towards the chemotherapy regimen. Furthermore, additional analysis on the uptake rate before chemotherapy may accurately predict treatment response. PMID:22966312

An analysis of science versus pseudoscience

NASA Astrophysics Data System (ADS)

Hooten, James T.

2011-12-01

This quantitative study identified distinctive features in archival datasets commissioned by the National Science Foundation (NSF) for Science and Engineering Indicators reports. The dependent variables included education level, and scores for science fact knowledge, science process knowledge, and pseudoscience beliefs. The dependent variables were aggregated into nine NSF-defined geographic regions and examined for the years 2004 and 2006. The variables were also examined over all years available in the dataset. Descriptive statistics were determined and tests for normality and homogeneity of variances were performed using Statistical Package for the Social Sciences. Analysis of Variance was used to test for statistically significant differences between the nine geographic regions for each of the four dependent variables. Statistical significance of 0.05 was used. Tukey post-hoc analysis was used to compute practical significance of differences between regions. Post-hoc power analysis using G*Power was used to calculate the probability of Type II errors. Tests for correlations across all years of the dependent variables were also performed. Pearson's r was used to indicate the strength of the relationship between the dependent variables. Small to medium differences in science literacy and education level were observed between many of the nine U.S. geographic regions. The most significant differences occurred when the West South Central region was compared to the New England and the Pacific regions. Belief in pseudoscience appeared to be distributed evenly across all U.S. geographic regions. Education level was a strong indicator of science literacy regardless of a respondent's region of residence. Recommendations for further study include more in-depth investigation to uncover the nature of the relationship between education level and belief in pseudoscience.

Comparative analysis of hazardous household waste in two Mexican regions.

PubMed

Delgado, Otoniel Buenrostro; Ojeda-Benítez, Sara; Márquez-Benavides, Liliana

2007-01-01

Household hazardous waste (HHW) generation in two Mexican regions was examined, a northern region (bordering with the USA) and a central region. The aim of this work was to determine the dynamics of solid waste generation and to be able to compare the results of both regions, regarding consumption patterns and solid waste generation rates. In the northern region, household solid waste was analysed quantitatively. In order to perform this analysis, the population was categorized into three socioeconomic strata (lower, middle, upper). Waste characterization revealed the presence of products that give origin to household hazardous waste. In the northern region (Mexicali city), household hazardous waste comprised 3.7% of municipal solid waste, the largest categories in this fraction were home care products (29.2%), cleaning products (19.5%) and batteries and electronic equipment (15.7%). In the central region, HHW comprised 1.03% of municipal solid waste; the main categories in this fraction were represented by cleaning products (39%), self care products (27.3%), and insecticides (14.4%). In Mexicali, the socioeconomic study demonstrated that the production of HHW is independent of the income level. Furthermore, the composition of the solid waste stream in both regions suggested the influence of another set of variables such as local climate, migration patterns and marketing coverage. Further research is needed in order to establish the effect of low quantities of HHW upon the environment and public health.

Usefulness of quantitative susceptibility mapping for the diagnosis of Parkinson disease.

PubMed

Murakami, Y; Kakeda, S; Watanabe, K; Ueda, I; Ogasawara, A; Moriya, J; Ide, S; Futatsuya, K; Sato, T; Okada, K; Uozumi, T; Tsuji, S; Liu, T; Wang, Y; Korogi, Y

2015-06-01

Quantitative susceptibility mapping allows overcoming several nonlocal restrictions of susceptibility-weighted and phase imaging and enables quantification of magnetic susceptibility. We compared the diagnostic accuracy of quantitative susceptibility mapping and R2* (1/T2*) mapping to discriminate between patients with Parkinson disease and controls. For 21 patients with Parkinson disease and 21 age- and sex-matched controls, 2 radiologists measured the quantitative susceptibility mapping values and R2* values in 6 brain structures (the thalamus, putamen, caudate nucleus, pallidum, substantia nigra, and red nucleus). The quantitative susceptibility mapping values and R2* values of the substantia nigra were significantly higher in patients with Parkinson disease (P < .01); measurements in other brain regions did not differ significantly between patients and controls. For the discrimination of patients with Parkinson disease from controls, receiver operating characteristic analysis suggested that the optimal cutoff values for the substantia nigra, based on the Youden Index, were >0.210 for quantitative susceptibility mapping and >28.8 for R2*. The sensitivity, specificity, and accuracy of quantitative susceptibility mapping were 90% (19 of 21), 86% (18 of 21), and 88% (37 of 42), respectively; for R2* mapping, they were 81% (17 of 21), 52% (11 of 21), and 67% (28 of 42). Pair-wise comparisons showed that the areas under the receiver operating characteristic curves were significantly larger for quantitative susceptibility mapping than for R2* mapping (0.91 versus 0.69, P < .05). Quantitative susceptibility mapping showed higher diagnostic performance than R2* mapping for the discrimination between patients with Parkinson disease and controls. © 2015 by American Journal of Neuroradiology.

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.

A joint analysis of the Drake equation and the Fermi paradox

NASA Astrophysics Data System (ADS)

Prantzos, Nikos

2013-07-01

I propose a unified framework for a joint analysis of the Drake equation and the Fermi paradox, which enables a simultaneous, quantitative study of both of them. The analysis is based on a simplified form of the Drake equation and on a fairly simple scheme for the colonization of the Milky Way. It appears that for sufficiently long-lived civilizations, colonization of the Galaxy is the only reasonable option to gain knowledge about other life forms. This argument allows one to define a region in the parameter space of the Drake equation, where the Fermi paradox definitely holds (`Strong Fermi paradox').

Validation of Simple Quantification Methods for (18)F-FP-CIT PET Using Automatic Delineation of Volumes of Interest Based on Statistical Probabilistic Anatomical Mapping and Isocontour Margin Setting.

PubMed

Kim, Yong-Il; Im, Hyung-Jun; Paeng, Jin Chul; Lee, Jae Sung; Eo, Jae Seon; Kim, Dong Hyun; Kim, Euishin E; Kang, Keon Wook; Chung, June-Key; Lee, Dong Soo

2012-12-01

(18)F-FP-CIT positron emission tomography (PET) is an effective imaging for dopamine transporters. In usual clinical practice, (18)F-FP-CIT PET is analyzed visually or quantified using manual delineation of a volume of interest (VOI) for the striatum. In this study, we suggested and validated two simple quantitative methods based on automatic VOI delineation using statistical probabilistic anatomical mapping (SPAM) and isocontour margin setting. Seventy-five (18)F-FP-CIT PET images acquired in routine clinical practice were used for this study. A study-specific image template was made and the subject images were normalized to the template. Afterwards, uptakes in the striatal regions and cerebellum were quantified using probabilistic VOI based on SPAM. A quantitative parameter, QSPAM, was calculated to simulate binding potential. Additionally, the functional volume of each striatal region and its uptake were measured in automatically delineated VOI using isocontour margin setting. Uptake-volume product (QUVP) was calculated for each striatal region. QSPAM and QUVP were compared with visual grading and the influence of cerebral atrophy on the measurements was tested. Image analyses were successful in all the cases. Both the QSPAM and QUVP were significantly different according to visual grading (P < 0.001). The agreements of QUVP or QSPAM with visual grading were slight to fair for the caudate nucleus (κ = 0.421 and 0.291, respectively) and good to perfect to the putamen (κ = 0.663 and 0.607, respectively). Also, QSPAM and QUVP had a significant correlation with each other (P < 0.001). Cerebral atrophy made a significant difference in QSPAM and QUVP of the caudate nuclei regions with decreased (18)F-FP-CIT uptake. Simple quantitative measurements of QSPAM and QUVP showed acceptable agreement with visual grading. Although QSPAM in some group may be influenced by cerebral atrophy, these simple methods are expected to be effective in the quantitative analysis of (18)F-FP-CIT PET in usual clinical practice.

Differentiating functional brain regions using optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gil, Daniel A.; Bow, Hansen C.; Shen, Jin-H.; Joos, Karen M.; Skala, Melissa C.

2017-02-01

The human brain is made up of functional regions governing movement, sensation, language, and cognition. Unintentional injury during neurosurgery can result in significant neurological deficits and morbidity. The current standard for localizing function to brain tissue during surgery, intraoperative electrical stimulation or recording, significantly increases the risk, time, and cost of the procedure. There is a need for a fast, cost-effective, and high-resolution intraoperative technique that can avoid damage to functional brain regions. We propose that optical coherence tomography (OCT) can fill this niche by imaging differences in the cellular composition and organization of functional brain areas. We hypothesized this would manifest as differences in the attenuation coefficient measured using OCT. Five functional regions (prefrontal, somatosensory, auditory, visual, and cerebellum) were imaged in ex vivo porcine brains (n=3), a model chosen due to a similar white/gray matter ratio as human brains. The attenuation coefficient was calculated using a depth-resolved model and quantitatively validated with Intralipid phantoms across a physiological range of attenuation coefficients (absolute difference < 0.1cm-1). Image analysis was performed on the attenuation coefficient images to derive quantitative endpoints. We observed a statistically significant difference among the median attenuation coefficients of these five regions (one-way ANOVA, p<0.05). Nissl-stained histology will be used to validate our results and correlate OCT-measured attenuation coefficients to neuronal density. Additional development and validation of OCT algorithms to discriminate brain regions are planned to improve the safety and efficacy of neurosurgical procedures such as biopsy, electrode placement, and tissue resection.

Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis.

PubMed

Debuc, Delia Cabrera; Salinas, Harry M; Ranganathan, Sudarshan; Tátrai, Erika; Gao, Wei; Shen, Meixiao; Wang, Jianhua; Somfai, Gábor M; Puliafito, Carmen A

2010-01-01

We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 microm and 26.71 microm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 microm and 0.6 and 1.76 microm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R(2)>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.

Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis

NASA Astrophysics Data System (ADS)

Cabrera Debuc, Delia; Salinas, Harry M.; Ranganathan, Sudarshan; Tátrai, Erika; Gao, Wei; Shen, Meixiao; Wang, Jianhua; Somfai, Gábor M.; Puliafito, Carmen A.

2010-07-01

We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 μm and 26.71 μm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 μm and 0.6 and 1.76 μm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R2>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.

Three-way analysis of the UPLC-PDA dataset for the multicomponent quantitation of hydrochlorothiazide and olmesartan medoxomil in tablets by parallel factor analysis and three-way partial least squares.

PubMed

Dinç, Erdal; Ertekin, Zehra Ceren

2016-01-01

An application of parallel factor analysis (PARAFAC) and three-way partial least squares (3W-PLS1) regression models to ultra-performance liquid chromatography-photodiode array detection (UPLC-PDA) data with co-eluted peaks in the same wavelength and time regions was described for the multicomponent quantitation of hydrochlorothiazide (HCT) and olmesartan medoxomil (OLM) in tablets. Three-way dataset of HCT and OLM in their binary mixtures containing telmisartan (IS) as an internal standard was recorded with a UPLC-PDA instrument. Firstly, the PARAFAC algorithm was applied for the decomposition of three-way UPLC-PDA data into the chromatographic, spectral and concentration profiles to quantify the concerned compounds. Secondly, 3W-PLS1 approach was subjected to the decomposition of a tensor consisting of three-way UPLC-PDA data into a set of triads to build 3W-PLS1 regression for the analysis of the same compounds in samples. For the proposed three-way analysis methods in the regression and prediction steps, the applicability and validity of PARAFAC and 3W-PLS1 models were checked by analyzing the synthetic mixture samples, inter-day and intra-day samples, and standard addition samples containing HCT and OLM. Two different three-way analysis methods, PARAFAC and 3W-PLS1, were successfully applied to the quantitative estimation of the solid dosage form containing HCT and OLM. Regression and prediction results provided from three-way analysis were compared with those obtained by traditional UPLC method. Copyright © 2015 Elsevier B.V. All rights reserved.

Sampling of illicit drugs for quantitative analysis--part II. Study of particle size and its influence on mass reduction.

PubMed

Bovens, M; Csesztregi, T; Franc, A; Nagy, J; Dujourdy, L

2014-01-01

The basic goal in sampling for the quantitative analysis of illicit drugs is to maintain the average concentration of the drug in the material from its original seized state (the primary sample) all the way through to the analytical sample, where the effect of particle size is most critical. The size of the largest particles of different authentic illicit drug materials, in their original state and after homogenisation, using manual or mechanical procedures, was measured using a microscope with a camera attachment. The comminution methods employed included pestle and mortar (manual) and various ball and knife mills (mechanical). The drugs investigated were amphetamine, heroin, cocaine and herbal cannabis. It was shown that comminution of illicit drug materials using these techniques reduces the nominal particle size from approximately 600 μm down to between 200 and 300 μm. It was demonstrated that the choice of 1 g increments for the primary samples of powdered drugs and cannabis resin, which were used in the heterogeneity part of our study (Part I) was correct for the routine quantitative analysis of illicit seized drugs. For herbal cannabis we found that the appropriate increment size was larger. Based on the results of this study we can generally state that: An analytical sample weight of between 20 and 35 mg of an illicit powdered drug, with an assumed purity of 5% or higher, would be considered appropriate and would generate an RSDsampling in the same region as the RSDanalysis for a typical quantitative method of analysis for the most common, powdered, illicit drugs. For herbal cannabis, with an assumed purity of 1% THC (tetrahydrocannabinol) or higher, an analytical sample weight of approximately 200 mg would be appropriate. In Part III we will pull together our homogeneity studies and particle size investigations and use them to devise sampling plans and sample preparations suitable for the quantitative instrumental analysis of the most common illicit drugs. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Identification and quantitative evaluation of the fiber structure in the pathological tissue using Mueller matrix microscope

NASA Astrophysics Data System (ADS)

Zhou, Jialing; He, Honghui; Wang, Ye; Ma, Hui

2017-02-01

Fiber structure changes in the various pathological processes, such as the increase of fibrosis in liver diseases, the derangement of fiber in cervical cancer and so on. Currently, clinical pathologic diagnosis is regarded as the golden criterion, but different doctors with discrepancy in knowledge and experience may obtain different conclusions. Up to a point, quantitative evaluation of the fiber structure in the pathological tissue can be of great service to quantitative diagnosis. Mueller matrix measurement is capable of probing comprehensive microstructural information of samples and different wavelength of lights can provide more information. In this paper, we use a Mueller matrix microscope with light sources in six different wavelength. We use unstained, dewaxing liver tissue slices in four stages and the pathological biopsy of the filtration channels from rabbit eyes as samples. We apply the Mueller matrix polar decomposition (MMPD) parameter δ which corresponds to retardance to liver slices. The mean value of abnormal region get bigger when the level of fibrosis get higher and light in short wavelength is more sensitive to the microstructure of fiber. On the other hand, we use the Mueller matrix transformation (MMT) parameter Φ which is associated to the angel of fast axis in the analysis of the slices of the filtration channels from rabbit eyes. The value of kurtosis and the value of skewness shows big difference between new born region and normal region and can reveal the arrangement of fiber. These results indicate that the Mueller matrix microscope has great potential in auxiliary diagnosis.

δ-aminolevulinic acid–induced protoporphyrin IX concentration correlates with histopathologic markers of malignancy in human gliomas: the need for quantitative fluorescence-guided resection to identify regions of increasing malignancy

PubMed Central

Valdés, Pablo A.; Kim, Anthony; Brantsch, Marco; Niu, Carolyn; Moses, Ziev B.; Tosteson, Tor D.; Wilson, Brian C.; Paulsen, Keith D.; Roberts, David W.; Harris, Brent T.

2011-01-01

Extent of resection is a major goal and prognostic factor in the treatment of gliomas. In this study we evaluate whether quantitative ex vivo tissue measurements of δ-aminolevulinic acid–induced protoporphyrin IX (PpIX) identify regions of increasing malignancy in low- and high-grade gliomas beyond the capabilities of current fluorescence imaging in patients undergoing fluorescence-guided resection (FGR). Surgical specimens were collected from 133 biopsies in 23 patients and processed for ex vivo neuropathological analysis: PpIX fluorimetry to measure PpIX concentrations (CPpIX) and Ki-67 immunohistochemistry to assess tissue proliferation. Samples displaying visible levels of fluorescence showed significantly higher levels of CPpIX and tissue proliferation. CPpIX was strongly correlated with histopathological score (nonparametric) and tissue proliferation (parametric), such that increasing levels of CPpIX were identified with regions of increasing malignancy. Furthermore, a large percentage of tumor-positive biopsy sites (∼40%) that were not visibly fluorescent under the operating microscope had levels of CPpIX greater than 0.1 µg/mL, which indicates that significant PpIX accumulation exists below the detection threshold of current fluorescence imaging. Although PpIX fluorescence is recognized as a visual biomarker for neurosurgical resection guidance, these data show that it is quantitatively related at the microscopic level to increasing malignancy in both low- and high-grade gliomas. This work suggests a need for improved PpIX fluorescence detection technologies to achieve better sensitivity and quantification of PpIX in tissue during surgery. PMID:21798847

A comparison of region-based and pixel-based CEUS kinetics parameters in the assessment of arthritis

NASA Astrophysics Data System (ADS)

Grisan, E.; Raffeiner, B.; Coran, A.; Rizzo, G.; Ciprian, L.; Stramare, R.

2014-03-01

Inflammatory rheumatic diseases are leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity and increased mortality. The gold-standard for diagnosing and differentiating arthritis is based on patient conditions and radiographic findings, as joint erosions or decalcification. However, early signs of arthritis are joint effusion, hypervascularization and synovial hypertrophy. In particular, vascularization has been shown to correlate with arthritis' destructive behavior, more than clinical assessment. Contrast Enhanced Ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. The evaluation of perfusion pattern rely on subjective semi-quantitative scales, that are able to capture the macroscopic degree of vascularization, but are unable to detect the subtler differences in kinetics perfusion parameters that might lead to a deeper understanding of disease progression and a better management of patients. Quantitative assessment is mostly performed by means of the Qontrast software package, that requires the user to define a region of interest, whose mean intensity curve is fitted with an exponential function. We show that using a more physiologically motivated perfusion curve, and by estimating the kinetics parameters separately pixel per pixel, the quantitative information gathered is able to differentiate more effectively different perfusion patterns. In particular, we will show that a pixel-based analysis is able to provide significant markers differentiating rheumatoid arthritis from simil-rheumatoid psoriatic arthritis, that have non-significant differences in clinical evaluation (DAS28), serological markers, or region-based parameters.

Feasibility of Rainwater Harvesting to fulfill potable water demand using quantitative water management in low-lying delta regions of Asia

NASA Astrophysics Data System (ADS)

Mahmood, A.; Hossain, F.

2016-12-01

Low-lying deltas of Asian region are usually densely populated and located in developing countries situated at the downstream end of major rivers. Extensive dam construction by the upstream countries has now caused water scarcity in large portions of low-lying deltas. Most inhabitants depend on shallow tube well for safe drinking water that tend to suffer from water quality issues (e.g. Arsenic contamination). In addition, people also get infected from water borne diseases like Cholera and Typhoid due to lack of safe drinking water. Developing a centralized piped network based water supply system is often not a feasible option in rural regions. Due to social acceptability, environment friendliness, lower capital and maintenance cost, rainwater harvesting can be the most sustainable option to supply safe drinking water in rural areas. In this study, first we estimate the monthly rainfall variability using long precipitation climatology from satellite precipitation data. The upper and lower bounds of monthly harvestable rainwater were estimated for each satellite precipitation grid. Taking this lower bound of monthly harvestable rainwater as input, we use quantitative water management concept to determine the percent of the time of the year potable water demand can be fulfilled. Analysis indicates that a 6 m³ reservoir tank can fulfill the potable water demand of a 6 person family throughout a year in almost all parts of this region.

Developing a Social, Cultural and Economic Report Card for a Regional Industrial Harbour.

PubMed

Pascoe, Sean; Tobin, Renae; Windle, Jill; Cannard, Toni; Marshall, Nadine; Kabir, Zobaidul; Flint, Nicole

2016-01-01

Report cards are increasingly used to provide ongoing snap-shots of progress towards specific ecosystem health goals, particularly in coastal regions where planners need to balance competing demands for coastal resources from a range of industries. While most previous report cards focus on the biophysical components of the system, there is a growing interest in including the social and economic implications of ecosystem management to provide a greater social-ecological system understanding. Such a report card was requested on the Gladstone Harbour area in central Queensland, Australia. Gladstone Harbour adjoins the southern Great Barrier Reef, and is also a major industrial and shipping port. Balancing social, economic and environmental interests is therefore of great concern to the regional managers. While environmental benchmarking procedures are well established within Australia (and elsewhere), a method for assessing social and economic performance of coastal management is generally lacking. The key aim of this study was to develop and pilot a system for the development of a report card relating to appropriate cultural, social and economic objectives. The approach developed uses a range of multicriteria decision analysis methods to assess and combine different qualitative and quantitative measures, including the use of Bayesian Belief Networks to combine the different measures and provide an overall quantitative score for each of the key management objectives. The approach developed is readily transferable for purposes of similar assessments in other regions.

Developing a Social, Cultural and Economic Report Card for a Regional Industrial Harbour

PubMed Central

Pascoe, Sean; Tobin, Renae; Windle, Jill; Cannard, Toni; Marshall, Nadine; Kabir, Zobaidul; Flint, Nicole

2016-01-01

Report cards are increasingly used to provide ongoing snap-shots of progress towards specific ecosystem health goals, particularly in coastal regions where planners need to balance competing demands for coastal resources from a range of industries. While most previous report cards focus on the biophysical components of the system, there is a growing interest in including the social and economic implications of ecosystem management to provide a greater social-ecological system understanding. Such a report card was requested on the Gladstone Harbour area in central Queensland, Australia. Gladstone Harbour adjoins the southern Great Barrier Reef, and is also a major industrial and shipping port. Balancing social, economic and environmental interests is therefore of great concern to the regional managers. While environmental benchmarking procedures are well established within Australia (and elsewhere), a method for assessing social and economic performance of coastal management is generally lacking. The key aim of this study was to develop and pilot a system for the development of a report card relating to appropriate cultural, social and economic objectives. The approach developed uses a range of multicriteria decision analysis methods to assess and combine different qualitative and quantitative measures, including the use of Bayesian Belief Networks to combine the different measures and provide an overall quantitative score for each of the key management objectives. The approach developed is readily transferable for purposes of similar assessments in other regions. PMID:26839949

Qualitative and Quantitative Analysis for Facial Complexion in Traditional Chinese Medicine

PubMed Central

Zhao, Changbo; Li, Guo-zheng; Li, Fufeng; Wang, Zhi; Liu, Chang

2014-01-01

Facial diagnosis is an important and very intuitive diagnostic method in Traditional Chinese Medicine (TCM). However, due to its qualitative and experience-based subjective property, traditional facial diagnosis has a certain limitation in clinical medicine. The computerized inspection method provides classification models to recognize facial complexion (including color and gloss). However, the previous works only study the classification problems of facial complexion, which is considered as qualitative analysis in our perspective. For quantitative analysis expectation, the severity or degree of facial complexion has not been reported yet. This paper aims to make both qualitative and quantitative analysis for facial complexion. We propose a novel feature representation of facial complexion from the whole face of patients. The features are established with four chromaticity bases splitting up by luminance distribution on CIELAB color space. Chromaticity bases are constructed from facial dominant color using two-level clustering; the optimal luminance distribution is simply implemented with experimental comparisons. The features are proved to be more distinctive than the previous facial complexion feature representation. Complexion recognition proceeds by training an SVM classifier with the optimal model parameters. In addition, further improved features are more developed by the weighted fusion of five local regions. Extensive experimental results show that the proposed features achieve highest facial color recognition performance with a total accuracy of 86.89%. And, furthermore, the proposed recognition framework could analyze both color and gloss degrees of facial complexion by learning a ranking function. PMID:24967342

Deficiency mapping of quantitative trait loci affecting longevity in Drosophila melanogaster.

PubMed Central

Pasyukova, E G; Vieira, C; Mackay, T F

2000-01-01

In a previous study, sex-specific quantitative trait loci (QTL) affecting adult longevity were mapped by linkage to polymorphic roo transposable element markers, in a population of recombinant inbred lines derived from the Oregon and 2b strains of Drosophila melanogaster. Two life span QTL were each located on chromosomes 2 and 3, within sections 33E-46C and 65D-85F on the cytological map, respectively. We used quantitative deficiency complementation mapping to further resolve the locations of life span QTL within these regions. The Oregon and 2b strains were each crossed to 47 deficiencies spanning cytological regions 32F-44E and 64C-76B, and quantitative failure of the QTL alleles to complement the deficiencies was assessed. We initially detected a minimum of five and four QTL in the chromosome 2 and 3 regions, respectively, illustrating that multiple linked factors contribute to each QTL detected by recombination mapping. The QTL locations inferred from deficiency mapping did not generally correspond to those of candidate genes affecting oxidative and thermal stress or glucose metabolism. The chromosome 2 QTL in the 35B-E region was further resolved to a minimum of three tightly linked QTL, containing six genetically defined loci, 24 genes, and predicted genes that are positional candidates corresponding to life span QTL. This region was also associated with quantitative variation in life span in a sample of 10 genotypes collected from nature. Quantitative deficiency complementation is an efficient method for fine-scale QTL mapping in Drosophila and can be further improved by controlling the background genotype of the strains to be tested. PMID:11063689

Measurement and interpretation of magnetic shear in solar active regions

NASA Technical Reports Server (NTRS)

Hagyard, M. J.; Rabin, D. M.

1986-01-01

In this paper a summary and synthesis are presented for results on the role of magnetic shear in the flare process that have been derived from the series of Flare Buildup Study Workshops in the Solar Maximum Analysis program. With emphasis on observations, the mechanisms that seem to produce the sheared magnetic configurations observed in flaring active regions are discussed. The spatial and temporal correlations of this shear with the onset of solar flares are determined from quantitative analyses of measurements of the vector magnetic field. The question of why some areas of sheared magnetic fields are the sites of flares and others are not is investigated observationally.

[Decreased hospital spending as a result of antibiotic prescriptions dispensed in community pharmacies. Results from the Midi-Pyrenees region.].

PubMed

Gallini, Adeline; Taboulet, Florence

2010-01-01

A contract between French hospitals and national health authorities was signed in early 2006 to improve the rational use of antibiotics in hospitals. The contract offers a financial reward in the event of decreased spending as a result of hospital prescriptions dispensed in community pharmacies compared to the previous year. The article describes the limitations relating to the financial rewards defined by the contract, particularly those concerning the measurement and relevance of the chosen indicator. Since no national data are currently available, quantitative results drawn from the Midi-Pyrénées region are used to illustrate the analysis.

Cortical orofacial motor representation in Old World monkeys, great apes, and humans. I. Quantitative analysis of cytoarchitecture.

PubMed

Sherwood, Chet C; Holloway, Ralph L; Erwin, Joseph M; Schleicher, Axel; Zilles, Karl; Hof, Patrick R

2004-01-01

Social life in anthropoid primates is mediated by interindividual communication, involving movements of the orofacial muscles for the production of vocalization and gestural expression. Although phylogenetic diversity has been reported in the auditory and visual communication systems of primates, little is known about the comparative neuroanatomy that subserves orofacial movement. The current study reports results from quantitative image analysis of the region corresponding to orofacial representation of primary motor cortex (Brodmann's area 4) in several catarrhine primate species (Macaca fascicularis, Papio anubis, Pongo pygmaeus, Gorilla gorilla, Pan troglodytes, and Homo sapiens) using the Grey Level Index method. This cortical region has been implicated in the execution of skilled motor activities such as voluntary facial expression and human speech. Density profiles of the laminar distribution of Nissl-stained neuronal somata were acquired from high-resolution images to quantify cytoarchitectural patterns. Despite general similarity in these profiles across catarrhines, multivariate analysis showed that cytoarchitectural patterns of individuals were more similar within-species versus between-species. Compared to Old World monkeys, the orofacial representation of area 4 in great apes and humans was characterized by an increased relative thickness of layer III and overall lower cell volume densities, providing more neuropil space for interconnections. These phylogenetic differences in microstructure might provide an anatomical substrate for the evolution of greater volitional fine motor control of facial expressions in great apes and humans. Copyright 2004 S. Karger AG, Basel

STEM_CELL: a software tool for electron microscopy: part 2--analysis of crystalline materials.

PubMed

Grillo, Vincenzo; Rossi, Francesca

2013-02-01

A new graphical software (STEM_CELL) for analysis of HRTEM and STEM-HAADF images is here introduced in detail. The advantage of the software, beyond its graphic interface, is to put together different analysis algorithms and simulation (described in an associated article) to produce novel analysis methodologies. Different implementations and improvements to state of the art approach are reported in the image analysis, filtering, normalization, background subtraction. In particular two important methodological results are here highlighted: (i) the definition of a procedure for atomic scale quantitative analysis of HAADF images, (ii) the extension of geometric phase analysis to large regions up to potentially 1μm through the use of under sampled images with aliasing effects. Copyright © 2012 Elsevier B.V. All rights reserved.

Four out of eight genes in a mouse chromosome 7 congenic donor region are candidate obesity genes.

PubMed

Sarahan, Kari A; Fisler, Janis S; Warden, Craig H

2011-09-22

We previously identified a region of mouse chromosome 7 that influences body fat mass in F2 littermates of congenic × background intercrosses. Current analyses revealed that alleles in the donor region of the subcongenic B6.C-D7Mit318 (318) promoted a twofold increase in adiposity in homozygous lines of 318 compared with background C57BL/6ByJ (B6By) mice. Parent-of-origin effects were discounted through cross-fostering studies and an F1 reciprocal cross. Mapping of the donor region revealed that it has a maximal size of 2.8 Mb (minimum 1.8 Mb) and contains a maximum of eight protein coding genes. Quantitative PCR in whole brain, liver, and gonadal white adipose tissue (GWAT) revealed differential expression between genotypes for three genes in females and two genes in males. Alpha-2,8-sialyltransferase 8B (St8sia2) showed reduced 318 mRNA levels in brain for females and males and in GWAT for females only. Both sexes of 318 mice had reduced Repulsive guidance molecule-a (Rgma) expression in GWAT. In brain, Family with sequence similarity 174 member b (Fam174b) had increased expression in 318 females, whereas Chromodomain helicase DNA binding protein 2 (Chd2-2) had reduced expression in 318 males. No donor region genes were differentially expressed in liver. Sequence analysis of coding exons for all genes in the 318 donor region revealed only one single nucleotide polymorphism that produced a nonsynonymous missense mutation, Gln7Pro, in Fam174b. Our findings highlight the difficulty of using expression and sequence to identify quantitative trait genes underlying obesity even in small genomic regions.

Space-time quantitative source apportionment of soil heavy metal concentration increments.

PubMed

Yang, Yong; Christakos, George; Guo, Mingwu; Xiao, Lu; Huang, Wei

2017-04-01

Assessing the space-time trends and detecting the sources of heavy metal accumulation in soils have important consequences in the prevention and treatment of soil heavy metal pollution. In this study, we collected soil samples in the eastern part of the Qingshan district, Wuhan city, Hubei Province, China, during the period 2010-2014. The Cd, Cu, Pb and Zn concentrations in soils exhibited a significant accumulation during 2010-2014. The spatiotemporal Kriging technique, based on a quantitative characterization of soil heavy metal concentration variations in terms of non-separable variogram models, was employed to estimate the spatiotemporal soil heavy metal distribution in the study region. Our findings showed that the Cd, Cu, and Zn concentrations have an obvious incremental tendency from the southwestern to the central part of the study region. However, the Pb concentrations exhibited an obvious tendency from the northern part to the central part of the region. Then, spatial overlay analysis was used to obtain absolute and relative concentration increments of adjacent 1- or 5-year periods during 2010-2014. The spatial distribution of soil heavy metal concentration increments showed that the larger increments occurred in the center of the study region. Lastly, the principal component analysis combined with the multiple linear regression method were employed to quantify the source apportionment of the soil heavy metal concentration increments in the region. Our results led to the conclusion that the sources of soil heavy metal concentration increments should be ascribed to industry, agriculture and traffic. In particular, 82.5% of soil heavy metal concentration increment during 2010-2014 was ascribed to industrial/agricultural activities sources. Using STK and SOA to obtain the spatial distribution of heavy metal concentration increments in soils. Using PCA-MLR to quantify the source apportionment of soil heavy metal concentration increments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Developmental specialization in the right intraparietal sulcus for the abstract representation of numerical magnitude.

PubMed

Holloway, Ian D; Ansari, Daniel

2010-11-01

Because number is an abstract quality of a set, the way in which a number is externally represented does not change its quantitative meaning. In this study, we examined the development of the brain regions that support format-independent representation of numerical magnitude. We asked children and adults to perform both symbolic (Hindu-Arabic numerals) and nonsymbolic (arrays of squares) numerical comparison tasks as well as two control tasks while their brains were scanned using fMRI. In a preliminary analysis, we calculated the conjunction between symbolic and nonsymbolic numerical comparison. We then examined in which brain regions this conjunction differed between children and adults. This analysis revealed a large network of visual and parietal regions that showed greater activation in adults relative to children. In our primary analysis, we examined age-related differences in the conjunction of symbolic and nonsymbolic comparison after subtracting the control tasks. This analysis revealed a much more limited set of regions including the right inferior parietal lobe near the intraparietal sulcus. In addition to showing increased activation to both symbolic and nonsymbolic magnitudes over and above activation related to response selection, this region showed age-related differences in the distance effect. Our findings demonstrate that the format-independent representation of numerical magnitude in the right inferior parietal lobe is the product of developmental processes of cortical specialization and highlight the importance of using appropriate control tasks when conducting developmental neuroimaging studies.

Bacterial diversity in different regions of gastrointestinal tract of Giant African snail (Achatina fulica).

PubMed

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-12-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. © 2012 The Authors. Published by Blackwell Publishing Ltd.

Bacterial diversity in different regions of gastrointestinal tract of Giant African Snail (Achatina fulica)

PubMed Central

Pawar, Kiran D; Banskar, Sunil; Rane, Shailendra D; Charan, Shakti S; Kulkarni, Girish J; Sawant, Shailesh S; Ghate, Hemant V; Patole, Milind S; Shouche, Yogesh S

2012-01-01

The gastrointestinal (GI) tract of invasive land snail Achatina fulica is known to harbor metabolically active bacterial communities. In this study, we assessed the bacterial diversity in the different regions of GI tract of Giant African snail, A. fulica by culture-independent and culture-dependent methods. Five 16S rRNA gene libraries from different regions of GI tract of active snails indicated that sequences affiliated to phylum γ-Proteobacteria dominated the esophagus, crop, intestine, and rectum libraries, whereas sequences affiliated to Tenericutes dominated the stomach library. On phylogenetic analysis, 30, 27, 9, 27, and 25 operational taxonomic units (OTUs) from esophagus, crop, stomach, intestine, and rectum libraries were identified, respectively. Estimations of the total bacterial diversity covered along with environmental cluster analysis showed highest bacterial diversity in the esophagus and lowest in the stomach. Thirty-three distinct bacterial isolates were obtained, which belonged to 12 genera of two major bacterial phyla namely γ-Proteobacteria and Firmicutes. Among these, Lactococcus lactis and Kurthia gibsonii were the dominant bacteria present in all GI tract regions. Quantitative real-time polymerase chain reaction (qPCR) analysis indicated significant differences in bacterial load in different GI tract regions of active and estivating snails. The difference in the bacterial load between the intestines of active and estivating snail was maximum. Principal component analysis (PCA) of terminal restriction fragment length polymorphism suggested that bacterial community structure changes only in intestine when snail enters estivation state. PMID:23233413

[Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

PubMed

Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

2013-11-01

In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

Quantitative photoacoustic assessment of ex-vivo lymph nodes of colorectal cancer patients

NASA Astrophysics Data System (ADS)

Sampathkumar, Ashwin; Mamou, Jonathan; Saegusa-Beercroft, Emi; Chitnis, Parag V.; Machi, Junji; Feleppa, Ernest J.

2015-03-01

Staging of cancers and selection of appropriate treatment requires histological examination of multiple dissected lymph nodes (LNs) per patient, so that a staggering number of nodes require histopathological examination, and the finite resources of pathology facilities create a severe processing bottleneck. Histologically examining the entire 3D volume of every dissected node is not feasible, and therefore, only the central region of each node is examined histologically, which results in severe sampling limitations. In this work, we assess the feasibility of using quantitative photoacoustics (QPA) to overcome the limitations imposed by current procedures and eliminate the resulting under sampling in node assessments. QPA is emerging as a new hybrid modality that assesses tissue properties and classifies tissue type based on multiple estimates derived from spectrum analysis of photoacoustic (PA) radiofrequency (RF) data and from statistical analysis of envelope-signal data derived from the RF signals. Our study seeks to use QPA to distinguish cancerous from non-cancerous regions of dissected LNs and hence serve as a reliable means of imaging and detecting small but clinically significant cancerous foci that would be missed by current methods. Dissected lymph nodes were placed in a water bath and PA signals were generated using a wavelength-tunable (680-950 nm) laser. A 26-MHz, f-2 transducer was used to sense the PA signals. We present an overview of our experimental setup; provide a statistical analysis of multi-wavelength classification parameters (mid-band fit, slope, intercept) obtained from the PA signal spectrum generated in the LNs; and compare QPA performance with our established quantitative ultrasound (QUS) techniques in distinguishing metastatic from non-cancerous tissue in dissected LNs. QPA-QUS methods offer a novel general means of tissue typing and evaluation in a broad range of disease-assessment applications, e.g., cardiac, intravascular, musculoskeletal, endocrine-gland, etc.

Genetic linkage analysis using pooled DNA and infrared detection of tailed STRP primer patterns

NASA Astrophysics Data System (ADS)

Oetting, William S.; Wildenberg, Scott C.; King, Richard A.

1996-04-01

The mapping of a disease locus to a specific chromosomal region is an important step in the eventual isolation and analysis of a disease causing gene. Conventional mapping methods analyze large multiplex families and/or smaller nuclear families to find linkage between the disease and a chromosome marker that maps to a known chromosomal region. This analysis is time consuming and tedious, typically requiring the determination of 30,000 genotypes or more. For appropriate populations, we have instead utilized pooled DNA samples for gene mapping which greatly reduces the amount of time necessary for an initial chromosomal screen. This technique assumes a common founder for the disease locus of interest and searches for a region of a chromosome shared between affected individuals. Our analysis involves the PCR amplification of short tandem repeat polymorphisms (STRP) to detect these shared regions. In order to reduce the cost of genotyping, we have designed unlabeled tailed PCR primers which, when combined with a labeled universal primer, provides for an alternative to synthesizing custom labeled primers. The STRP pattern is visualized with an infrared fluorescence based automated DNA sequencer and the patterns quantitated by densitometric analysis of the allele pattern. Differences in the distribution of alleles between pools of affected and unaffected individuals, including a reduction in the number of alleles in the affected pool, indicate the sharing of a region of a chromosome. We have found this method effective for markers 10 - 15 cM away from the disease locus for a recessive genetic disease.

Quantitative holographic interferometry applied to combustion and compressible flow research

NASA Astrophysics Data System (ADS)

Bryanston-Cross, Peter J.; Towers, D. P.

1993-03-01

The application of holographic interferometry to phase object analysis is described. Emphasis has been given to a method of extracting quantitative information automatically from the interferometric fringe data. To achieve this a carrier frequency has been added to the holographic data. This has made it possible, firstly to form a phase map using a fast Fourier transform (FFT) algorithm. Then to `solve,' or unwrap, this image to give a contiguous density map using a minimum weight spanning tree (MST) noise immune algorithm, known as fringe analysis (FRAN). Applications of this work to a burner flame and a compressible flow are presented. In both cases the spatial frequency of the fringes exceed the resolvable limit of conventional digital framestores. Therefore, a flatbed scanner with a resolution of 3200 X 2400 pixels has been used to produce very high resolution digital images from photographs. This approach has allowed the processing of data despite the presence of caustics, generated by strong thermal gradients at the edge of the combustion field. A similar example is presented from the analysis of a compressible transonic flow in the shock wave and trailing edge regions.

Combining FT-IR spectroscopy and multivariate analysis for qualitative and quantitative analysis of the cell wall composition changes during apples development.

PubMed

Szymanska-Chargot, M; Chylinska, M; Kruk, B; Zdunek, A

2015-01-22

The aim of this work was to quantitatively and qualitatively determine the composition of the cell wall material from apples during development by means of Fourier transform infrared (FT-IR) spectroscopy. The FT-IR region of 1500-800 cm(-1), containing characteristic bands for galacturonic acid, hemicellulose and cellulose, was examined using principal component analysis (PCA), k-means clustering and partial least squares (PLS). The samples were differentiated by development stage and cultivar using PCA and k-means clustering. PLS calibration models for galacturonic acid, hemicellulose and cellulose content from FT-IR spectra were developed and validated with the reference data. PLS models were tested using the root-mean-square errors of cross-validation for contents of galacturonic acid, hemicellulose and cellulose which was 8.30 mg/g, 4.08% and 1.74%, respectively. It was proven that FT-IR spectroscopy combined with chemometric methods has potential for fast and reliable determination of the main constituents of fruit cell walls. Copyright © 2014 Elsevier Ltd. All rights reserved.

Eifel maars: Quantitative shape characterization of juvenile ash particles (Eifel Volcanic Field, Germany)

NASA Astrophysics Data System (ADS)

Rausch, Juanita; Grobéty, Bernard; Vonlanthen, Pierre

2015-01-01

The Eifel region in western central Germany is the type locality for maar volcanism, which is classically interpreted to be the result of explosive eruptions due to shallow interaction between magma and external water (i.e. phreatomagmatic eruptions). Sedimentary structures, deposit features and particle morphology found in many maar deposits of the West Eifel Volcanic Field (WEVF), in contrast to deposits in the East Eifel Volcanic Field (EEVF), lack the diagnostic criteria of typical phreatomagmatic deposits. The aim of this study was to determine quantitatively the shape of WEVF and EEVF maar ash particles in order to infer the governing eruption style in Eifel maar volcanoes. The quantitative shape characterization was done by analyzing fractal dimensions of particle contours (125-250 μm sieve fraction) obtained from Scanning electron microscopy (SEM) and SEM micro-computed tomography (SEM micro-CT) images. The fractal analysis (dilation method) and the fractal spectrum technique confirmed that the WEVF and EEVF maar particles have contrasting multifractal shapes. Whereas the low small-scale dimensions of EEVF particles (Eppelsberg Green Unit) coincide with previously published values for phreatomagmatic particles, the WEVF particles (Meerfelder Maar, Pulvermaar and Ulmener Maar) have larger values indicating more complex small-scale features, which are characteristic for magmatic particles. These quantitative results are strengthening the qualitative microscopic observations, that the studied WEVF maar eruptions are rather dominated by magmatic processes. The different eruption styles in the two volcanic fields can be explained by the different geological and hydrological settings found in both regions and the different chemical compositions of the magmas.

Localization and quantitative co-localization of enamelin with amelogenin.

PubMed

Gallon, Victoria; Chen, Lisha; Yang, Xiudong; Moradian-Oldak, Janet

2013-08-01

Enamelin and amelogenin are vital proteins in enamel formation. The cooperative function of these two proteins controls crystal nucleation and morphology in vitro. We quantitatively analyzed the co-localization between enamelin and amelogenin by confocal microscopy and using two antibodies, one raised against a sequence in the porcine 32 kDa enamelin region and the other raised against full-length recombinant mouse amelogenin. We further investigated the interaction of the porcine 32 kDa enamelin and recombinant amelogenin using immuno-gold labeling. This study reports the quantitative co-localization results for postnatal days 1-8 mandibular mouse molars. We show that amelogenin and enamelin are secreted into the extracellular matrix on the cuspal slopes of the molars at day 1 and that secretion continues to at least day 8. Quantitative co-localization analysis (QCA) was performed in several different configurations using large (45 μm height, 33 μm width) and small (7 μm diameter) regions of interest to elucidate any patterns. Co-localization patterns in day 8 samples revealed that enamelin and amelogenin co-localize near the secretory face of the ameloblasts and appear to be secreted approximately in a 1:1 ratio. The degree of co-localization decreases as the enamel matures, both along the secretory face of ameloblasts and throughout the entire thickness of the enamel. Immuno-reactivity against enamelin is concentrated along the secretory face of ameloblasts, supporting the theory that this protein together with amelogenin is intimately involved in mineral induction at the beginning of enamel formation. Copyright © 2013 Elsevier Inc. All rights reserved.

Assessment of metabolic bone diseases by quantitative computed tomography

NASA Technical Reports Server (NTRS)

Richardson, M. L.; Genant, H. K.; Cann, C. E.; Ettinger, B.; Gordan, G. S.; Kolb, F. O.; Reiser, U. J.

1985-01-01

Advances in the radiologic sciences have permitted the development of numerous noninvasive techniques for measuring the mineral content of bone, with varying degrees of precision, accuracy, and sensitivity. The techniques of standard radiography, radiogrammetry, photodensitometry, Compton scattering, neutron activation analysis, single and dual photon absorptiometry, and quantitative computed tomography (QCT) are described and reviewed in depth. Results from previous cross-sectional and longitudinal QCT investigations are given. They then describe a current investigation in which they studied 269 subjects, including 173 normal women, 34 patients with hyperparathyroidism, 24 patients with steroid-induced osteoporosis, and 38 men with idiopathic osteoporosis. Spinal quantitative computed tomography, radiogrammetry, and single photon absorptiometry were performed, and a spinal fracture index was calculated on all patients. The authors found a disproportionate loss of spinal trabecular mineral compared to appendicular mineral in the men with idiopathic osteoporosis and the patients with steroid-induced osteoporosis. They observed roughly equivalent mineral loss in both the appendicular and axial regions in the hyperparathyroid patients. The appendicular cortical measurements correlated moderately well with each other but less well with spinal trabecular QCT. The spinal fracture index correlated well with QCT and less well with the appendicular measurements. Knowledge of appendicular cortical mineral status is important in its own right but is not a valid predictor of axial trabecular mineral status, which may be disproportionately decreased in certain diseases. Quantitative CT provides a reliable means of assessing the latter region of the skeleton, correlates well with the spinal fracture index (a semiquantitative measurement of end-organ failure), and offers the clinician a sensitive means of following the effects of therapy.

Complementary biomarker-based methods for characterising Arctic sea ice conditions: A case study comparison between multivariate analysis and the PIP25 index

NASA Astrophysics Data System (ADS)

Köseoğlu, Denizcan; Belt, Simon T.; Smik, Lukas; Yao, Haoyi; Panieri, Giuliana; Knies, Jochen

2018-02-01

The discovery of IP25 as a qualitative biomarker proxy for Arctic sea ice and subsequent introduction of the so-called PIP25 index for semi-quantitative descriptions of sea ice conditions has significantly advanced our understanding of long-term paleo Arctic sea ice conditions over the past decade. We investigated the potential for classification tree (CT) models to provide a further approach to paleo Arctic sea ice reconstruction through analysis of a suite of highly branched isoprenoid (HBI) biomarkers in ca. 200 surface sediments from the Barents Sea. Four CT models constructed using different HBI assemblages revealed IP25 and an HBI triene as the most appropriate classifiers of sea ice conditions, achieving a >90% cross-validated classification rate. Additionally, lower model performance for locations in the Marginal Ice Zone (MIZ) highlighted difficulties in characterisation of this climatically-sensitive region. CT model classification and semi-quantitative PIP25-derived estimates of spring sea ice concentration (SpSIC) for four downcore records from the region were consistent, although agreement between proxy and satellite/observational records was weaker for a core from the west Svalbard margin, likely due to the highly variable sea ice conditions. The automatic selection of appropriate biomarkers for description of sea ice conditions, quantitative model assessment, and insensitivity to the c-factor used in the calculation of the PIP25 index are key attributes of the CT approach, and we provide an initial comparative assessment between these potentially complementary methods. The CT model should be capable of generating longer-term temporal shifts in sea ice conditions for the climatically sensitive Barents Sea.

Chronic obstructive pulmonary disease: quantitative and visual ventilation pattern analysis at xenon ventilation CT performed by using a dual-energy technique.

PubMed

Park, Eun-Ah; Goo, Jin Mo; Park, Sang Joon; Lee, Hyun Ju; Lee, Chang Hyun; Park, Chang Min; Yoo, Chul-Gyu; Kim, Jong Hyo

2010-09-01

To evaluate the potential of xenon ventilation computed tomography (CT) in the quantitative and visual analysis of chronic obstructive pulmonary disease (COPD). This study was approved by the institutional review board. After informed consent was obtained, 32 patients with COPD underwent CT performed before the administration of xenon, two-phase xenon ventilation CT with wash-in (WI) and wash-out (WO) periods, and pulmonary function testing (PFT). For quantitative analysis, results of PFT were compared with attenuation parameters from prexenon images and xenon parameters from xenon-enhanced images in the following three areas at each phase: whole lung, lung with normal attenuation, and low-attenuating lung (LAL). For visual analysis, ventilation patterns were categorized according to the pattern of xenon attenuation in the area of structural abnormalities compared with that in the normal-looking background on a per-lobe basis: pattern A consisted of isoattenuation or high attenuation in the WI period and isoattenuation in the WO period; pattern B, isoattenuation or high attenuation in the WI period and high attenuation in the WO period; pattern C, low attenuation in both the WI and WO periods; and pattern D, low attenuation in the WI period and isoattenuation or high attenuation in the WO period. Among various attenuation and xenon parameters, xenon parameters of the LAL in the WO period showed the best inverse correlation with results of PFT (P < .0001). At visual analysis, while emphysema (which affected 99 lobes) commonly showed pattern A or B, airway diseases such as obstructive bronchiolitis (n = 5) and bronchiectasis (n = 2) and areas with a mucus plug (n = 1) or centrilobular nodules (n = 5) showed pattern D or C. WI and WO xenon ventilation CT is feasible for the simultaneous regional evaluation of structural and ventilation abnormalities both quantitatively and qualitatively in patients with COPD. (c) RSNA, 2010.

Alpha-A crystallin: quantitation of C-terminal modification during lens aging

NASA Technical Reports Server (NTRS)

Takemoto, L.; Gopalakrishnan, S.; Spooner, B. S. (Principal Investigator)

1994-01-01

Previous studies have demonstrated that the C-terminal region of alpha-A crystallin is susceptible to age-dependent, posttranslational modification. To quantitate the amount of modification, alpha-A crystallin was purified from total proteins of the aging bovine lens, then digested with lys-C endoproteinase. Reverse phase, high pressure liquid chromatography was used to resolve and quantitate the resulting peptides, to determine the amount of C-terminal peptide relative to peptides from other regions of the protein that have not been reported to undergo modification. The results indicate that relative to alpha-A crystallin from newborn lens, posttranslational modification has occurred in approximately 45-55% of the C-terminal region from mature lens. These results demonstrate extensive modification of the C-terminal region of alpha-A crystallin from the mature lens, indicating that during the aging process, posttranslational modifications in this region may make significant contributions to the aggregated state and/or molecular chaperone properties of the molecule.

Alzheimer's disease detection using 11C-PiB with improved partial volume effect correction

NASA Astrophysics Data System (ADS)

Raniga, Parnesh; Bourgeat, Pierrick; Fripp, Jurgen; Acosta, Oscar; Ourselin, Sebastien; Rowe, Christopher; Villemagne, Victor L.; Salvado, Olivier

2009-02-01

Despite the increasing use of 11C-PiB in research into Alzheimer's disease (AD), there are few standardized analysis procedures that have been reported or published. This is especially true with regards to partial volume effects (PVE) and partial volume correction. Due to the nature of PET physics and acquisition, PET images exhibit relatively low spatial resolution compared to other modalities, resulting in bias of quantitative results. Although previous studies have applied PVE correction techniques on 11C-PiB data, the results have not been quantitatively evaluated and compared against uncorrected data. The aim of this study is threefold. Firstly, a realistic synthetic phantom was created to quantify PVE. Secondly, MRI partial volume estimate segmentations were used to improve voxel-based PVE correction instead of using hard segmentations. Thirdly, quantification of PVE correction was evaluated on 34 subjects (AD=10, Normal Controls (NC)=24), including 12 PiB positive NC. Regional analysis was performed using the Anatomical Automatic Labeling (AAL) template, which was registered to each patient. Regions of interest were restricted to the gray matter (GM) defined by the MR segmentation. Average normalized intensity of the neocortex and selected regions were used to evaluate the discrimination power between AD and NC both with and without PVE correction. Receiver Operating Characteristic (ROC) curves were computed for the binary discrimination task. The phantom study revealed signal losses due to PVE between 10 to 40 % which were mostly recovered to within 5% after correction. Better classification was achieved after PVE correction, resulting in higher areas under ROC curves.

Analysis of Lard in Lipstick Formulation Using FTIR Spectroscopy and Multivariate Calibration: A Comparison of Three Extraction Methods.

PubMed

Waskitho, Dri; Lukitaningsih, Endang; Sudjadi; Rohman, Abdul

2016-01-01

Analysis of lard extracted from lipstick formulation containing castor oil has been performed using FTIR spectroscopic method combined with multivariate calibration. Three different extraction methods were compared, namely saponification method followed by liquid/liquid extraction with hexane/dichlorometane/ethanol/water, saponification method followed by liquid/liquid extraction with dichloromethane/ethanol/water, and Bligh & Dyer method using chloroform/methanol/water as extracting solvent. Qualitative and quantitative analysis of lard were performed using principle component (PCA) and partial least square (PLS) analysis, respectively. The results showed that, in all samples prepared by the three extraction methods, PCA was capable of identifying lard at wavelength region of 1200-800 cm -1 with the best result was obtained by Bligh & Dyer method. Furthermore, PLS analysis at the same wavelength region used for qualification showed that Bligh and Dyer was the most suitable extraction method with the highest determination coefficient (R 2 ) and the lowest root mean square error of calibration (RMSEC) as well as root mean square error of prediction (RMSEP) values.

Quantitative susceptibility map analysis in preterm neonates with germinal matrix-intraventricular hemorrhage.

PubMed

Tortora, Domenico; Severino, Mariasavina; Sedlacik, Jan; Toselli, Benedetta; Malova, Mariya; Parodi, Alessandro; Morana, Giovanni; Fato, Marco Massimo; Ramenghi, Luca Antonio; Rossi, Andrea

2018-05-10

Germinal matrix-intraventricular hemorrhage (GMH-IVH) is a common form of intracranial hemorrhage occurring in preterm neonates that may affect normal brain development. Although the primary lesion is easily identified on MRI by the presence of blood products, its exact extent may not be recognizable with conventional sequences. Quantitative susceptibility mapping (QSM) quantify the spatial distribution of magnetic susceptibility within biological tissues, including blood degradation products. To evaluate magnetic susceptibility of normal-appearing white (WM) and gray matter regions in preterm neonates with and without GMH-IVH. Retrospective case-control. A total of 127 preterm neonates studied at term equivalent age: 20 had mild GMH-IVH (average gestational age 28.7 ± 2.1 weeks), 15 had severe GMH-IVH (average gestational age 29.3 ± 1.8 weeks), and 92 had normal brain MRI (average gestational age 29.8 ± 1.8 weeks). QSM at 1.5 Tesla. QSM analysis was performed for each brain hemisphere with a region of interest-based approach including five WM regions (centrum semiovale, frontal, parietal, temporal, and cerebellum), and a subcortical gray matter region (basal ganglia/thalami). Changes in magnetic susceptibility were explored using a one-way analysis of covariance, according to GMH-IVH severity (P < 0.05). In preterm neonates with normal brain MRI, all white and subcortical gray matter regions had negative magnetic susceptibility values (diamagnetic). Neonates with severe GMH-IVH showed higher positive magnetic susceptibility values (i.e. paramagnetic) in the centrum semiovale (0.0019 versus -0.0014 ppm; P < 0.001), temporal WM (0.0011 versus -0.0012 ppm; P = 0.037), and parietal WM (0.0005 versus -0.0001 ppm; P = 0.002) compared with controls. No differences in magnetic susceptibility were observed between neonates with mild GMH-IVH and controls (P = 0.236). Paramagnetic susceptibility changes occur in several normal-appearing WM regions of neonates with severe GMH-IVH, likely related to the accumulation of hemosiderin/ferritin iron secondary to diffusion of extracellular hemoglobin from the ventricle into the periventricular WM. 4 Technical Efficacy: Stage 3 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Markers of oxidative damage to lipids, nucleic acids and proteins and antioxidant enzymes activities in Alzheimer's disease brain: A meta-analysis in human pathological specimens.

PubMed

Zabel, Matthew; Nackenoff, Alex; Kirsch, Wolff M; Harrison, Fiona E; Perry, George; Schrag, Matthew

2018-02-01

Oxidative stress and decreased cellular responsiveness to oxidative stress are thought to influence brain aging and Alzheimer's disease, but the specific patterns of oxidative damage and the underlying mechanism leading to this damage are not definitively known. The objective of this study was to define the pattern of changes in oxidative-stress related markers by brain region in human Alzheimer's disease and mild cognitive impairment brain tissue. Observational case-control studies were identified from systematic queries of PubMed, ISI Web of Science and Scopus databases and studies were evaluated with appropriate quality measures. The data was used to construct a region-by-region meta-analysis of malondialdehyde, 4-hydroxynonenal, protein carbonylation, 8-hydroxyguanine levels and superoxide dismutase, glutathione peroxidase, glutathione reductase and catalase activities. We also evaluated ascorbic acid, tocopherol, uric acid and glutathione levels. The analysis was complicated in several cases by publication bias and/or outlier data. We found that malondialdehyde levels were slightly increased in the temporal and occipital lobes and hippocampus, but this analysis was significantly impacted by publication bias. 4-hydroxynonenal levels were unchanged in every brain region. There was no change in 8-hydroxyguanine level in any brain region and protein carbonylation levels were unchanged except for a slight increase in the occipital lobe. Superoxide dismutase, glutathione peroxidase and reductase and catalase activities were not decreased in any brain region. There was limited data reporting non-enzymatic antioxidant levels in Alzheimer's disease brain, although glutathione and tocopherol levels appear to be unchanged. Minimal quantitative data is available from brain tissue from patients with mild cognitive impairment. While there is modest evidence supporting minor regional changes in markers of oxidative damage, this analysis fails to identify a consistent pattern of pro-oxidative changes and accumulation of oxidative damage in bulk tissue analysis in the setting of Alzheimer's disease, as has been widely reported. Copyright © 2017 Elsevier Inc. All rights reserved.

Electric Field Quantitative Measurement System and Method

NASA Technical Reports Server (NTRS)

Generazio, Edward R. (Inventor)

2016-01-01

A method and system are provided for making a quantitative measurement of an electric field. A plurality of antennas separated from one another by known distances are arrayed in a region that extends in at least one dimension. A voltage difference between at least one selected pair of antennas is measured. Each voltage difference is divided by the known distance associated with the selected pair of antennas corresponding thereto to generate a resulting quantity. The plurality of resulting quantities defined over the region quantitatively describe an electric field therein.

Volumetric Analysis of Regional Variability in the Cerebellum of Children with Dyslexia

PubMed Central

Stuebing, Karla; Juranek, Jenifer; Fletcher, Jack M.

2013-01-01

Cerebellar deficits and subsequent impairment in procedural learning may contribute to both motor difficulties and reading impairment in dyslexia. We used quantitative magnetic resonance imaging to investigate the role of regional variation in cerebellar anatomy in children with single-word decoding impairments (N=23), children with impairment in fluency alone (N=8), and typically developing children (N=16). Children with decoding impairments (dyslexia) demonstrated no statistically significant differences in overall grey and white matter volumes or cerebellar asymmetry; however, reduced volume in the anterior lobe of the cerebellum relative to typically developing children was observed. These results implicate cerebellar involvement in dyslexia and establish an important foundation for future research on the connectivity of the cerebellum and cortical regions typically associated with reading impairment. PMID:23828023

Volumetric analysis of regional variability in the cerebellum of children with dyslexia.

PubMed

Fernandez, Vindia G; Stuebing, Karla; Juranek, Jenifer; Fletcher, Jack M

2013-12-01

Cerebellar deficits and subsequent impairment in procedural learning may contribute to both motor difficulties and reading impairment in dyslexia. We used quantitative magnetic resonance imaging to investigate the role of regional variation in cerebellar anatomy in children with single-word decoding impairments (N = 23), children with impairment in fluency alone (N = 8), and typically developing children (N = 16). Children with decoding impairments (dyslexia) demonstrated no statistically significant differences in overall grey and white matter volumes or cerebellar asymmetry; however, reduced volume in the anterior lobe of the cerebellum relative to typically developing children was observed. These results implicate cerebellar involvement in dyslexia and establish an important foundation for future research on the connectivity of the cerebellum and cortical regions typically associated with reading impairment.

Use of local noise power spectrum and wavelet analysis in quantitative image quality assurance for EPIDs

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

Lee, Soyoung

Purpose: To investigate the use of local noise power spectrum (NPS) to characterize image noise and wavelet analysis to isolate defective pixels and inter-subpanel flat-fielding artifacts for quantitative quality assurance (QA) of electronic portal imaging devices (EPIDs). Methods: A total of 93 image sets including custom-made bar-pattern images and open exposure images were collected from four iViewGT a-Si EPID systems over three years. Global quantitative metrics such as modulation transform function (MTF), NPS, and detective quantum efficiency (DQE) were computed for each image set. Local NPS was also calculated for individual subpanels by sampling region of interests within each subpanelmore » of the EPID. The 1D NPS, obtained by radially averaging the 2D NPS, was fitted to a power-law function. The r-square value of the linear regression analysis was used as a singular metric to characterize the noise properties of individual subpanels of the EPID. The sensitivity of the local NPS was first compared with the global quantitative metrics using historical image sets. It was then compared with two commonly used commercial QA systems with images collected after applying two different EPID calibration methods (single-level gain and multilevel gain). To detect isolated defective pixels and inter-subpanel flat-fielding artifacts, Haar wavelet transform was applied on the images. Results: Global quantitative metrics including MTF, NPS, and DQE showed little change over the period of data collection. On the contrary, a strong correlation between the local NPS (r-square values) and the variation of the EPID noise condition was observed. The local NPS analysis indicated image quality improvement with the r-square values increased from 0.80 ± 0.03 (before calibration) to 0.85 ± 0.03 (after single-level gain calibration) and to 0.96 ± 0.03 (after multilevel gain calibration), while the commercial QA systems failed to distinguish the image quality improvement between the two calibration methods. With wavelet analysis, defective pixels and inter-subpanel flat-fielding artifacts were clearly identified as spikes after thresholding the inversely transformed images. Conclusions: The proposed local NPS (r-square values) showed superior sensitivity to the noise level variations of individual subpanels compared with global quantitative metrics such as MTF, NPS, and DQE. Wavelet analysis was effective in detecting isolated defective pixels and inter-subpanel flat-fielding artifacts. The proposed methods are promising for the early detection of imaging artifacts of EPIDs.« less

Chemical fingerprinting and source tracing of obsidian: the central Mediterranean trade in black gold.

PubMed

Tykot, Robert H

2002-08-01

Chemical fingerprinting using major or trace element composition is used to characterize the Mediterranean island sources of obsidian and can even differentiate as many as nine flows in the Monte Arci region of Sardinia. Analysis of significant numbers of obsidian artifacts from Neolithic sites in the central Mediterranean reveals specific patterns of source exploitation and suggests particular trade mechanisms and routes. The use of techniques such as X-ray fluorescence, the electron microprobe, neutron activation analysis, and laser ablation ICP mass spectrometry are emphasized in order to produce quantitative results while minimizing damage to valuable artifacts.

2D- and 3D-quantitative structure-activity relationship studies for a series of phenazine N,N'-dioxide as antitumour agents.

PubMed

Cunha, Jonathan Da; Lavaggi, María Laura; Abasolo, María Inés; Cerecetto, Hugo; González, Mercedes

2011-12-01

Hypoxic regions of tumours are associated with increased resistance to radiation and chemotherapy. Nevertheless, hypoxia has been used as a tool for specific activation of some antitumour prodrugs, named bioreductive agents. Phenazine dioxides are an example of such bioreductive prodrugs. Our 2D-quantitative structure activity relationship studies established that phenazine dioxides electronic and lipophilic descriptors are related to survival fraction in oxia or in hypoxia. Additionally, statistically significant models, derived by partial least squares, were obtained between survival fraction in oxia and comparative molecular field analysis standard model (r² = 0.755, q² = 0.505 and F = 26.70) or comparative molecular similarity indices analysis-combined steric and electrostatic fields (r² = 0.757, q² = 0.527 and F = 14.93), and survival fraction in hypoxia and comparative molecular field analysis standard model (r² = 0.736, q² = 0.521 and F = 18.63) or comparative molecular similarity indices analysis-hydrogen bond acceptor field (r² = 0.858, q² = 0.737 and F = 27.19). Categorical classification was used for the biological parameter selective cytotoxicity emerging also good models, derived by soft independent modelling of class analogy, with both comparative molecular field analysis standard model (96% of overall classification accuracy) and comparative molecular similarity indices analysis-steric field (92% of overall classification accuracy). 2D- and 3D-quantitative structure-activity relationships models provided important insights into the chemical and structural basis involved in the molecular recognition process of these phenazines as bioreductive agents and should be useful for the design of new structurally related analogues with improved potency. © 2011 John Wiley & Sons A/S.

Pleiotropy Analysis of Quantitative Traits at Gene Level by Multivariate Functional Linear Models

PubMed Central

Wang, Yifan; Liu, Aiyi; Mills, James L.; Boehnke, Michael; Wilson, Alexander F.; Bailey-Wilson, Joan E.; Xiong, Momiao; Wu, Colin O.; Fan, Ruzong

2015-01-01

In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution tests based on Pillai–Bartlett trace, Hotelling–Lawley trace, and Wilks’s Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case. PMID:25809955

Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models.

PubMed

Wang, Yifan; Liu, Aiyi; Mills, James L; Boehnke, Michael; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao; Wu, Colin O; Fan, Ruzong

2015-05-01

In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution tests based on Pillai-Bartlett trace, Hotelling-Lawley trace, and Wilks's Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case. © 2015 WILEY PERIODICALS, INC.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes.

PubMed

Marone, Daniela; Russo, Maria A; Laidò, Giovanni; De Vita, Pasquale; Papa, Roberto; Blanco, Antonio; Gadaleta, Agata; Rubiales, Diego; Mastrangelo, Anna M

2013-08-19

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2-6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes

PubMed Central

2013-01-01

Background Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Results Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2–6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. Conclusions The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat. PMID:23957646

Quantitative regional and sub-regional analysis of femoral and tibial subchondral bone mineral density (sBMD) using computed tomography (CT): comparison of non-osteoarthritic (OA) and severe OA knees.

PubMed

Omoumi, P; Babel, H; Jolles, B M; Favre, J

2017-11-01

This study aimed to compare subchondral bone mineral density (sBMD) between non-radiographic osteoarthritic (OA) and medial femorotibial OA knees, using computed tomography (CT). CT exams from 16 non-radiographic OA (KL grade < 2) and 16 severe medial OA (KL grade ≥ 3) knees (average age of 61.7 ± 3 and 62.2 ± 5 years old respectively, 50% male in each group), were retrospectively analyzed. CT exams were segmented and 3D maps of sBMD based on the CT number in the most superficial 3 mm of femoral and tibial subchondral bone were computed. Average sBMD and medial-to-lateral sBMD ratios were calculated for total load-bearing regions and for sub-regions of interest in the femur and tibia. The analysis of total load-bearing regions did not reveal any significant difference between groups, except for the lateral tibia, where OA knees had lower sBMD. Sub-regional analysis unveiled differences with some sub-regions of the femur and tibia presenting significantly lower (in the lateral compartment) or higher (in the medial compartment) sBMD in OA knees compared to non-OA knees. The M/L sBMD ratios were significantly higher for OA knees compared to non-OA knees for all regions and sub-regions, except for the internal sub-regions. sBMD locally differs between non-OA and OA knees, in agreement with prior knowledge on biomechanics. CT proved to be a valuable tool for 3D analysis of femoral and tibial sBMD, which can be used in future studies to describe the chronology of sBMD alterations and improve our understanding of the role of subchondral bone in knee OA. Copyright © 2017 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

The Determinant Factors of Regional Development Toward Land Use Change in Deli Serdang

NASA Astrophysics Data System (ADS)

Lindarto, D.; Sirojuzilam; Badaruddin; Dwira

2017-03-01

The concept of regional development Mebidangro (Medan, Binjai, Deli Serdang, and Karo) creating neighboring region hinterland Medan city with Deli Serdang Regency especially in Tembung village, Percut Sei Tuan District. Population structure in Tembung shows occurrence condition of rural-urban change which seen from the sprawl land use change. The aim of the study is to reveal the genius locus as one of land use change factors. The study conducted with quantitative approach intended at obtaining variables which describing several factors forming land use change. Descriptive approach intended to give an idea, justification, and fact-finding with correct interpretation. Data collected through a purposive sampling of 300 respondents who have built the house between 2010 till 2014. With overlay figure/ground technique, scoring analysis, descriptive quantitative and SEM (Structural Equational Models) gained a result that place character/genius locus (p=0,007) potentially as one of the main land use change driving factors besides accessibility (p=0,039), infrastructure (p=0,005), social-economic p=0,038). Topographic (p=0,663) was inversely potentially. The implication of the findings is required intensive control in space utilization considering the rapid change in land use transformation that tend to have the negative impact of urban sprawl.

Quantitative proteome analysis of barley seeds using ruthenium(II)-tris-(bathophenanthroline-disulphonate) staining.

PubMed

Witzel, Katja; Surabhi, Giridara-Kumar; Jyothsnakumari, Gottimukkala; Sudhakar, Chinta; Matros, Andrea; Mock, Hans-Peter

2007-04-01

This paper describes the application of the recently introduced fluorescence stain Ruthenium(II)-tris-(bathophenanthroline-disulphonate) (RuBP) on a comparative proteome analysis of two phenotypically different barley lines. We carried out an analysis of protein patterns from 2-D gels of the parental lines of the Oregon Wolfe Barley mapping population DOM and REC and stained with either the conventional colloidal Coomassie Brilliant Blue (cCBB) or with the novel RuBP solution. We wished to experimentally verify the usefulness of such a stain in evaluating the complex pattern of a seed proteome, in comparison to the previously used cCBB staining technique. To validate the efficiency of visualization by both stains, we first compared the overall number of detected protein spots. On average, 790 spots were visible by cCBB staining and 1200 spots by RuBP staining. Then, the intensity of a set of spots was assessed, and changes in relative abundance were determined using image analysis software. As expected, staining with RuBP performed better in quantitation in terms of sensitivity and dynamic range. Furthermore, spots from a cultivar-specific region in the protein map were chosen for identification to asses the gain of biological information due to the staining procedure. From this particular region, eight spots were visualized exclusively by RuBP and identification was successful for all spots, proving the ability to identify even very low abundant proteins. Performance in MS analysis was comparable for both protein stains. Proteins were identified by MALDI-TOF MS peptide mass fingerprinting. This approach was not successful for all spots, due to the restricted entry number for barley in the database. Therefore, we subsequently used LC-ESI-Q-TOF MS/MS and de novo sequencing for identification. Because only an insufficient number of proteins from barley is annotated, an EST-based identification strategy was chosen for our experiment. We wished to test whether under these limitations the application of a more sensitive stain would lead to a more advanced proteome approach. In summary, we demonstrate here that the application of RuBP as an economical but reliable and sensitive fluorescence stain is highly suitable for quantitative proteome analysis of plant seeds.

Quantitative 3D reconstruction of airway and pulmonary vascular trees using HRCT

NASA Astrophysics Data System (ADS)

Wood, Susan A.; Hoford, John D.; Hoffman, Eric A.; Zerhouni, Elias A.; Mitzner, Wayne A.

1993-07-01

Accurate quantitative measurements of airway and vascular dimensions are essential to evaluate function in the normal and diseased lung. In this report, a novel method is described for three-dimensional extraction and analysis of pulmonary tree structures using data from High Resolution Computed Tomography (HRCT). Serially scanned two-dimensional slices of the lower left lobe of isolated dog lungs were stacked to create a volume of data. Airway and vascular trees were three-dimensionally extracted using a three dimensional seeded region growing algorithm based on difference in CT number between wall and lumen. To obtain quantitative data, we reduced each tree to its central axis. From the central axis, branch length is measured as the distance between two successive branch points, branch angle is measured as the angle produced by two daughter branches, and cross sectional area is measured from a plane perpendicular to the central axis point. Data derived from these methods can be used to localize and quantify structural differences both during changing physiologic conditions and in pathologic lungs.

Quantitative EEG and its Correlation with Cardiovascular, Cognition and mood State: an Integrated Study in Simulated Microgravity

NASA Astrophysics Data System (ADS)

Zhang, Jianyuan; Hu, Bin; Chen, Wenjuan; Moore, Philip; Xu, Tingting; Dong, Qunxi; Liu, Zhenyu; Luo, Yuejia; Chen, Shanguang

2014-12-01

The focus of the study is the estimation of the effects of microgravity on the central nervous activity and its underlying influencing mechanisms. To validate the microgravity-induced physiological and psychological effects on EEG, quantitative EEG features, cardiovascular indicators, mood state, and cognitive performances data collection was achieved during a 45 day period using a -6°head-down bed rest (HDBR) integrated approach. The results demonstrated significant differences in EEG data, as an increased Theta wave, a decreased Beta wave and a reduced complexity of brain, accompanied with an increased heart rate and pulse rate, decreased positive emotion, and degraded emotion conflict monitoring performance. The canonical correlation analysis (CCA) based cardiovascular and cognitive related EEG model showed the cardiovascular effect on EEG mainly affected bilateral temporal region and the cognitive effect impacted parietal-occipital and frontal regions. The results obtained in the study support the use of an approach which combines a multi-factor influential mechanism hypothesis. The changes in the EEG data may be influenced by both cardiovascular and cognitive effects.

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient

PubMed Central

2011-01-01

Background Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. Methods We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. Results In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. Conclusions This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus. PMID:22044463

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient.

PubMed

Thonberg, Håkan; Fallström, Marie; Björkström, Jenny; Schoumans, Jacqueline; Nennesmo, Inger; Graff, Caroline

2011-11-01

Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus.

Perioperative Assessment of Myocardial Deformation

PubMed Central

Duncan, Andra E.; Alfirevic, Andrej; Sessler, Daniel I.; Popovic, Zoran B.; Thomas, James D.

2014-01-01

Evaluation of left ventricular performance improves risk assessment and guides anesthetic decisions. However, the most common echocardiographic measure of myocardial function, the left ventricular ejection fraction (LVEF), has important limitations. LVEF is limited by subjective interpretation which reduces accuracy and reproducibility, and LVEF assesses global function without characterizing regional myocardial abnormalities. An alternative objective echocardiographic measure of myocardial function is thus needed. Myocardial deformation analysis, which performs quantitative assessment of global and regional myocardial function, may be useful for perioperative care of surgical patients. Myocardial deformation analysis evaluates left ventricular mechanics by quantifying strain and strain rate. Strain describes percent change in myocardial length in the longitudinal (from base to apex) and circumferential (encircling the short-axis of the ventricle) direction and change in thickness in the radial direction. Segmental strain describes regional myocardial function. Strain is a negative number when the ventricle shortens longitudinally or circumferentially and is positive with radial thickening. Reference values for normal longitudinal strain from a recent meta-analysis using transthoracic echocardiography are (mean ± SD) −19.7 ± 0.4%, while radial and circumferential strain are 47.3 ± 1.9 and −23.3 ± 0.7%, respectively. The speed of myocardial deformation is also important and is characterized by strain rate. Longitudinal systolic strain rate in healthy subjects averages −1.10 ± 0.16 sec−1. Assessment of myocardial deformation requires consideration of both strain (change in deformation), which correlates with LVEF, and strain rate (speed of deformation), which correlates with rate of rise of left ventricular pressure (dP/dt). Myocardial deformation analysis also evaluates ventricular relaxation, twist, and untwist, providing new and noninvasive methods to assess components of myocardial systolic and diastolic function. Myocardial deformation analysis is based on either Doppler or a non-Doppler technique, called speckle-tracking echocardiography. Myocardial deformation analysis provides quantitative measures of global and regional myocardial function for use in the perioperative care of the surgical patient. For example, coronary graft occlusion after coronary artery bypass grafting is detected by an acute reduction in strain in the affected coronary artery territory. In addition, assessment of left ventricular mechanics detects underlying myocardial pathology before abnormalities become apparent on conventional echocardiography. Certainly, patients with aortic regurgitation demonstrate reduced longitudinal strain before reduction in LVEF occurs, which allows detection of subclinical left ventricular dysfunction and predicts increased risk for heart failure and impaired myocardial function after surgical repair. In this review we describe the principles, techniques, and clinical application of myocardial deformation analysis. PMID:24557101

Allele-specific methylated multiplex real-time quantitative PCR (ASMM RTQ-PCR), a powerful method for diagnosing loss of imprinting of the 11p15 region in Russell Silver and Beckwith Wiedemann syndromes.

PubMed

Azzi, Salah; Steunou, Virginie; Rousseau, Alexandra; Rossignol, Sylvie; Thibaud, Nathalie; Danton, Fabienne; Le Jule, Marilyne; Gicquel, Christine; Le Bouc, Yves; Netchine, Irène

2011-02-01

Many human syndromes involve a loss of imprinting (LOI) due to a loss (LOM) or a gain of DNA methylation (GOM). Most LOI occur as mosaics and can therefore be difficult to detect with conventional methods. The human imprinted 11p15 region is crucial for the control of fetal growth, and LOI at this locus is associated with two clinical disorders with opposite phenotypes: Beckwith-Wiedemann syndrome (BWS), characterized by fetal overgrowth and a high risk of tumors, and Russell-Silver syndrome (RSS), characterized by intrauterine and postnatal growth restriction. Until recently, we have been using Southern blotting for the diagnosis of RSS and BWS. We describe here a powerful quantitative technique, allele-specific methylated multiplex real-time quantitative PCR (ASMM RTQ-PCR), for the diagnosis of these two complex disorders. We first checked the specificity of the probes and primers used for ASMM RTQ-PCR. We then carried out statistical validation for this method, on both retrospective and prospective populations of patients. This analysis demonstrated that ASMM RTQ-PCR is more sensitive than Southern blotting for detecting low degree of LOI. Moreover, ASMM RTQ-PCR is a very rapid, reliable, simple, safe, and cost effective method. © 2011 Wiley-Liss, Inc.

Quantitative MR assessment of structural changes in white matter of children treated for ALL

NASA Astrophysics Data System (ADS)

Reddick, Wilburn E.; Glass, John O.; Mulhern, Raymond K.

2001-07-01

Our research builds on the hypothesis that white matter damage resulting from therapy spans a continuum of severity that can be reliably probed using non-invasive MR technology. This project focuses on children treated for ALL with a regimen containing seven courses of high-dose methotrexate (HDMTX) which is known to cause leukoencephalopathy. Axial FLAIR, T1-, T2-, and PD-weighted images were acquired, registered and then analyzed with a hybrid neural network segmentation algorithm to identify normal brain parenchyma and leukoencephalopathy. Quantitative T1 and T2 maps were also analyzed at the level of the basal ganglia and the centrum semiovale. The segmented images were used as mask to identify regions of normal appearing white matter (NAWM) and leukoencephalopathy in the quantitative T1 and T2 maps. We assessed the longitudinal changes in volume, T1 and T2 in NAWM and leukoencephalopathy for 42 patients. The segmentation analysis revealed that 69% of patients had leukoencephalopathy after receiving seven courses of HDMTX. The leukoencephalopathy affected approximately 17% of the patients' white matter volume on average (range 2% - 38%). Relaxation rates in the NAWM were not significantly changed between the 1st and 7th courses. Regions of leukoencephalopathy exhibited a 13% elevation in T1 and a 37% elevation in T2 relaxation rates.

Quantitative analysis of collagens and fibronectin expression in human right ventricular hypertrophy.

PubMed

Peters, T H; Sharma, H S; Yilmaz, E; Bogers, A J

1999-06-30

One of the main features in human tetralogy of Fallot (TF) is right ventricular hypertrophy (RVH) due to pressure (sub-pulmonary stenosis) and volume overload (ventricular septal defect). Currently, primary correction at a young age is the treatment of choice. To unravel the role of extracellular matrix in RVH, we examined myocardial expression of collagens and fibronectin in TF patients with primary correction (TF1, age 0.7 +/- 0.2 yr.), secondary surgery (TF2, age 36.9 +/- 4.6 yr), and in age-matched control patients. Sirius red staining quantified by video imaging showed significantly increased interstitial staining for collagens in both TF1 and TF2 groups as compared to respective controls. Fibronectin was expressed in extracellular spaces, perivascular regions, and in some cardiomyocytes. Quantitative analysis of fibronectin revealed increased expression in only TF1 group as compared to respective control. Our results indicate an increased amount of myocardial extracellular matrix deposition as a sign of fibrosis during RVH in patients with TF.

Quantitative analysis of gallstones using laser-induced breakdown spectroscopy

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

Singh, Vivek K.; Singh, Vinita; Rai, Awadhesh K.

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 spectramore » 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.« less

Simulation of UV atomic radiation for application in exhaust plume spectrometry

NASA Astrophysics Data System (ADS)

Wallace, T. L.; Powers, W. T.; Cooper, A. E.

1993-06-01

Quantitative analysis of exhaust plume spectral data has long been a goal of developers of advanced engine health monitoring systems which incorporate optical measurements of rocket exhaust constituents. Discussed herein is the status of present efforts to model and predict atomic radiation spectra and infer free-atom densities from emission/absorption measurements as part of the Optical Plume Anomaly Detection (OPAD) program at Marshall Space Flight Center (MSFC). A brief examination of the mathematical formalism is provided in the context of predicting radiation from the Mach disk region of the SSME exhaust flow at nominal conditions during ground level testing at MSFC. Computational results are provided for Chromium and Copper at selected transitions which indicate a strong dependence upon broadening parameter values determining the absorption-emission line shape. Representative plots of recent spectral data from the Stennis Space Center (SSC) Diagnostic Test Facility (DTF) rocket engine are presented and compared to numerical results from the present self-absorbing model; a comprehensive quantitative analysis will be reported at a later date.

Over-seasons analysis of quantitative trait loci affecting phenolic content and antioxidant capacity in raspberry.

PubMed

Dobson, Patricia; Graham, Julie; Stewart, D; Brennan, Rex; Hackett, Christine A; McDougall, Gordon J

2012-05-30

This study examined the total phenol content (TPC) and total anthocyanin content (TAC) in ripe fruit of progeny of a mapping population generated from a cross between the European red raspberry cv. Glen Moy ( Rubus ideaus var. idaeus) and the North American red raspberry cv. Latham ( Rubus ideaus var. strigosus) over five seasons in two different growing environments. Measurements of antioxidant capacity (FRAP and TEAC) were also carried out. TPC was highly correlated with TEAC and FRAP across the entire data set. The subset of anthocyanin content was genotype-dependent but also correlated with TPC, although the proportion of anthocyanin compounds varied between progeny. Quantitative trait locus (QTL) analysis was carried out, and key markers were tested for consistency of effects over sites and years. Four regions, on linkage groups 2, 3, 5, and 6, were identified. These agree with QTLs from a previous study over a single season and indicate that QTL effects were robust over seasons.

Experiment K-7-18: Effects of Spaceflight in the Muscle Adductor Longus of Rats Flown in the Soviet Biosatellite Cosmos 2044. Part 2; Quantitative Autoradiographic Analysis of Gaba (Benzodiazepine) and Muscarinic (Cholinergic) Receptors in the Forebrain of Rats Flown on Cosmos 2044

NASA Technical Reports Server (NTRS)

Wu, L.; Daunton, N. G.; Krasnov, I. B.; DAmelio, F.; Hyde, T. M.; Sigworth, S. K.

1994-01-01

Quantitative autoradiographic analysis of receptors for GABA and acetylcholine in the forebrain of rats flown on COSMOS 2044 was undertaken as part of a joint US-Soviet study to determine the effects of microgravity on the central nervous system, and in particular on the sensory and motor portions of the forebrain. Changes in binding of these receptors in tissue from animals exposed to microgravity would provide evidence for possible changes in neural processing as a result of exposure to microgravity. Tritium-labelled diazepam and Quinuclidinyl-benzilate (QNB) were used to visualize GABA (benzodiazepine) and muscarinic (cholinergic) receptors, respectively. The density of tritium-labelled radioligands bound to various regions in the forebrain of both flight and control animals were measured from autoradiograms. Data from rats flown in space and from ground-based control animals that were not exposed to microgravity were compared.

Quantitative imaging of protein targets in the human brain with PET

NASA Astrophysics Data System (ADS)

Gunn, Roger N.; Slifstein, Mark; Searle, Graham E.; Price, Julie C.

2015-11-01

PET imaging of proteins in the human brain with high affinity radiolabelled molecules has a history stretching back over 30 years. During this period the portfolio of protein targets that can be imaged has increased significantly through successes in radioligand discovery and development. This portfolio now spans six major categories of proteins; G-protein coupled receptors, membrane transporters, ligand gated ion channels, enzymes, misfolded proteins and tryptophan-rich sensory proteins. In parallel to these achievements in radiochemical sciences there have also been significant advances in the quantitative analysis and interpretation of the imaging data including the development of methods for image registration, image segmentation, tracer compartmental modeling, reference tissue kinetic analysis and partial volume correction. In this review, we analyze the activity of the field around each of the protein targets in order to give a perspective on the historical focus and the possible future trajectory of the field. The important neurobiology and pharmacology is introduced for each of the six protein classes and we present established radioligands for each that have successfully transitioned to quantitative imaging in humans. We present a standard quantitative analysis workflow for these radioligands which takes the dynamic PET data, associated blood and anatomical MRI data as the inputs to a series of image processing and bio-mathematical modeling steps before outputting the outcome measure of interest on either a regional or parametric image basis. The quantitative outcome measures are then used in a range of different imaging studies including tracer discovery and development studies, cross sectional studies, classification studies, intervention studies and longitudinal studies. Finally we consider some of the confounds, challenges and subtleties that arise in practice when trying to quantify and interpret PET neuroimaging data including motion artifacts, partial volume effects, age effects, image registration and normalization, input functions and metabolites, parametric imaging, receptor internalization and genetic factors.

Application of the LEPS technique for Quantitative Precipitation Forecasting (QPF) in Southern Italy: a preliminary study

NASA Astrophysics Data System (ADS)

Federico, S.; Avolio, E.; Bellecci, C.; Colacino, M.; Walko, R. L.

2006-03-01

This paper reports preliminary results for a Limited area model Ensemble Prediction System (LEPS), based on RAMS (Regional Atmospheric Modelling System), for eight case studies of moderate-intense precipitation over Calabria, the southernmost tip of the Italian peninsula. LEPS aims to transfer the benefits of a probabilistic forecast from global to regional scales in countries where local orographic forcing is a key factor to force convection. To accomplish this task and to limit computational time in an operational implementation of LEPS, we perform a cluster analysis of ECMWF-EPS runs. Starting from the 51 members that form the ECMWF-EPS we generate five clusters. For each cluster a representative member is selected and used to provide initial and dynamic boundary conditions to RAMS, whose integrations generate LEPS. RAMS runs have 12-km horizontal resolution. To analyze the impact of enhanced horizontal resolution on quantitative precipitation forecasts, LEPS forecasts are compared to a full Brute Force (BF) ensemble. This ensemble is based on RAMS, has 36 km horizontal resolution and is generated by 51 members, nested in each ECMWF-EPS member. LEPS and BF results are compared subjectively and by objective scores. Subjective analysis is based on precipitation and probability maps of case studies whereas objective analysis is made by deterministic and probabilistic scores. Scores and maps are calculated by comparing ensemble precipitation forecasts against reports from the Calabria regional raingauge network. Results show that LEPS provided better rainfall predictions than BF for all case studies selected. This strongly suggests the importance of the enhanced horizontal resolution, compared to ensemble population, for Calabria for these cases. To further explore the impact of local physiographic features on QPF (Quantitative Precipitation Forecasting), LEPS results are also compared with a 6-km horizontal resolution deterministic forecast. Due to local and mesoscale forcing, the high resolution forecast (Hi-Res) has better performance compared to the ensemble mean for rainfall thresholds larger than 10mm but it tends to overestimate precipitation for lower amounts. This yields larger false alarms that have a detrimental effect on objective scores for lower thresholds. To exploit the advantages of a probabilistic forecast compared to a deterministic one, the relation between the ECMWF-EPS 700 hPa geopotential height spread and LEPS performance is analyzed. Results are promising even if additional studies are required.

Whole-body PET parametric imaging employing direct 4D nested reconstruction and a generalized non-linear Patlak model

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Rahmim, Arman

2014-03-01

Graphical analysis is employed in the research setting to provide quantitative estimation of PET tracer kinetics from dynamic images at a single bed. Recently, we proposed a multi-bed dynamic acquisition framework enabling clinically feasible whole-body parametric PET imaging by employing post-reconstruction parameter estimation. In addition, by incorporating linear Patlak modeling within the system matrix, we enabled direct 4D reconstruction in order to effectively circumvent noise amplification in dynamic whole-body imaging. However, direct 4D Patlak reconstruction exhibits a relatively slow convergence due to the presence of non-sparse spatial correlations in temporal kinetic analysis. In addition, the standard Patlak model does not account for reversible uptake, thus underestimating the influx rate Ki. We have developed a novel whole-body PET parametric reconstruction framework in the STIR platform, a widely employed open-source reconstruction toolkit, a) enabling accelerated convergence of direct 4D multi-bed reconstruction, by employing a nested algorithm to decouple the temporal parameter estimation from the spatial image update process, and b) enhancing the quantitative performance particularly in regions with reversible uptake, by pursuing a non-linear generalized Patlak 4D nested reconstruction algorithm. A set of published kinetic parameters and the XCAT phantom were employed for the simulation of dynamic multi-bed acquisitions. Quantitative analysis on the Ki images demonstrated considerable acceleration in the convergence of the nested 4D whole-body Patlak algorithm. In addition, our simulated and patient whole-body data in the postreconstruction domain indicated the quantitative benefits of our extended generalized Patlak 4D nested reconstruction for tumor diagnosis and treatment response monitoring.

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives.

PubMed

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure-activity relationship (3D-QSAR) and three-dimensional quantitative structure-selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q (2) values of 0.753 and 0.770, and r (2) values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2'-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure-property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature.

Design and prediction of new anticoagulants as a selective Factor IXa inhibitor via three-dimensional quantitative structure-property relationships of amidinobenzothiophene derivatives

PubMed Central

Gao, Jia-Suo; Tong, Xu-Peng; Chang, Yi-Qun; He, Yu-Xuan; Mei, Yu-Dan; Tan, Pei-Hong; Guo, Jia-Liang; Liao, Guo-Chao; Xiao, Gao-Keng; Chen, Wei-Min; Zhou, Shu-Feng; Sun, Ping-Hua

2015-01-01

Factor IXa (FIXa), a blood coagulation factor, is specifically inhibited at the initiation stage of the coagulation cascade, promising an excellent approach for developing selective and safe anticoagulants. Eighty-four amidinobenzothiophene antithrombotic derivatives targeting FIXa were selected to establish three-dimensional quantitative structure–activity relationship (3D-QSAR) and three-dimensional quantitative structure–selectivity relationship (3D-QSSR) models using comparative molecular field analysis and comparative similarity indices analysis methods. Internal and external cross-validation techniques were investigated as well as region focusing and bootstrapping. The satisfactory q2 values of 0.753 and 0.770, and r2 values of 0.940 and 0.965 for 3D-QSAR and 3D-QSSR, respectively, indicated that the models are available to predict both the inhibitory activity and selectivity on FIXa against Factor Xa, the activated status of Factor X. This work revealed that the steric, hydrophobic, and H-bond factors should appropriately be taken into account in future rational design, especially the modifications at the 2′-position of the benzene and the 6-position of the benzothiophene in the R group, providing helpful clues to design more active and selective FIXa inhibitors for the treatment of thrombosis. On the basis of the three-dimensional quantitative structure–property relationships, 16 new potent molecules have been designed and are predicted to be more active and selective than Compound 33, which has the best activity as reported in the literature. PMID:25848211

Smartphone-Based Accurate Analysis of Retinal Vasculature towards Point-of-Care Diagnostics

PubMed Central

Xu, Xiayu; Ding, Wenxiang; Wang, Xuemin; Cao, Ruofan; Zhang, Maiye; Lv, Peilin; Xu, Feng

2016-01-01

Retinal vasculature analysis is important for the early diagnostics of various eye and systemic diseases, making it a potentially useful biomarker, especially for resource-limited regions and countries. Here we developed a smartphone-based retinal image analysis system for point-of-care diagnostics that is able to load a fundus image, segment retinal vessels, analyze individual vessel width, and store or uplink results. The proposed system was not only evaluated on widely used public databases and compared with the state-of-the-art methods, but also validated on clinical images directly acquired with a smartphone. An Android app is also developed to facilitate on-site application of the proposed methods. Both visual assessment and quantitative assessment showed that the proposed methods achieved comparable results to the state-of-the-art methods that require high-standard workstations. The proposed system holds great potential for the early diagnostics of various diseases, such as diabetic retinopathy, for resource-limited regions and countries. PMID:27698369

Analysis of Protein Kinetics Using Fluorescence Recovery After Photobleaching (FRAP).

PubMed

Giakoumakis, Nickolaos Nikiforos; Rapsomaniki, Maria Anna; Lygerou, Zoi

2017-01-01

Fluorescence recovery after photobleaching (FRAP) is a cutting-edge live-cell functional imaging technique that enables the exploration of protein dynamics in individual cells and thus permits the elucidation of protein mobility, function, and interactions at a single-cell level. During a typical FRAP experiment, fluorescent molecules in a defined region of interest within the cell are bleached by a short and powerful laser pulse, while the recovery of the fluorescence in the region is monitored over time by time-lapse microscopy. FRAP experimental setup and image acquisition involve a number of steps that need to be carefully executed to avoid technical artifacts. Equally important is the subsequent computational analysis of FRAP raw data, to derive quantitative information on protein diffusion and binding parameters. Here we present an integrated in vivo and in silico protocol for the analysis of protein kinetics using FRAP. We focus on the most commonly encountered challenges and technical or computational pitfalls and their troubleshooting so that valid and robust insight into protein dynamics within living cells is gained.

Separation of distinct photoexcitation species in femtosecond transient absorption microscopy

DOE PAGES

Xiao, Kai; Ma, Ying -Zhong; Simpson, Mary Jane; ...

2016-02-03

Femtosecond transient absorption microscopy is a novel chemical imaging capability with simultaneous high spatial and temporal resolution. Although several powerful data analysis approaches have been developed and successfully applied to separate distinct chemical species in such images, the application of such analysis to distinguish different photoexcited species is rare. In this paper, we demonstrate a combined approach based on phasor and linear decomposition analysis on a microscopic level that allows us to separate the contributions of both the excitons and free charge carriers in the observed transient absorption response of a composite organometallic lead halide perovskite film. We found spatialmore » regions where the transient absorption response was predominately a result of excitons and others where it was predominately due to charge carriers, and regions consisting of signals from both contributors. Lastly, quantitative decomposition of the transient absorption response curves further enabled us to reveal the relative contribution of each photoexcitation to the measured response at spatially resolved locations in the film.« less

Cluster analysis of quantitative parametric maps from DCE-MRI: application in evaluating heterogeneity of tumor response to antiangiogenic treatment.

PubMed

Longo, Dario Livio; Dastrù, Walter; Consolino, Lorena; Espak, Miklos; Arigoni, Maddalena; Cavallo, Federica; Aime, Silvio

2015-07-01

The objective of this study was to compare a clustering approach to conventional analysis methods for assessing changes in pharmacokinetic parameters obtained from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) during antiangiogenic treatment in a breast cancer model. BALB/c mice bearing established transplantable her2+ tumors were treated with a DNA-based antiangiogenic vaccine or with an empty plasmid (untreated group). DCE-MRI was carried out by administering a dose of 0.05 mmol/kg of Gadocoletic acid trisodium salt, a Gd-based blood pool contrast agent (CA) at 1T. Changes in pharmacokinetic estimates (K(trans) and vp) in a nine-day interval were compared between treated and untreated groups on a voxel-by-voxel analysis. The tumor response to therapy was assessed by a clustering approach and compared with conventional summary statistics, with sub-regions analysis and with histogram analysis. Both the K(trans) and vp estimates, following blood-pool CA injection, showed marked and spatial heterogeneous changes with antiangiogenic treatment. Averaged values for the whole tumor region, as well as from the rim/core sub-regions analysis were unable to assess the antiangiogenic response. Histogram analysis resulted in significant changes only in the vp estimates (p<0.05). The proposed clustering approach depicted marked changes in both the K(trans) and vp estimates, with significant spatial heterogeneity in vp maps in response to treatment (p<0.05), provided that DCE-MRI data are properly clustered in three or four sub-regions. This study demonstrated the value of cluster analysis applied to pharmacokinetic DCE-MRI parametric maps for assessing tumor response to antiangiogenic therapy. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantitative Differentiation of LV Myocardium with and without Layer-Specific Fibrosis Using MRI in Hypertrophic Cardiomyopathy and Layer-Specific Strain TTE Analysis.

PubMed

Funabashi, Nobusada; Takaoka, Hiroyuki; Ozawa, Koya; Kamata, Tomoko; Uehara, Masae; Komuro, Issei; Kobayashi, Yoshio

2018-05-30

To achieve further risk stratification in hypertrophic cardiomyopathy (HCM) patients, we localized and quantified layer-specific LVM fibrosis on MRI in HCM patients using regional layer-specific peak longitudinal strain (PLS) and peak circumferential strain (PCS) in LV myocardium (LVM) on speckle tracking transthoracic echocardiography (TTE). A total of 18 HCM patients (14 males; 58 ± 17 years) underwent 1.5T-MRI and TTE. PLS and PCS in each layer of the LVM (endocardium, epicardium, and whole-layer myocardium) were calculated for 17 AHA-defined lesions. MRI assessment showed that fibrosis was classified as endocardial, epicardial, or whole-layer (= either or both of these). Regional PLS was smaller in fibrotic endocardial lesions than in non-fibrotic endocardial lesions (P = 0.004). To detect LV endocardial lesions with fibrosis, ROC curves of regional PLS revealed an area under the curve (AUC) of 0.609 and a best cut-off point of 13.5%, with sensitivity of 65.3% and specificity of 54.3%. Regional PLS was also smaller in fibrotic epicardial lesions than in non-fibrotic epicardial lesions (P < 0.001). To detect LV epicardial lesions with fibrosis, ROC curves of PLS revealed an AUC of 0.684 and a best cut-off point of 9.5%, with sensitivity of 73.5% and specificity of 55.5%. Using whole-layer myocardium analysis, PLS was smaller in fibrotic lesions than in non-fibrotic lesions (P < 0.001). To detect whole-layer LV lesions with fibrosis, ROC curves of regional PLS revealed an AUC of 0.674 and a best cut-off point of 12.5%, with sensitivity of 79.0% and specificity of 50.7%. There were no significant differences in PCS of LV myocardium (endocardium, epicardium, and whole-layer) between fibrotic and non-fibrotic lesions. Quantitative regional PLS but not PCS in LV endocardium, epicardium, and whole-layer myocardium provides useful non-invasive information for layer-specific localization of fibrosis in HCM patients.

Quantitative kinetic analysis of PET amyloid imaging agents [(11)C]BF227 and [(18)F]FACT in human brain.

PubMed

Shidahara, Miho; Watabe, Hiroshi; Tashiro, Manabu; Okamura, Nobuyuki; Furumoto, Shozo; Watanuki, Shoichi; Furukawa, Katsutoshi; Arakawa, Yuma; Funaki, Yoshihito; Iwata, Ren; Gonda, Kohsuke; Kudo, Yukitsuka; Arai, Hiroyuki; Ishiwata, Kiichi; Yanai, Kazuhiko

2015-09-01

The purpose of this study was to compare two amyloid imaging agents, [(11)C]BF227 and [(18)F]FACT (derivative from [(11)C]BF227) through quantitative pharmacokinetics analysis in human brain. Positron emission tomography studies were performed on six elderly healthy control (HC) subjects and seven probable Alzheimer's disease (AD) patients with [(11)C]BF227 and 10 HC subjects and 10 probable AD patients with [(18)F]FACT. Data from nine regions of interest were analyzed by several approaches, namely non-linear least-squared fitting methods with arterial input functions (one-tissue compartment model(1TCM), two-tissue compartment model (2TCM)), Logan plot, and linearized methods with reference region (Reference Logan plot (RefLogan), MRTM0, MRTM2). We also evaluated SUV and SUVR for both tracers. The parameters estimated by several approaches were compared between two tracers for detectability of differences between HC and AD patients. For [(11)C]BF227, there were no significant difference of VT (2TCM, 1TCM) and SUV in all regions (Student t-test; p<0.05) and significant differences in the DVRs (Logan, RefLogan, and MRTM2) and SUVRs in six neocortical regions (p<0.05) between the HC and AD groups. For [(18)F]FACT, significant differences in DVRs (RefLogan, MRTM0, and MRTM2) were observed in more than four neocortical regions between the HC and AD groups (p<0.05), and the significant differences were found in SUVRs for two neocortical regions (inferior frontal coretex and lateral temporal coretex). Our results showed that both tracers can clearly distinguish between HC and AD groups although the pharmacokinetics and distribution patterns in brain for two tracers were substantially different. This study revealed that although the PET amyloid imaging agents [(11)C]BF227 and [(18)F]FACT have similar chemical and biological properties, they have different pharmacokinetics, and caution must be paid for usage of the tracers. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantitative Magnetic Resonance Diffusion-Weighted Imaging Evaluation of the Supratentorial Brain Regions in Patients Diagnosed with Brainstem Variant of Posterior Reversible Encephalopathy Syndrome: A Preliminary Study.

PubMed

Chen, Tai-Yuan; Wu, Te-Chang; Ko, Ching-Chung; Feng, I-Jung; Tsui, Yu-Kun; Lin, Chien-Jen; Chen, Jeon-Hor; Lin, Ching-Po

2017-07-01

Posterior reversible encephalopathy syndrome (PRES) is a clinicoradiologic entity with several causes, characterized by rapid onset of symptoms and typical neuroimaging features, which usually resolve if promptly recognized and treated. Brainstem variant of PRES presents with vasogenic edema in brainstem regions on magnetic resonance (MR) images and there is sparing of the supratentorial regions. Because PRES is usually caused by a hypertensive crisis, which would likely have a systemic effect and global manifestations on the brain tissue, we thus proposed that some microscopic abnormalities of the supratentorial regions could be detected with diffusion-weighted imaging (DWI) using apparent diffusion coefficient (ADC) analysis in brainstem variant of PRES and hypothesized that "normal-looking" supratentorial regions will increase water diffusion. We retrospectively identified patients with PRES who underwent brain magnetic resonance imaging studies. We identified 11 brainstem variants of PRES patients, who formed the study cohort, and 11 typical PRES patients and 20 normal control subjects as the comparison cohorts for this study. Nineteen regions of interest were drawn and systematically placed. The mean ADC values were measured and compared among these 3 groups. ADC values of the typical PRES group were consistently elevated compared with those in normal control subjects. ADC values of the brainstem variant group were consistently elevated compared with those in normal control subjects. ADC values of the typical PRES group and brainstem variant group did not differ significantly, except for the pons area. Quantitative MR DWI may aid in the evaluation of supratentorial microscopic abnormalities in brainstem variant of PRES patients. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Diffuse Reflectance Infrared Fourier Transform Spectroscopy for the Determination of Asbestos Species in Bulk Building Materials

PubMed Central

Accardo, Grazia; Cioffi, Raffaeke; Colangelo, Francesco; d’Angelo, Raffaele; De Stefano, Luca; Paglietti, Fderica

2014-01-01

Diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy is a well-known technique for thin film characterization. Since all asbestos species exhibit intense adsorptions peaks in the 4000–400 cm−1 region of the infrared spectrum, a quantitative analysis of asbestos in bulk samples by DRIFT is possible. In this work, different quantitative analytical procedures have been used to quantify chrysotile content in bulk materials produced by building requalification: partial least squares (PLS) chemometrics, the Linear Calibration Curve Method (LCM) and the Method of Additions (MoA). Each method has its own pros and cons, but all give affordable results for material characterization: the amount of asbestos (around 10%, weight by weight) can be determined with precision and accuracy (errors less than 0.1). PMID:28788467

Combining emission inventory and isotope ratio analyses for quantitative source apportionment of heavy metals in agricultural soil.

PubMed

Chen, Lian; Zhou, Shenglu; Wu, Shaohua; Wang, Chunhui; Li, Baojie; Li, Yan; Wang, Junxiao

2018-08-01

Two quantitative methods (emission inventory and isotope ratio analysis) were combined to apportion source contributions of heavy metals entering agricultural soils in the Lihe River watershed (Taihu region, east China). Source apportionment based on the emission inventory method indicated that for Cd, Cr, Cu, Pb, and Zn, the mean percentage input from atmospheric deposition was highest (62-85%), followed by irrigation (12-27%) and fertilization (1-14%). Thus, the heavy metals were derived mainly from industrial activities and traffic emissions. For Ni the combined percentage input from irrigation and fertilization was approximately 20% higher than that from atmospheric deposition, indicating that Ni was mainly derived from agricultural activities. Based on isotope ratio analysis, atmospheric deposition accounted for 57-93% of Pb entering soil, with the mean value of 69.3%, which indicates that this was the major source of Pb entering soil in the study area. The mean contributions of irrigation and fertilization to Pb pollution of soil ranged from 0% to 10%, indicating that they played only a marginally important role. Overall, the results obtained using the two methods were similar. This study provides a reliable approach for source apportionment of heavy metals entering agricultural soils in the study area, and clearly have potential application for future studies in other regions. Copyright © 2018 Elsevier Ltd. All rights reserved.

Surgical task analysis of simulated laparoscopic cholecystectomy with a navigation system.

PubMed

Sugino, T; Kawahira, H; Nakamura, R

2014-09-01

   Advanced surgical procedures, which have become complex and difficult, increase the burden of surgeons. Quantitative analysis of surgical procedures can improve training, reduce variability, and enable optimization of surgical procedures. To this end, a surgical task analysis system was developed that uses only surgical navigation information.    Division of the surgical procedure, task progress analysis, and task efficiency analysis were done. First, the procedure was divided into five stages. Second, the operating time and progress rate were recorded to document task progress during specific stages, including the dissecting task. Third, the speed of the surgical instrument motion (mean velocity and acceleration), as well as the size and overlap ratio of the approximate ellipse of the location log data distribution, was computed to estimate the task efficiency during each stage. These analysis methods were evaluated based on experimental validation with two groups of surgeons, i.e., skilled and "other" surgeons. The performance metrics and analytical parameters included incidents during the operation, the surgical environment, and the surgeon's skills or habits.    Comparison of groups revealed that skilled surgeons tended to perform the procedure in less time and involved smaller regions; they also manipulated the surgical instruments more gently.    Surgical task analysis developed for quantitative assessment of surgical procedures and surgical performance may provide practical methods and metrics for objective evaluation of surgical expertise.

Functional ankle instability as a risk factor for osteoarthritis: using T2-mapping to analyze early cartilage degeneration in the ankle joint of young athletes.

PubMed

Golditz, T; Steib, S; Pfeifer, K; Uder, M; Gelse, K; Janka, R; Hennig, F F; Welsch, G H

2014-10-01

The aim of this study was to investigate, using T2-mapping, the impact of functional instability in the ankle joint on the development of early cartilage damage. Ethical approval for this study was provided. Thirty-six volunteers from the university sports program were divided into three groups according to their ankle status: functional ankle instability (FAI, initial ankle sprain with residual instability); ankle sprain Copers (initial sprain, without residual instability); and controls (without a history of ankle injuries). Quantitative T2-mapping magnetic resonance imaging (MRI) was performed at the beginning ('early-unloading') and at the end ('late-unloading') of the MR-examination, with a mean time span of 27 min. Zonal region-of-interest T2-mapping was performed on the talar and tibial cartilage in the deep and superficial layers. The inter-group comparisons of T2-values were analyzed using paired and unpaired t-tests. Statistical analysis of variance was performed. T2-values showed significant to highly significant differences in 11 of 12 regions throughout the groups. In early-unloading, the FAI-group showed a significant increase in quantitative T2-values in the medial, talar regions (P = 0.008, P = 0.027), whereas the Coper-group showed this enhancement in the central-lateral regions (P = 0.05). Especially the comparison of early-loading to late-unloading values revealed significantly decreasing T2-values over time laterally and significantly increasing T2-values medially in the FAI-group, which were not present in the Coper- or control-group. Functional instability causes unbalanced loading in the ankle joint, resulting in cartilage alterations as assessed by quantitative T2-mapping. This approach can visualize and localize early cartilage abnormalities, possibly enabling specific treatment options to prevent osteoarthritis in young athletes. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay.

PubMed

Reiner-Benaim, Anat; Yekutieli, Daniel; Letwin, Noah E; Elmer, Gregory I; Lee, Norman H; Kafkafi, Neri; Benjamini, Yoav

2007-09-01

Gene expression and phenotypic functionality can best be associated when they are measured quantitatively within the same experiment. The analysis of such a complex experiment is presented, searching for associations between measures of exploratory behavior in mice and gene expression in brain regions. The analysis of such experiments raises several methodological problems. First and foremost, the size of the pool of potential discoveries being screened is enormous yet only few biologically relevant findings are expected, making the problem of multiple testing especially severe. We present solutions based on screening by testing related hypotheses, then testing the hypotheses of interest. In one variant the subset is selected directly, in the other one a tree of hypotheses is tested hierarchical; both variants control the False Discovery Rate (FDR). Other problems in such experiments are in the fact that the level of data aggregation may be different for the quantitative traits (one per animal) and gene expression measurements (pooled across animals); in that the association may not be linear; and in the resolution of interest only few replications exist. We offer solutions to these problems as well. The hierarchical FDR testing strategies presented here can serve beyond the structure of our motivating example study to any complex microarray study. Supplementary data are available at Bioinformatics online.

Contrast-enhanced magnetic resonance imaging of pulmonary lesions: description of a technique aiming clinical practice.

PubMed

Koenigkam-Santos, Marcel; Optazaite, Elzbieta; Sommer, Gregor; Safi, Seyer; Heussel, Claus Peter; Kauczor, Hans-Ulrich; Puderbach, Michael

2015-01-01

To propose a technique for evaluation of pulmonary lesions using contrast-enhanced MRI; to assess morphological patterns of enhancement and correlate quantitative analysis with histopathology. Thirty-six patients were prospectively studied. Volumetric-interpolated T1W images were obtained during consecutive breath holds after bolus triggered contrast injection. Volume coverage of first three acquisitions was limited (higher temporal resolution) and last acquisition obtained at 4th min. Two radiologists individually evaluated the patterns of enhancement. Region-of-interest-based signal intensity (SI)-time curves were created to assess quantitative parameters. Readers agreed moderately to substantially concerning lesions' enhancement pattern. SI-time curves could be created for all lesions. In comparison to benign, malignant lesions showed higher values of maximum enhancement, early peak, slope and 4th min enhancement. Early peak >15% showed 100% sensitivity to detect malignancy, maximum enhancement >40% showed 100% specificity. The proposed technique is robust, simple to perform and can be applied in clinical scenario. It allows visual evaluation of enhancement pattern/progression together with creation of SI-time curves and assessment of derived quantitative parameters. Perfusion analysis was highly sensitive to detect malignancy, in accordance to what is recommended by most recent guidelines on imaging evaluation of pulmonary lesions. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quantitative analysis of the effect of environmental-scanning electron microscopy on collagenous tissues.

PubMed

Lee, Woowon; Toussaint, Kimani C

2018-05-31

Environmental-scanning electron microscopy (ESEM) is routinely applied to various biological samples due to its ability to maintain a wet environment while imaging; moreover, the technique obviates the need for sample coating. However, there is limited research carried out on electron-beam (e-beam) induced tissue damage resulting from using the ESEM. In this paper, we use quantitative second-harmonic generation (SHG) microscopy to examine the effects of e-beam exposure from the ESEM on collagenous tissue samples prepared as either fixed, frozen, wet or dehydrated. Quantitative SHG analysis of tissues, before and after ESEM e-beam exposure in low-vacuum mode, reveals evidence of cross-linking of collagen fibers, however there are no structural differences observed in fixed tissue. Meanwhile wet-mode ESEM appears to radically alter the structure from a regular fibrous arrangement to a more random fiber orientation. We also confirm that ESEM images of collagenous tissues show higher spatial resolution compared to SHG microscopy, but the relative tradeoff with collagen specificity reduces its effectiveness in quantifying collagen fiber organization. Our work provides insight on both the limitations of the ESEM for tissue imaging, and the potential opportunity to use as a complementary technique when imaging fine features in the non-collagenous regions of tissue samples.

High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

PubMed

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

PubMed

Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

2018-01-01

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

Quantitative trait loci detection of Edwardsiella tarda resistance in Japanese flounder Paralichthys olivaceus using bulked segregant analysis

NASA Astrophysics Data System (ADS)

Wang, Xiaoxia; Xu, Wenteng; Liu, Yang; Wang, Lei; Sun, Hejun; Wang, Lei; Chen, Songlin

2016-11-01

In recent years, Edwardsiella tarda has become one of the most deadly pathogens of Japanese flounder ( Paralichthys olivaceus), causing serious annual losses in commercial production. In contrast to the rapid advances in the aquaculture of P. olivaceus, the study of E. tarda resistance-related markers has lagged behind, hindering the development of a disease-resistant strain. Thus, a marker-trait association analysis was initiated, combining bulked segregant analysis (BSA) and quantitative trait loci (QTL) mapping. Based on 180 microsatellite loci across all chromosomes, 106 individuals from the F1333 (♀: F0768 ×♂: F0915) (Nomenclature rule: F+year+family number) were used to detect simple sequence repeats (SSRs) and QTLs associated with E. tarda resistance. After a genomic scan, three markers (Scaffold 404-21589, Scaffold 404-21594 and Scaffold 270-13812) from the same linkage group (LG)-1 exhibited a significant difference between DNA, pooled/bulked from the resistant and susceptible groups (P <0.001). Therefore, 106 individuals were genotyped using all the SSR markers in LG1 by single marker analysis. Two different analytical models were then employed to detect SSR markers with different levels of significance in LG1, where 17 and 18 SSR markers were identified, respectively. Each model found three resistance-related QTLs by composite interval mapping (CIM). These six QTLs, designated qE1-6, explained 16.0%-89.5% of the phenotypic variance. Two of the QTLs, qE-2 and qE-4, were located at the 66.7 cM region, which was considered a major candidate region for E. tarda resistance. This study will provide valuable data for further investigations of E. tarda resistance genes and facilitate the selective breeding of disease-resistant Japanese flounder in the future.

1996 PAMS hydrocarbon QA studies in EPA Region II: Part II. Trends and insights

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

Teitz, A.; Kantz, M.

1997-12-31

Comparison of ambient air samples between EPA Region II and the PAMS monitoring organizations within the Region, and comparisons among EPA Regions I, II, and III, revealed the following analytical trends: (1) Agreement between laboratories was typically between 10-20% for many of the PAMS analytes found at higher concentrations, i.e., butane, isopentane, benzene, toluene, and m/p-xylene; (2) Nafion dryer systems tended to underestimate the amount of acetylene by 35-50%; (3) Isobutylene co-elution with 1-butene proved difficult to resolve unless a 100 meter DB-1 or a regular length PLOT GC column was used; (4) Organizations that monitor for polar compounds foundmore » that co-elution of ethanol/acetone can interfere with the analysis of 1-pentene; (5) Analytical systems capable of polar analyses can have co-elution and/or misidentification of these aldehydes, typically in the styrene/heptanal/o-xylene regions of the chromatogram; and (6) Tetrachloroethylene was found to interfere with octane quantitation in some analyses.« less

Urban sprawl and air quality in large US cities.

PubMed

Stone, Brian

2008-03-01

This study presents the results of a paper of urban spatial structure and exceedances of the 8-h national ambient air quality standard for ozone in 45 large US metropolitan regions. Through the integration of a published index of sprawl with metropolitan level data on annual ozone exceedances, precursor emissions, and regional climate over a 13-year period, the association between the extent of urban decentralization and the average number of ozone exceedances per year, while controlling for precursor emissions and temperature, is measured. The results of this analysis support the hypothesis that large metropolitan regions ranking highly on a quantitative index of sprawl experience a greater number of ozone exceedances than more spatially compact metropolitan regions. Importantly, this relationship was found to hold when controlling for population size, average ozone season temperatures, and regional emissions of nitrogen oxides and volatile organic compounds, suggesting that urban spatial structure may have effects on ozone formation that are independent of its effects on precursor emissions from transportation, industry, and power generation facilities.

High Prevalence of Tula Hantavirus in Common Voles in The Netherlands.

PubMed

Maas, Miriam; de Vries, Ankje; van Roon, Annika; Takumi, Katsuhisa; van der Giessen, Joke; Rockx, Barry

2017-03-01

Tula virus (TULV) is a zoonotic hantavirus. Knowledge about TULV in the Netherlands is very scarce. Therefore in 2014, 49 common voles (Microtus arvalis) from a region in the south of the Netherlands, and in 2015, 241 common voles from regions in the north of the Netherlands were tested with the TULV quantitative RT-PCR. In the southern region, prevalence of TULV was 41% (20/49). In the northern regions, prevalence ranged from 12% (4/34) to 45% (17/38). Phylogenetic analysis of the obtained sequences showed that the regions fall within different clusters. Voles from the south were also tested on-site for the presence of hantavirus antibodies, but serology results were poorly associated with qRT-PCR results. These findings suggest that TULV may be more widespread than previously thought. No human TULV cases have been reported thus far in the Netherlands, but differentiation between infection by TULV or the closely related Puumala virus is not made in humans in the Netherlands, thus cases may be misdiagnosed.

Evidence Accumulation and Choice Maintenance Are Dissociated in Human Perceptual Decision Making

PubMed Central

Pedersen, Mads Lund; Endestad, Tor; Biele, Guido

2015-01-01

Perceptual decision making in monkeys relies on decision neurons, which accumulate evidence and maintain choices until a response is given. In humans, several brain regions have been proposed to accumulate evidence, but it is unknown if these regions also maintain choices. To test if accumulator regions in humans also maintain decisions we compared delayed and self-paced responses during a face/house discrimination decision making task. Computational modeling and fMRI results revealed dissociated processes of evidence accumulation and decision maintenance, with potential accumulator activations found in the dorsomedial prefrontal cortex, right inferior frontal gyrus and bilateral insula. Potential maintenance activation spanned the frontal pole, temporal gyri, precuneus and the lateral occipital and frontal orbital cortices. Results of a quantitative reverse inference meta-analysis performed to differentiate the functions associated with the identified regions did not narrow down potential accumulation regions, but suggested that response-maintenance might rely on a verbalization of the response. PMID:26510176

XANES analyses of silicon crystalline irradiated by nitrogen/oxygen ions.

PubMed

Yoshida, T; Hara, T; Li, T; Yoshida, H; Tanabe, T

2001-03-01

X-ray absorption techniques have been applied to the characterization of 5 keV nitrogen / oxygen ions implanted silicon samples. The depth selective measurement of XANES by recording in PEY mode and the quantitative analysis by superposition of XANES spectra were carried out to elucidate the depth profile of implanted ions. It has been revealed that the silicon nitride phase were formed in silicon after prolonged N+ irradiation and it extended over the deep part of the damaged region from the surface. On the other hand, for the O+ irradiation, silicon dioxide phase were produced only in the shallow part of the damaged region, i.e., the silicon dioxide phase likely broke off during the irradiation.

Functional-analytical capabilities of GIS technology in the study of water use risks

NASA Astrophysics Data System (ADS)

Nevidimova, O. G.; Yankovich, E. P.; Yankovich, K. S.

2015-02-01

Regional security aspects of economic activities are of great importance for legal regulation in environmental management. This has become a critical issue due to climate change, especially in regions where severe climate conditions have a great impact on almost all types of natural resource uses. A detailed analysis of climate and hydrological situation in Tomsk Oblast considering water use risks was carried out. Based on developed author's techniques an informational and analytical database was created using ArcGIS software platform, which combines statistical (quantitative) and spatial characteristics of natural hazards and socio-economic factors. This system was employed to perform areal zoning according to the degree of water use risks involved.

DICOM image quantification secondary capture (DICOM IQSC) integrated with numeric results, regions, and curves: implementation and applications in nuclear medicine

NASA Astrophysics Data System (ADS)

Cao, Xinhua; Xu, Xiaoyin; Voss, Stephan

2017-03-01

In this paper, we describe an enhanced DICOM Secondary Capture (SC) that integrates Image Quantification (IQ) results, Regions of Interest (ROIs), and Time Activity Curves (TACs) with screen shots by embedding extra medical imaging information into a standard DICOM header. A software toolkit of DICOM IQSC has been developed to implement the SC-centered information integration of quantitative analysis for routine practice of nuclear medicine. Primary experiments show that the DICOM IQSC method is simple and easy to implement seamlessly integrating post-processing workstations with PACS for archiving and retrieving IQ information. Additional DICOM IQSC applications in routine nuclear medicine and clinic research are also discussed.

A new efficient method for color image compression based on visual attention mechanism

NASA Astrophysics Data System (ADS)

Shao, Xiaoguang; Gao, Kun; Lv, Lily; Ni, Guoqiang

2010-11-01

One of the key procedures in color image compression is to extract its region of interests (ROIs) and evaluate different compression ratios. A new non-uniform color image compression algorithm with high efficiency is proposed in this paper by using a biology-motivated selective attention model for the effective extraction of ROIs in natural images. When the ROIs have been extracted and labeled in the image, the subsequent work is to encode the ROIs and other regions with different compression ratios via popular JPEG algorithm. Furthermore, experiment results and quantitative and qualitative analysis in the paper show perfect performance when comparing with other traditional color image compression approaches.

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.

Detection, monitoring, and quantitative analysis of wildfires with the BIRD satellite

NASA Astrophysics Data System (ADS)

Oertel, Dieter A.; Briess, Klaus; Lorenz, Eckehard; Skrbek, Wolfgang; Zhukov, Boris

2004-02-01

Increasing concern about environment and interest to avoid losses led to growing demands on space borne fire detection, monitoring and quantitative parameter estimation of wildfires. The global change research community intends to quantify the amount of gaseous and particulate matter emitted from vegetation fires, peat fires and coal seam fires. The DLR Institute of Space Sensor Technology and Planetary Exploration (Berlin-Adlershof) developed a small satellite called BIRD (Bi-spectral Infrared Detection) which carries a sensor package specially designed for fire detection. BIRD was launched as a piggy-back satellite on October 22, 2001 with ISRO"s Polar Satellite Launch Vehicle (PSLV). It is circling the Earth on a polar and sun-synchronous orbit at an altitude of 572 km and it is providing unique data for detailed analysis of high temperature events on Earth surface. The BIRD sensor package is dedicated for high resolution and reliable fire recognition. Active fire analysis is possible in the sub-pixel domain. The leading channel for fire detection and monitoring is the MIR channel at 3.8 μm. The rejection of false alarms is based on procedures using MIR/NIR (Middle Infra Red/Near Infra Red) and MIR/TIR (Middle Infra Red/Thermal Infra Red) radiance ratio thresholds. Unique results of BIRD wildfire detection and analysis over fire prone regions in Australia and Asia will be presented. BIRD successfully demonstrates innovative fire recognition technology for small satellites which permit to retrieve quantitative characteristics of active burning wildfires, such as the equivalent fire temperature, fire area, radiative energy release, fire front length and fire front strength.

The quantitative evaluation of cholinergic markers in spatial memory improvement induced by nicotine-bucladesine combination in rats.

PubMed

Azami, Kian; Etminani, Maryam; Tabrizian, Kaveh; Salar, Fatemeh; Belaran, Maryam; Hosseini, Asieh; Hosseini-Sharifabad, Ali; Sharifzadeh, Mohammad

2010-06-25

We previously showed that post-training intra-hippocampal infusion of nicotine-bucladesine combination enhanced spatial memory retention in the Morris water maze. Here we investigated the role of cholinergic markers in nicotine-bucladesine combination-induced memory improvement. We assessed the expression of choline acetyltransferase (ChAT) and vesicular acetylcholine transporter (VAChT) in CA1 region of the hippocampus and medial septal area (MSA) of the brain. Post-training bilateral infusion of a low concentration of either nicotine or bucladesine into the CA1 region of the hippocampus did not affect spatial memory significantly. Quantitative immunostaining analysis of optical density in CA1 regions and evaluation of immunopositive neurons in medial septal area of brain sections from all combination groups revealed a significant increase (P<0.001) in the ChAT and VAChT immunoreactivity. The maximum increase was observed with combination of 10-microM/side bucladesine and 0.5 microg/side nicotine and in a concentration dependent manner. Also, increase in the optical density and amount of ChAT and VAChT immunostaining correlated with the decrease in escape latency and traveled distance in rats treated with nicotine and low dose of bucladesine. Taken together, these results suggest that significant increases of ChAT and VAChT protein expressions in the CA1 region and medial septal area are the possible mechanisms of spatial memory improvement induced by nicotine-bucladesine combination. (c) 2010 Elsevier B.V. All rights reserved.

Choosing optimum station configurations for summarizing water quality characteristics, in 1994 Annual Report, San Francisco Estuary Regional Monitoring Program for Trace Substances: San Francisco Estuary Institute

USGS Publications Warehouse

Cloern, James E.; Cole, Brian E.; Caffrey, J.M.

1996-01-01

In this report, we focus on selection of an “optimum” station configuration for the channel of San Francisco Bay for vertical profiling of water quality. Our analysis is based on the monthly cruises conducted by the USGS under the auspices of the Regional Monitoring Program for Trace Substances (Caffrey et al. 1994; SFEI 1994). The underlying rationale for undertaking the analysis is that the distribution of trace substances is structured, at least in part, by the same forces acting on water quality parameters. This must be true to some extent, as trace substance concentrations are partially dependent on water quality characteristics such as salinity. On the other hand, the quantitative importance of these parameters in accounting for overall variability in individual trace substances is unknown. Furthermore, trace substances have their own unique sources, and these sources may dominate their distribution.

The neuroplastic effect of working memory training in healthy volunteers and patients with schizophrenia: Implications for cognitive rehabilitation.

PubMed

Li, Xu; Xiao, Ya-hui; Zhao, Qing; Leung, Ada W W; Cheung, Eric F C; Chan, Raymond C K

2015-08-01

We conducted an activation likelihood estimation (ALE) meta-analysis to quantitatively review the existing working memory (WM) training studies that investigated neural activation changes both in healthy individuals and patients with schizophrenia. ALE analysis of studies in healthy individuals indicates a widespread distribution of activation changes with WM training in the frontal and parietal regions, especially the dorsolateral prefrontal cortex, the medial frontal cortex and the precuneus, as well as subcortical regions such as the insula and the striatum. WM training is also accompanied by activation changes in patients with schizophrenia, mainly in the dorsolateral prefrontal cortex, the precuneus and the fusiform gyrus. Our results demonstrate that WM training is accompanied by changes in neural activation patterns in healthy individuals, which may provide the basis for understanding neuroplastic changes in patients with schizophrenia. Copyright © 2015 Elsevier Ltd. All rights reserved.

A sequential factorial analysis approach to characterize the effects of uncertainties for supporting air quality management

NASA Astrophysics Data System (ADS)

Wang, S.; Huang, G. H.; Veawab, A.

2013-03-01

This study proposes a sequential factorial analysis (SFA) approach for supporting regional air quality management under uncertainty. SFA is capable not only of examining the interactive effects of input parameters, but also of analyzing the effects of constraints. When there are too many factors involved in practical applications, SFA has the advantage of conducting a sequence of factorial analyses for characterizing the effects of factors in a systematic manner. The factor-screening strategy employed in SFA is effective in greatly reducing the computational effort. The proposed SFA approach is applied to a regional air quality management problem for demonstrating its applicability. The results indicate that the effects of factors are evaluated quantitatively, which can help decision makers identify the key factors that have significant influence on system performance and explore the valuable information that may be veiled beneath their interrelationships.

Boundary element analysis of corrosion problems for pumps and pipes

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

Miyasaka, M.; Amaya, K.; Kishimoto, K.

1995-12-31

Three-dimensional (3D) and axi-symmetric boundary element methods (BEM) were developed to quantitatively estimate cathodic protection and macro-cell corrosion. For 3D analysis, a multiple-region method (MRM) was developed in addition to a single-region method (SRM). The validity and usefulness of the BEMs were demonstrated by comparing numerical results with experimental data from galvanic corrosion systems of a cylindrical model and a seawater pipe, and from a cathodic protection system of an actual seawater pump. It was shown that a highly accurate analysis could be performed for fluid machines handling seawater with complex 3D fields (e.g. seawater pump) by taking account ofmore » flow rate and time dependencies of polarization curve. Compared to the 3D BEM, the axi-symmetric BEM permitted large reductions in numbers of elements and nodes, which greatly simplified analysis of axi-symmetric fields such as pipes. Computational accuracy and CPU time were compared between analyses using two approximation methods for polarization curves: a logarithmic-approximation method and a linear-approximation method.« less

Imitation and speech: commonalities within Broca's area.

PubMed

Kühn, Simone; Brass, Marcel; Gallinat, Jürgen

2013-11-01

The so-called embodiment of communication has attracted considerable interest. Recently a growing number of studies have proposed a link between Broca's area's involvement in action processing and its involvement in speech. The present quantitative meta-analysis set out to test whether neuroimaging studies on imitation and overt speech show overlap within inferior frontal gyrus. By means of activation likelihood estimation (ALE), we investigated concurrence of brain regions activated by object-free hand imitation studies as well as overt speech studies including simple syllable and more complex word production. We found direct overlap between imitation and speech in bilateral pars opercularis (BA 44) within Broca's area. Subtraction analyses revealed no unique localization neither for speech nor for imitation. To verify the potential of ALE subtraction analysis to detect unique involvement within Broca's area, we contrasted the results of a meta-analysis on motor inhibition and imitation and found separable regions involved for imitation. This is the first meta-analysis to compare the neural correlates of imitation and overt speech. The results are in line with the proposed evolutionary roots of speech in imitation.

Cytogenetic Analysis of Segregation Distortion in Drosophila Melanogaster: The Cytological Organization of the Responder (Rsp) Locus

PubMed Central

Pimpinelli, S.; Dimitri, P.

1989-01-01

The segregation distortion phenomenon occurs in Drosophila melanogaster males carrying an SD second chromosome and an SD(+) homolog. In such males the SD chromosome is transmitted to the progeny more frequently than the expected 50% because of an abnormal differentiation of the SD(+)-bearing sperms. Three major loci are involved in this phenomenon: SD and Rsp, associated with the SD and SD(+) chromosome, respectively, and E(SD). In the present work we performed a cytogenetic analysis of the Rsp locus which was known to map to the centromeric heterochromatin of the second chromosome. Hoechst- and N-banding techniques were used to characterize chromosomes carrying Responder insensitive (Rsp(i)), Responder sensitive (Rsp(s)) and Responder supersensitive (Rsp(ss)) alleles. Our results locate the Rsp locus to the h39 region of 2R heterochromatin. This region is a Hoechstbright, N-banding negative heterochromatic block adjacent to the centromere. Quantitative variations of the h39 region were observed. The degree of sensitivity to Sd was found to be directly correlated with the physical size of that region, demonstrating that the Rsp locus is composed of repeated DNA. PMID:2470640

The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae.

PubMed

García-Ríos, Estéfani; Morard, Miguel; Parts, Leopold; Liti, Gianni; Guillamón, José M

2017-02-14

Low-temperature growth and fermentation of wine yeast can enhance wine aroma and make them highly desirable traits for the industry. Elucidating response to cold in Saccharomyces cerevisiae is, therefore, of paramount importance to select or genetically improve new wine strains. As most enological traits of industrial importance in yeasts, adaptation to low temperature is a polygenic trait regulated by many interacting loci. In order to unravel the genetic determinants of low-temperature fermentation, we mapped quantitative trait loci (QTLs) by bulk segregant analyses in the F13 offspring of two Saccharomyces cerevisiae industrial strains with divergent performance at low temperature. We detected four genomic regions involved in the adaptation at low temperature, three of them located in the subtelomeric regions (chromosomes XIII, XV and XVI) and one in the chromosome XIV. The QTL analysis revealed that subtelomeric regions play a key role in defining individual variation, which emphasizes the importance of these regions' adaptive nature. The reciprocal hemizygosity analysis (RHA), run to validate the genes involved in low-temperature fermentation, showed that genetic variation in mitochondrial proteins, maintenance of correct asymmetry and distribution of phospholipid in the plasma membrane are key determinants of low-temperature adaptation.

Analysis of the Relationship Between the Solar X-Ray Radiation Intensity and the D-Region Electron Density Using Satellite and Ground-Based Radio Data

NASA Astrophysics Data System (ADS)

Nina, Aleksandra; Čadež, Vladimir M.; Bajčetić, Jovan; Mitrović, Srdjan T.; Popović, Luka Č.

2018-04-01

Increases in the X-ray radiation that is emitted during a solar X-ray flare induce significant changes in the ionospheric D region. Because of the numerous complex processes in the ionosphere and the characteristics of the radiation and plasma, the causal-consequential relationship between the X-ray radiation and ionospheric parameters is not easily determined. In addition, modeling the ionospheric D-region plasma parameters is very difficult because of the lack of data for numerous time- and space-dependent physical quantities. In this article we first give a qualitative analysis of the relationship between the electron density and the recorded solar X-ray intensity. After this, we analyze the differences in the relationships between the D-region response and various X-ray radiation properties. The quantitative study is performed for data observed on 5 May 2010 in the time period between 11:40 UT - 12:40 UT when the GOES 14 satellite detected a considerable X-ray intensity increase. Modeling the electron density is based on characteristics of the 23.4 kHz signal emitted in Germany and recorded by the receiver in Serbia.

Assessing White Matter Microstructure in Brain Regions with Different Myelin Architecture Using MRI.

PubMed

Groeschel, Samuel; Hagberg, Gisela E; Schultz, Thomas; Balla, Dávid Z; Klose, Uwe; Hauser, Till-Karsten; Nägele, Thomas; Bieri, Oliver; Prasloski, Thomas; MacKay, Alex L; Krägeloh-Mann, Ingeborg; Scheffler, Klaus

2016-01-01

We investigate how known differences in myelin architecture between regions along the cortico-spinal tract and frontal white matter (WM) in 19 healthy adolescents are reflected in several quantitative MRI parameters that have been proposed to non-invasively probe WM microstructure. In a clinically feasible scan time, both conventional imaging sequences as well as microstructural MRI parameters were assessed in order to quantitatively characterise WM regions that are known to differ in the thickness of their myelin sheaths, and in the presence of crossing or parallel fibre organisation. We found that diffusion imaging, MR spectroscopy (MRS), myelin water fraction (MWF), Magnetization Transfer Imaging, and Quantitative Susceptibility Mapping were myelin-sensitive in different ways, giving complementary information for characterising WM microstructure with different underlying fibre architecture. From the diffusion parameters, neurite density (NODDI) was found to be more sensitive than fractional anisotropy (FA), underlining the limitation of FA in WM crossing fibre regions. In terms of sensitivity to different myelin content, we found that MWF, the mean diffusivity and chemical-shift imaging based MRS yielded the best discrimination between areas. Multimodal assessment of WM microstructure was possible within clinically feasible scan times using a broad combination of quantitative microstructural MRI sequences. By assessing new microstructural WM parameters we were able to provide normative data and discuss their interpretation in regions with different myelin architecture, as well as their possible application as biomarker for WM disorders.

Image Patch Analysis of Sunspots and Active Regions

NASA Astrophysics Data System (ADS)

Moon, K.; Delouille, V.; Hero, A.

2017-12-01

The flare productivity of an active region has been observed to be related to its spatial complexity. Separating active regions that are quiet from potentially eruptive ones is a key issue in space weather applications. Traditional classification schemes such as Mount Wilson and McIntosh have been effective in relating an active region large scale magnetic configuration to its ability to produce eruptive events. However, their qualitative nature does not use all of the information present in the observations. In our work, we present an image patch analysis for characterizing sunspots and active regions. We first propose fine-scale quantitative descriptors for an active region's complexity such as intrinsic dimension, and we relate them to the Mount Wilson classification. Second, we introduce a new clustering of active regions that is based on the local geometry observed in Line of Sight magnetogram and continuum images. To obtain this local geometry, we use a reduced-dimension representation of an active region that is obtained by factoring the corresponding data matrix comprised of local image patches using the singular value decomposition. The resulting factorizations of active regions can be compared via the definition of appropriate metrics on the factors. The distances obtained from these metrics are then used to cluster the active regions. Results. We find that these metrics result in natural clusterings of active regions. The clusterings are related to large scale descriptors of an active region such as its size, its local magnetic field distribution, and its complexity as measured by the Mount Wilson classification scheme. We also find that including data focused on the neutral line of an active region can result in an increased correspondence between our clustering results and other active region descriptors such as the Mount Wilson classifications and the R-value.

Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens.

PubMed

Shoura, Massa J; Gabdank, Idan; Hansen, Loren; Merker, Jason; Gotlib, Jason; Levene, Stephen D; Fire, Andrew Z

2017-10-05

Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples. Copyright © 2017 Shoura et al.

Quantitative Trait Loci for BMD in an SM/J by NZB/BlNJ Intercross Population and Identification of Trps1 as a Probable Candidate Gene

PubMed Central

Ishimori, Naoki; Stylianou, Ioannis M; Korstanje, Ron; Marion, Michael A; Li, Renhua; Donahue, Leah Rae; Rosen, Clifford J; Beamer, Wesley G; Paigen, Beverly; Churchill, Gary A

2008-01-01

Identification of genes that regulate BMD will enhance our understanding of osteoporosis and could provide novel molecular targets for treatment or prevention. We generated a mouse intercross population and carried out a quantitative trait locus (QTL) analysis of 143 female and 124 male F2 progeny from progenitor strains SM/J and NZB/BlNJ using whole body and vertebral areal BMD (aBMD) as measured by DXA. We found that both whole body and vertebral aBMD was affected by two loci on chromosome 9: one with a significant epistatic interaction on distal chromosome 8 and the other with a sex-specific effect. Two additional significant QTLs were identified on chromosome 12, and several suggestive ones were identified on chromosomes 5, 8, 15, and 19. The chromosome 9, 12, and 15 loci have been previously identified in other crosses. SNP-based haplotype analysis of the progenitor strains identified blocks within the QTL region that distinguish the low allele strains from the high allele strains, significantly narrowing the QTL region and reducing the possible candidate genes to 98 for chromosome 9, 31 for chromosome 12, and only 2 for chromosome 15. Trps1 is the most probable candidate gene for the chromosome 15 QTL. The sex-specific effects may help to elucidate the BMD differences between males and females. This study shows the power of statistical modeling to resolve linked QTLs and the use of haplotype analysis in narrowing the list of candidates. PMID:18442308

Marginal fit and photoelastic stress analysis of CAD-CAM and overcast 3-unit implant-supported frameworks.

PubMed

Presotto, Anna Gabriella Camacho; Bhering, Cláudia Lopes Brilhante; Mesquita, Marcelo Ferraz; Barão, Valentim Adelino Ricardo

2017-03-01

Several studies have shown the superiority of computer-assisted design and computer-assisted manufacturing (CAD-CAM) technology compared with conventional casting. However, an advanced technology exists for casting procedures (the overcasting technique), which may serve as an acceptable and affordable alternative to CAD-CAM technology for fabricating 3-unit implant-supported fixed dental prostheses (FDPs). The purpose of this in vitro study was to evaluate, using quantitative photoelastic analysis, the effect of the prosthetic framework fabrication method (CAD-CAM and overcasting) on the marginal fit and stress transmitted to implants. The correlation between marginal fit and stress was also investigated. Three-unit implant-supported FDP frameworks were made using the CAD-CAM (n=10) and overcasting (n=10) methods. The frameworks were waxed to simulate a mandibular first premolar (PM region) to first molar (M region) FDP using overcast mini-abutment cylinders. The wax patterns were overcast (overcast experimental group) or scanned to obtain the frameworks (CAD-CAM control group). All frameworks were fabricated from cobalt-chromium (CoCr) alloy. The marginal fit was analyzed according to the single-screw test protocol, obtaining an average value for each region (M and PM) and each framework. The frameworks were tightened for the photoelastic model with standardized 10-Ncm torque. Stress was measured by quantitative photoelastic analysis. The results were submitted to the Student t test, 2-way ANOVA, and Pearson correlation test (α=.05). The framework fabrication method (FM) and evaluation site (ES; M and PM regions) did not affect the marginal fit values (P=.559 for FM and P=.065 for ES) and stress (P=.685 for FM and P=.468 for ES) in the implant-supported system. Positive correlations between marginal fit and stress were observed (CAD-CAM: r=0.922; P<.001; overcast: r=0.908; P<.001). CAD-CAM and overcasting methods present similar marginal fit and stress values for 3-unit FDP frameworks. The decreased marginal fit of frameworks induces greater stress in the implant-supported system. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Black phosphorus-assisted laser desorption ionization mass spectrometry for the determination of low-molecular-weight compounds in biofluids.

PubMed

He, Xiao-Mei; Ding, Jun; Yu, Lei; Hussain, Dilshad; Feng, Yu-Qi

2016-09-01

Quantitative analysis of small molecules by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been a challenging task due to matrix-derived interferences in low m/z region and poor reproducibility of MS signal response. In this study, we developed an approach by applying black phosphorus (BP) as a matrix-assisted laser desorption ionization (MALDI) matrix for the quantitative analysis of small molecules for the first time. Black phosphorus-assisted laser desorption/ionization mass spectrometry (BP/ALDI-MS) showed clear background and exhibited superior detection sensitivity toward quaternary ammonium compounds compared to carbon-based materials. By combining stable isotope labeling (SIL) strategy with BP/ALDI-MS (SIL-BP/ALDI-MS), a variety of analytes labeled with quaternary ammonium group were sensitively detected. Moreover, the isotope-labeled forms of analytes also served as internal standards, which broadened the analyte coverage of BP/ALDI-MS and improved the reproducibility of MS signals. Based on these advantages, a reliable method for quantitative analysis of aldehydes from complex biological samples (saliva, urine, and serum) was successfully established. Good linearities were obtained for five aldehydes in the range of 0.1-20.0 μM with correlation coefficients (R (2)) larger than 0.9928. The LODs were found to be 20 to 100 nM. Reproducibility of the method was obtained with intra-day and inter-day relative standard deviations (RSDs) less than 10.4 %, and the recoveries in saliva samples ranged from 91.4 to 117.1 %. Taken together, the proposed SIL-BP/ALDI-MS strategy has proved to be a reliable tool for quantitative analysis of aldehydes from complex samples. Graphical Abstract An approach for the determination of small molecules was developed by using black phosphorus (BP) as a matrix-assisted laser desorption ionization (MALDI) matrix.

Geoscience data visualization and analysis using GeoMapApp

NASA Astrophysics Data System (ADS)

Ferrini, Vicki; Carbotte, Suzanne; Ryan, William; Chan, Samantha

2013-04-01

Increased availability of geoscience data resources has resulted in new opportunities for developing visualization and analysis tools that not only promote data integration and synthesis, but also facilitate quantitative cross-disciplinary access to data. Interdisciplinary investigations, in particular, frequently require visualizations and quantitative access to specialized data resources across disciplines, which has historically required specialist knowledge of data formats and software tools. GeoMapApp (www.geomapapp.org) is a free online data visualization and analysis tool that provides direct quantitative access to a wide variety of geoscience data for a broad international interdisciplinary user community. While GeoMapApp provides access to online data resources, it can also be packaged to work offline through the deployment of a small portable hard drive. This mode of operation can be particularly useful during field programs to provide functionality and direct access to data when a network connection is not possible. Hundreds of data sets from a variety of repositories are directly accessible in GeoMapApp, without the need for the user to understand the specifics of file formats or data reduction procedures. Available data include global and regional gridded data, images, as well as tabular and vector datasets. In addition to basic visualization and data discovery functionality, users are provided with simple tools for creating customized maps and visualizations and to quantitatively interrogate data. Specialized data portals with advanced functionality are also provided for power users to further analyze data resources and access underlying component datasets. Users may import and analyze their own geospatial datasets by loading local versions of geospatial data and can access content made available through Web Feature Services (WFS) and Web Map Services (WMS). Once data are loaded in GeoMapApp, a variety options are provided to export data and/or 2D/3D visualizations into common formats including grids, images, text files, spreadsheets, etc. Examples of interdisciplinary investigations that make use of GeoMapApp visualization and analysis functionality will be provided.

Fluvial drainage networks: the fractal approach as an improvement of quantitative geomorphic analyses

NASA Astrophysics Data System (ADS)

Melelli, Laura; Liucci, Luisa; Vergari, Francesca; Ciccacci, Sirio; Del Monte, Maurizio

2014-05-01

Drainage basins are primary landscape units for geomorphological investigations. Both hillslopes and river drainage system are fundamental components in drainage basins analysis. As other geomorphological systems, also the drainage basins aim to an equilibrium condition where the sequence of erosion, transport and sedimentation approach to a condition of minimum energy effort. This state is revealed by a typical geometry of landforms and of drainage net. Several morphometric indexes can measure how much a drainage basin is far from the theoretical equilibrium configuration, revealing possible external disarray. In active tectonic areas, the drainage basins have a primary importance in order to highlight style, amount and rate of tectonic impulses, and morphometric indexes allow to estimate the tectonic activity classes of different sectors in a study area. Moreover, drainage rivers are characterized by a self-similarity structure; this promotes the use of fractals theory to investigate the system. In this study, fractals techniques are employed together with quantitative geomorphological analysis to study the Upper Tiber Valley (UTV), a tectonic intermontane basin located in northern Apennines (Umbria, central Italy). The area is the result of different tectonic phases. From Late Pliocene until present time the UTV is strongly controlled by a regional uplift and by an extensional phase with different sets of normal faults playing a fundamental role in basin morphology. Thirty-four basins are taken into account for the quantitative analysis, twenty on the left side of the basin, the others on the right side. Using fractals dimension of drainage networks, Horton's laws results, concavity and steepness indexes, and hypsometric curves, this study aims to obtain an evolutionary model of the UTV, where the uplift is compared to local subsidence induced by normal fault activity. The results highlight a well defined difference between western and eastern tributary basins, suggesting a greater disequilibrium in the last ones. The quantitative analysis points out the segments of the basin boundaries where the fault activity is more efficient and the resulting geomorphological implications.

Quantitative analysis applied to contrast medium extravasation by using the computed-tomography number within the region of interest

NASA Astrophysics Data System (ADS)

Lee, Jae-Seung; Im, In-Chul; Kim, Moon-Jib; Goo, Eun-Hoe; Kim, Sun-Ju; Kim, Kwang; Kwak, Byung-Joon

2014-02-01

The present study was carried out to present a method to analyze extravasation quantitatively by measuring the computed tomography (CT) number after determining the region of interest (ROI) in the CT images obtained from patients suspected of extravasation induced by contrast medium auto-injection. To achieve this, we divided the study subjects into a group of patients who incurred extravasation and a group of patients who underwent routine scans without incurring extravasation. The CT numbers at IV sites were obtained as reference values, and CT numbers at extravasation sites and hepatic portal veins, respectively, were obtained as relative values. Thereupon, the predicted time for extravasation ( T EP ) and the predicted ratio for extravasation ( R EP ) of an extravasation site were obtained and analyzed quantitatively. In the case of extravasation induced by a dual auto-injector, the values of the CT numbers were confirmed to be lower and the extravasation site to be enlarged when compared to the extravasation induced by a single autoinjector. This is because the physiological saline introduced after the injection of the contrast agent diluted the concentration of the extravasated contrast agent. Additionally, the T EP caused by the auto-injector was about 40 seconds, and we could perform a precise quantitative assessment of the site suspected of extravasation. In conclusion, the dual auto-injection method, despite its advantage of reducing the volume of contrast agent and improving the quality of images for patients with good vascular integrity, was judged to be likely to increase the risk of extravasation and aggravate outcomes for patients with poor vascular integrity by enlarging extravasation sites.

Optical Basicity and Nepheline Crystallization in High Alumina Glasses

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

Rodriguez, Carmen P.; McCloy, John S.; Schweiger, M. J.

2011-02-25

The purpose of this study was to find compositions that increase waste loading of high-alumina wastes beyond what is currently acceptable while avoiding crystallization of nepheline (NaAlSiO4) on slow cooling. Nepheline crystallization has been shown to have a large impact on the chemical durability of high-level waste glasses. It was hypothesized that there would be some composition regions where high-alumina would not result in nepheline crystal production, compositions not currently allowed by the nepheline discriminator. Optical basicity (OB) and the nepheline discriminator (ND) are two ways of describing a given complex glass composition. This report presents the theoretical and experimentalmore » basis for these models. They are being studied together in a quadrant system as metrics to explore nepheline crystallization and chemical durability as a function of waste glass composition. These metrics were calculated for glasses with existing data and also for theoretical glasses to explore nepheline formation in Quadrant IV (passes OB metric but fails ND metric), where glasses are presumed to have good chemical durability. Several of these compositions were chosen, and glasses were made to fill poorly represented regions in Quadrant IV. To evaluate nepheline formation and chemical durability of these glasses, quantitative X-ray diffraction (XRD) analysis and the Product Consistency Test were conducted. A large amount of quantitative XRD data is collected here, both from new glasses and from glasses of previous studies that had not previously performed quantitative XRD on the phase assemblage. Appendix A critically discusses a large dataset to be considered for future quantitative studies on nepheline formation in glass. Appendix B provides a theoretical justification for choice of the oxide coefficients used to compute the OB criterion for nepheline formation.« less

Atlas-based analysis of cardiac shape and function: correction of regional shape bias due to imaging protocol for population studies.

PubMed

Medrano-Gracia, Pau; Cowan, Brett R; Bluemke, David A; Finn, J Paul; Kadish, Alan H; Lee, Daniel C; Lima, Joao A C; Suinesiaputra, Avan; Young, Alistair A

2013-09-13

Cardiovascular imaging studies generate a wealth of data which is typically used only for individual study endpoints. By pooling data from multiple sources, quantitative comparisons can be made of regional wall motion abnormalities between different cohorts, enabling reuse of valuable data. Atlas-based analysis provides precise quantification of shape and motion differences between disease groups and normal subjects. However, subtle shape differences may arise due to differences in imaging protocol between studies. A mathematical model describing regional wall motion and shape was used to establish a coordinate system registered to the cardiac anatomy. The atlas was applied to data contributed to the Cardiac Atlas Project from two independent studies which used different imaging protocols: steady state free precession (SSFP) and gradient recalled echo (GRE) cardiovascular magnetic resonance (CMR). Shape bias due to imaging protocol was corrected using an atlas-based transformation which was generated from a set of 46 volunteers who were imaged with both protocols. Shape bias between GRE and SSFP was regionally variable, and was effectively removed using the atlas-based transformation. Global mass and volume bias was also corrected by this method. Regional shape differences between cohorts were more statistically significant after removing regional artifacts due to imaging protocol bias. Bias arising from imaging protocol can be both global and regional in nature, and is effectively corrected using an atlas-based transformation, enabling direct comparison of regional wall motion abnormalities between cohorts acquired in separate studies.

Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

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

Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard

2008-01-10

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched inmore » bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early-embryonic transcriptional regulation, and a significant proportion may be nonfunctional. Surprisingly, for five of the six factors, their recognition sites are not unambiguously more constrained evolutionarily than the immediate flanking DNA, even in more highly bound and presumably functional regions, indicating that comparative DNA sequence analysis is limited in its ability to identify functional transcription factor targets.« less

[11C]Flumazenil PET in patients with epilepsy with dual pathology.

PubMed

Juhász, C; Nagy, F; Muzik, O; Watson, C; Shah, J; Chugani, H T

1999-05-01

Coexistence of hippocampal sclerosis and a potentially epileptogenic cortical lesion is referred to as dual pathology and can be responsible for poor surgical outcome in patients with medically intractable partial epilepsy. [11C]Flumazenil (FMZ) positron emission tomography (PET) is a sensitive method for visualizing epileptogenic foci. In this study of 12 patients with dual pathology, we addressed the sensitivity of FMZ PET to detect hippocampal abnormalities and compared magnetic resonance imaging (MRI) with visual as well as quantitative FMZ PET findings. All patients underwent volumetric MRI, prolonged video-EEG monitoring, and glucose metabolism PET before the FMZ PET. MRI-coregistered partial volume-corrected PET images were used to measure FMZ-binding asymmetries by using asymmetry indices (AIs) in the whole hippocampus and in three (anterior, middle, and posterior) hippocampal subregions. Cortical sites of decreased FMZ binding also were evaluated by using AIs for regions with MRI-verified cortical lesions as well as for non-lesional areas with visually detected asymmetry. Abnormally decreased FMZ binding could be detected by quantitative analysis in the atrophic hippocampus of all 12 patients, including three patients with discordant or inconclusive EEG findings. Decreased FMZ binding was restricted to only one subregion of the hippocampus in three patients. Areas of decreased cortical FMZ binding were obvious visually in all patients. Decreased FMZ binding was detected visually in nonlesional cortical areas in four patients. The AIs for these nonlesional regions with visual asymmetry were significantly lower than those for regions showing MRI lesions (paired t test, p = 0.0075). Visual as well as quantitative analyses of FMZ-binding asymmetry are sensitive methods to detect decreased benzodiazepine-receptor binding in the hippocampus and neocortex of patients with dual pathology. MRI-defined hippocampal atrophy is always associated with decreased FMZ binding, although the latter may be localized to only one sub-region within the hippocampus. FMZ PET abnormalities can occur in areas with normal appearance on MRI, but FMZ-binding asymmetry of these regions is lower when compared with that of lesional areas. FMZ PET can be especially helpful when MRI and EEG findings of patients with intractable epilepsy are discordant.

Computed Tomography Studies of Lung Mechanics

PubMed Central

Simon, Brett A.; Christensen, Gary E.; Low, Daniel A.; Reinhardt, Joseph M.

2005-01-01

The study of lung mechanics has progressed from global descriptions of lung pressure and volume relationships to the high-resolution, three-dimensional, quantitative measurement of dynamic regional mechanical properties and displacements. X-ray computed tomography (CT) imaging is ideally suited to the study of regional lung mechanics in intact subjects because of its high spatial and temporal resolution, correlation of functional data with anatomic detail, increasing volumetric data acquisition, and the unique relationship between CT density and lung air content. This review presents an overview of CT measurement principles and limitations for the study of regional mechanics, reviews some of the early work that set the stage for modern imaging approaches and impacted the understanding and management of patients with acute lung injury, and presents evolving novel approaches for the analysis and application of dynamic volumetric lung image data. PMID:16352757

VHF and UHF radar observations of equatorial F region ionospheric irregularities and background densities

NASA Astrophysics Data System (ADS)

Towle, D. M.

1980-02-01

A series of measurements of the properties of equatorial ionospheric irregularities were made at Kwajalein, Marshall Islands (M.I.) in August 1977 and July-August 1978. These measurements, sponsored by the Defense Nuclear Agency (DNA), involved coordinated ground-based and in situ sensors. The ARPA Long-Range Tracking and Instrumentation Radar (ALTAIR), operated by Lincoln Laboratory, obtained backscatter and transmission data during five nights in August 1977 and eight nights in July-August 1978. This report describes the ALTAIR data from the night of August 11, 1978, which yield direct quantitative measurements of 1-m and 3/8-m irregularities and of plasma depleted regions. These plasma depleted regions, previously predicted on the basis of theoretical analysis and in situ data, were observed during the decay phase and not the generative phase of the field-aligned irregularities.

Impact of Emissions and Long-Range Transport on Multi-Decadal Aerosol Trends: Implications for Air Quality and Climate

NASA Technical Reports Server (NTRS)

Chin, Mian

2012-01-01

We present a global model analysis of the impact of long-range transport and anthropogenic emissions on the aerosol trends in the major pollution regions in the northern hemisphere and in the Arctic in the past three decades. We will use the Goddard Chemistry Aerosol Radiation and Transport (GOCART) model to analyze the multi-spatial and temporal scale data, including observations from Terra, Aqua, and CALIPSO satellites and from the long-term surface monitoring stations. We will analyze the source attribution (SA) and source-receptor (SR) relationships in North America, Europe, East Asia, South Asia, and the Arctic at the surface and free troposphere and establish the quantitative linkages between emissions from different source regions. We will discuss the implications for regional air quality and climate change.

An ultrastructural analysis of the epithelial-fiber interface (EFI) in primate lenses.

PubMed

Kuszak, J R; Novak, L A; Brown, H G

1995-11-01

The purpose of this study was to conduct a comprehensive ultrastructural analysis of the epithelial-fiber interface (EFI) in normal adult primate (Macaque nemestrina and fascicularis; 6-9 years old, n = 10) lenses. Scanning electron microscopy (SEM) was used to initially characterize the gross size, shape and three-dimensional organization of central zone (cz) epithelial cells and the anterior ends of elongating fibers beneath these cells. This fiducial information was essential to properly orient lens pieces in freeze fracture specimen carriers for the production of replicas with unambiguously identifiable EFI. Transmission electron microscopy (TEM) of replicas and thin-sectioned material were used to ultrastructurally analyse the cz EFI. TEM thin-sectioned material was also used to ultrastructurally analyse the pregerminative (pgz), germinative (gz) and transitional zone (tz) EFI. Correlative SEM and TEM of cz EFI components revealed that the apical membrane of both epithelial and elongating fiber cells were irregularly polygonal in shape, and aligned in parallel as smooth, concave-convex surfaces. However, whereas epithelial cell apical surfaces had minimal size variation, elongating fibers were larger and considerably variable in size. Quantitative analysis of > 10000 micron2 cz elongating fiber apical surfaces failed to detect any gap junctions defined in freeze fracture replicas as complementary aggregates of transmembrane proteins (connexons) conjoined across a narrowed extracellular space. However, a comparable frequency of vesicular events was noted in this region as quantified previously in adult and embryonic chick lens. Correlative TEM analysis > 1500 linear micrometers of thin-sectioned EFI from this region confirmed the presence of epithelial-epithelial gap junctions, elongating fiber-elongating fiber gap junctions, and an extreme paucity of epithelial-elongating fiber gap junctions. In contrast, TEM analysis of > 1000 linear micrometers of thin-sectioned pgz, gz and tz EFI, confirmed the presence of epithelial-epithelial gap junctions, elongating fiber-elongating fiber gap junctions, numerous epithelial-elongating fiber adherens junctions and a few epithelial-elongating fiber gap junctions. Thus, the results of this and previous quantitative morphological and physiological studies (electronic and dye coupling) demonstrate that there is limited coupling between cz epithelial cells and underlying elongating fibers. Furthermore, the absence of gap junctional plaques in cz EFI freeze-fracture replicas and either pentalaminar or septalaminar profiles in correlative thin-sections, suggests that this limited coupling could be mediated via isolated gap junction channels. However, the results of this and previous quantitative studies further show that a greater degree of coupling exists across the pgz, gz and tz regions of the EFI and that this coupling is likely to be mediated by gap junction plaques. Finally, this and other studies continue to demonstrate that transcytotic processes play a role in lens physiology at the EFI.

Quantitative Hyperspectral Reflectance Imaging

PubMed Central

Klein, Marvin E.; Aalderink, Bernard J.; Padoan, Roberto; de Bruin, Gerrit; Steemers, Ted A.G.

2008-01-01

Hyperspectral imaging is a non-destructive optical analysis technique that can for instance be used to obtain information from cultural heritage objects unavailable with conventional colour or multi-spectral photography. This technique can be used to distinguish and recognize materials, to enhance the visibility of faint or obscured features, to detect signs of degradation and study the effect of environmental conditions on the object. We describe the basic concept, working principles, construction and performance of a laboratory instrument specifically developed for the analysis of historical documents. The instrument measures calibrated spectral reflectance images at 70 wavelengths ranging from 365 to 1100 nm (near-ultraviolet, visible and near-infrared). By using a wavelength tunable narrow-bandwidth light-source, the light energy used to illuminate the measured object is minimal, so that any light-induced degradation can be excluded. Basic analysis of the hyperspectral data includes a qualitative comparison of the spectral images and the extraction of quantitative data such as mean spectral reflectance curves and statistical information from user-defined regions-of-interest. More sophisticated mathematical feature extraction and classification techniques can be used to map areas on the document, where different types of ink had been applied or where one ink shows various degrees of degradation. The developed quantitative hyperspectral imager is currently in use by the Nationaal Archief (National Archives of The Netherlands) to study degradation effects of artificial samples and original documents, exposed in their permanent exhibition area or stored in their deposit rooms. PMID:27873831

Two-way and three-way approaches to ultra high performance liquid chromatography-photodiode array dataset for the quantitative resolution of a two-component mixture containing ciprofloxacin and ornidazole.

PubMed

Dinç, Erdal; Ertekin, Zehra Ceren; Büker, Eda

2016-09-01

Two-way and three-way calibration models were applied to ultra high performance liquid chromatography with photodiode array data with coeluted peaks in the same wavelength and time regions for the simultaneous quantitation of ciprofloxacin and ornidazole in tablets. The chromatographic data cube (tensor) was obtained by recording chromatographic spectra of the standard and sample solutions containing ciprofloxacin and ornidazole with sulfadiazine as an internal standard as a function of time and wavelength. Parallel factor analysis and trilinear partial least squares were used as three-way calibrations for the decomposition of the tensor, whereas three-way unfolded partial least squares was applied as a two-way calibration to the unfolded dataset obtained from the data array of ultra high performance liquid chromatography with photodiode array detection. The validity and ability of two-way and three-way analysis methods were tested by analyzing validation samples: synthetic mixture, interday and intraday samples, and standard addition samples. Results obtained from two-way and three-way calibrations were compared to those provided by traditional ultra high performance liquid chromatography. The proposed methods, parallel factor analysis, trilinear partial least squares, unfolded partial least squares, and traditional ultra high performance liquid chromatography were successfully applied to the quantitative estimation of the solid dosage form containing ciprofloxacin and ornidazole. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Resected Brain Tissue, Seizure Onset Zone and Quantitative EEG Measures: Towards Prediction of Post-Surgical Seizure Control

PubMed Central

Andrzejak, Ralph G.; Hauf, Martinus; Pollo, Claudio; Müller, Markus; Weisstanner, Christian; Wiest, Roland; Schindler, Kaspar

2015-01-01

Background Epilepsy surgery is a potentially curative treatment option for pharmacoresistent patients. If non-invasive methods alone do not allow to delineate the epileptogenic brain areas the surgical candidates undergo long-term monitoring with intracranial EEG. Visual EEG analysis is then used to identify the seizure onset zone for targeted resection as a standard procedure. Methods Despite of its great potential to assess the epileptogenicty of brain tissue, quantitative EEG analysis has not yet found its way into routine clinical practice. To demonstrate that quantitative EEG may yield clinically highly relevant information we retrospectively investigated how post-operative seizure control is associated with four selected EEG measures evaluated in the resected brain tissue and the seizure onset zone. Importantly, the exact spatial location of the intracranial electrodes was determined by coregistration of pre-operative MRI and post-implantation CT and coregistration with post-resection MRI was used to delineate the extent of tissue resection. Using data-driven thresholding, quantitative EEG results were separated into normally contributing and salient channels. Results In patients with favorable post-surgical seizure control a significantly larger fraction of salient channels in three of the four quantitative EEG measures was resected than in patients with unfavorable outcome in terms of seizure control (median over the whole peri-ictal recordings). The same statistics revealed no association with post-operative seizure control when EEG channels contributing to the seizure onset zone were studied. Conclusions We conclude that quantitative EEG measures provide clinically relevant and objective markers of target tissue, which may be used to optimize epilepsy surgery. The finding that differentiation between favorable and unfavorable outcome was better for the fraction of salient values in the resected brain tissue than in the seizure onset zone is consistent with growing evidence that spatially extended networks might be more relevant for seizure generation, evolution and termination than a single highly localized brain region (i.e. a “focus”) where seizures start. PMID:26513359

SYN-JEM: A Quantitative Job-Exposure Matrix for Five Lung Carcinogens.

PubMed

Peters, Susan; Vermeulen, Roel; Portengen, Lützen; Olsson, Ann; Kendzia, Benjamin; Vincent, Raymond; Savary, Barbara; Lavoué, Jérôme; Cavallo, Domenico; Cattaneo, Andrea; Mirabelli, Dario; Plato, Nils; Fevotte, Joelle; Pesch, Beate; Brüning, Thomas; Straif, Kurt; Kromhout, Hans

2016-08-01

The use of measurement data in occupational exposure assessment allows more quantitative analyses of possible exposure-response relations. We describe a quantitative exposure assessment approach for five lung carcinogens (i.e. asbestos, chromium-VI, nickel, polycyclic aromatic hydrocarbons (by its proxy benzo(a)pyrene (BaP)) and respirable crystalline silica). A quantitative job-exposure matrix (JEM) was developed based on statistical modeling of large quantities of personal measurements. Empirical linear models were developed using personal occupational exposure measurements (n = 102306) from Europe and Canada, as well as auxiliary information like job (industry), year of sampling, region, an a priori exposure rating of each job (none, low, and high exposed), sampling and analytical methods, and sampling duration. The model outcomes were used to create a JEM with a quantitative estimate of the level of exposure by job, year, and region. Decreasing time trends were observed for all agents between the 1970s and 2009, ranging from -1.2% per year for personal BaP and nickel exposures to -10.7% for asbestos (in the time period before an asbestos ban was implemented). Regional differences in exposure concentrations (adjusted for measured jobs, years of measurement, and sampling method and duration) varied by agent, ranging from a factor 3.3 for chromium-VI up to a factor 10.5 for asbestos. We estimated time-, job-, and region-specific exposure levels for four (asbestos, chromium-VI, nickel, and RCS) out of five considered lung carcinogens. Through statistical modeling of large amounts of personal occupational exposure measurement data we were able to derive a quantitative JEM to be used in community-based studies. © The Author 2016. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Linearization improves the repeatability of quantitative dynamic contrast-enhanced MRI.

PubMed

Jones, Kyle M; Pagel, Mark D; Cárdenas-Rodríguez, Julio

2018-04-01

The purpose of this study was to compare the repeatabilities of the linear and nonlinear Tofts and reference region models (RRM) for dynamic contrast-enhanced MRI (DCE-MRI). Simulated and experimental DCE-MRI data from 12 rats with a flank tumor of C6 glioma acquired over three consecutive days were analyzed using four quantitative and semi-quantitative DCE-MRI metrics. The quantitative methods used were: 1) linear Tofts model (LTM), 2) non-linear Tofts model (NTM), 3) linear RRM (LRRM), and 4) non-linear RRM (NRRM). The following semi-quantitative metrics were used: 1) maximum enhancement ratio (MER), 2) time to peak (TTP), 3) initial area under the curve (iauc64), and 4) slope. LTM and NTM were used to estimate K trans , while LRRM and NRRM were used to estimate K trans relative to muscle (R Ktrans ). Repeatability was assessed by calculating the within-subject coefficient of variation (wSCV) and the percent intra-subject variation (iSV) determined with the Gage R&R analysis. The iSV for R Ktrans using LRRM was two-fold lower compared to NRRM at all simulated and experimental conditions. A similar trend was observed for the Tofts model, where LTM was at least 50% more repeatable than the NTM under all experimental and simulated conditions. The semi-quantitative metrics iauc64 and MER were as equally repeatable as K trans and R Ktrans estimated by LTM and LRRM respectively. The iSV for iauc64 and MER were significantly lower than the iSV for slope and TTP. In simulations and experimental results, linearization improves the repeatability of quantitative DCE-MRI by at least 30%, making it as repeatable as semi-quantitative metrics. Copyright © 2017 Elsevier Inc. All rights reserved.

Clinical comparison of branched DNA and reverse transcriptase-PCR and nucleic acid sequence-based amplification assay for the quantitation of circulating recombinant form_BC HIV-1 RNA in plasma.

PubMed

Pan, Pinliang; Tao, Xiaoxia; Zhang, Qi; Xing, Wenge; Sun, Xianguang; Pei, Lijian; Jiang, Yan

2007-12-01

To investigate the correlation between three viral load assays for circulating recombinant form (CRF)_BC. Recent studies in HIV-1 molecular epidemiology, reveals that CRF_BC is the dominant subtype of HIV-1 virus in mainland China, representing over 45% of the HIV-1 infected population. The performances of nucleic acid sequence-based amplification (NASBA), branched DNA (bDNA) and reverse transcriptase polymerase chain reaction (RT-PCR) were compared for the HIV-1 viral load detection and quantitation of CRF_BC in China. Sixteen HIV-1 positive and three HIV-1 negative samples were collected. Sequencing of the positive samples in the gp41 region was conducted. The HIV-1 viral load values were determined using bDNA, RT-PCR and NASBA assays. Deming regression analysis with SPSS 12.0 (SPS Inc., Chicago, Illinois, USA) was performed for data analysis. Sequencing and phylogenetic analysis of env gene (gp41) region of the 16 HIV-1 positive clinical specimens from Guizhou Province in southwest China revealed the dominance of the subtype CRF_BC in that region. A good correlation of their viral load values was observed among three assays. Pearson's correlation between RT-PCR and bDNA is 0.969, Lg(VL)RT-PCR = 0.969 * Lg(VL)bDNA + 0.55; Pearson's correlation between RT-PCR and NASBA is 0.968, Lg(VL)RT-PCR = 0.968 * Lg(VL)NASBA + 0.937; Pearson's correlation between NASBA and bDNA is 0.980, Lg(VL)NASBA = 0.980 * Lg(VL)bDNA - 0.318. When testing with 3 different assays, RT-PCR, bDNA and NASBA, the group of 16 HIV-1 positive samples showed the viral load value was highest for RT-PCR, followed by bDNA then NASBA, which is consistent with the former results in subtype B. The three viral load assays are highly correlative for CRF_BC in China.

Usefulness of myocardial parametric imaging to evaluate myocardial viability in experimental and in clinical studies

PubMed Central

Korosoglou, G; Hansen, A; Bekeredjian, R; Filusch, A; Hardt, S; Wolf, D; Schellberg, D; Katus, H A; Kuecherer, H

2006-01-01

Objective To evaluate whether myocardial parametric imaging (MPI) is superior to visual assessment for the evaluation of myocardial viability. Methods and results Myocardial contrast echocardiography (MCE) was assessed in 11 pigs before, during, and after left anterior descending coronary artery occlusion and in 32 patients with ischaemic heart disease by using intravenous SonoVue administration. In experimental studies perfusion defect area assessment by MPI was compared with visually guided perfusion defect planimetry. Histological assessment of necrotic tissue was the standard reference. In clinical studies viability was assessed on a segmental level by (1) visual analysis of myocardial opacification; (2) quantitative estimation of myocardial blood flow in regions of interest; and (3) MPI. Functional recovery between three and six months after revascularisation was the standard reference. In experimental studies, compared with visually guided perfusion defect planimetry, planimetric assessment of infarct size by MPI correlated more significantly with histology (r2  =  0.92 versus r2  =  0.56) and had a lower intraobserver variability (4% v 15%, p < 0.05). In clinical studies, MPI had higher specificity (66% v 43%, p < 0.05) than visual MCE and good accuracy (81%) for viability detection. It was less time consuming (3.4 (1.6) v 9.2 (2.4) minutes per image, p < 0.05) than quantitative blood flow estimation by regions of interest and increased the agreement between observers interpreting myocardial perfusion (κ  =  0.87 v κ  =  0.75, p < 0.05). Conclusion MPI is useful for the evaluation of myocardial viability both in animals and in patients. It is less time consuming than quantification analysis by regions of interest and less observer dependent than visual analysis. Thus, strategies incorporating this technique may be valuable for the evaluation of myocardial viability in clinical routine. PMID:15939722

Skeleton-based region competition for automated gray matter and white matter segmentation of human brain MR images

NASA Astrophysics Data System (ADS)

Chu, Yong; Chen, Ya-Fang; Su, Min-Ying; Nalcioglu, Orhan

2005-04-01

Image segmentation is an essential process for quantitative analysis. Segmentation of brain tissues in magnetic resonance (MR) images is very important for understanding the structural-functional relationship for various pathological conditions, such as dementia vs. normal brain aging. Different brain regions are responsible for certain functions and may have specific implication for diagnosis. Segmentation may facilitate the analysis of different brain regions to aid in early diagnosis. Region competition has been recently proposed as an effective method for image segmentation by minimizing a generalized Bayes/MDL criterion. However, it is sensitive to initial conditions - the "seeds", therefore an optimal choice of "seeds" is necessary for accurate segmentation. In this paper, we present a new skeleton-based region competition algorithm for automated gray and white matter segmentation. Skeletons can be considered as good "seed regions" since they provide the morphological a priori information, thus guarantee a correct initial condition. Intensity gradient information is also added to the global energy function to achieve a precise boundary localization. This algorithm was applied to perform gray and white matter segmentation using simulated MRI images from a realistic digital brain phantom. Nine different brain regions were manually outlined for evaluation of the performance in these separate regions. The results were compared to the gold-standard measure to calculate the true positive and true negative percentages. In general, this method worked well with a 96% accuracy, although the performance varied in different regions. We conclude that the skeleton-based region competition is an effective method for gray and white matter segmentation.

Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon

PubMed Central

Gharbi, Karim; Glover, Kevin A; Stone, Louise C; MacDonald, Elizabeth S; Matthews, Louise; Grimholt, Unni; Stear, Michael J

2009-01-01

Background Genetic variation has been shown to play a significant role in determining susceptibility to the salmon louse, Lepeophtheirus salmonis. However, the mechanisms involved in differential response to infection remain poorly understood. Recent findings in Atlantic salmon (Salmo salar) have provided evidence for a potential link between marker variation at the major histocompatibility complex (MHC) and differences in lice abundance among infected siblings, suggesting that MHC genes can modulate susceptibility to the parasite. In this study, we used quantitative trait locus (QTL) analysis to test the effect of genomic regions linked to MHC class I and II on linkage groups (LG) 15 and 6, respectively. Results Significant QTL effects were detected on both LG 6 and LG 15 in sire-based analysis but the QTL regions remained unresolved due to a lack of recombination between markers. In dam-based analysis, a significant QTL was identified on LG 6, which accounted for 12.9% of within-family variance in lice abundance. However, the QTL was located at the opposite end of DAA, with no significant overlap with the MHC class II region. Interestingly, QTL modelling also revealed evidence of sex-linked differences in lice abundance, indicating that males and females may have different susceptibility to infection. Conclusion Overall, QTL analysis provided relatively weak support for a proximal effect of classical MHC regions on lice abundance, which can partly be explained by linkage to other genes controlling susceptibility to L. salmonis on the same chromosome. PMID:19397823

Novel methods of imaging and analysis for the thermoregulatory sweat test.

PubMed

Carroll, Michael Sean; Reed, David W; Kuntz, Nancy L; Weese-Mayer, Debra Ellyn

2018-06-07

The thermoregulatory sweat test (TST) can be central to the identification and management of disorders affecting sudomotor function and small sensory and autonomic nerve fibers, but the cumbersome nature of the standard testing protocol has prevented its widespread adoption. A high resolution, quantitative, clean and simple assay of sweating could significantly improve identification and management of these disorders. Images from 89 clinical TSTs were analyzed retrospectively using two novel techniques. First, using the standard indicator powder, skin surface sweat distributions were determined algorithmically for each patient. Second, a fundamentally novel method using thermal imaging of forced evaporative cooling was evaluated through comparison with the standard technique. Correlation and receiver operating characteristic analyses were used to determine the degree of match between these methods, and the potential limits of thermal imaging were examined through cumulative analysis of all studied patients. Algorithmic encoding of sweating and non-sweating regions produces a more objective analysis for clinical decision making. Additionally, results from the forced cooling method correspond well with those from indicator powder imaging, with a correlation across spatial regions of -0.78 (CI: -0.84 to -0.71). The method works similarly across body regions, and frame-by-frame analysis suggests the ability to identify sweating regions within about 1 second of imaging. While algorithmic encoding can enhance the standard sweat testing protocol, thermal imaging with forced evaporative cooling can dramatically improve the TST by making it less time-consuming and more patient-friendly than the current approach.

Identifying metastatic breast tumors using textural kinetic features of a contrast based habitat in DCE-MRI

NASA Astrophysics Data System (ADS)

Chaudhury, Baishali; Zhou, Mu; Goldgof, Dmitry B.; Hall, Lawrence O.; Gatenby, Robert A.; Gillies, Robert J.; Drukteinis, Jennifer S.

2015-03-01

The ability to identify aggressive tumors from indolent tumors using quantitative analysis on dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) would dramatically change the breast cancer treatment paradigm. With this prognostic information, patients with aggressive tumors that have the ability to spread to distant sites outside of the breast could be selected for more aggressive treatment and surveillance regimens. Conversely, patients with tumors that do not have the propensity to metastasize could be treated less aggressively, avoiding some of the morbidity associated with surgery, radiation and chemotherapy. We propose a computer aided detection framework to determine which breast cancers will metastasize to the loco-regional lymph nodes as well as which tumors will eventually go on to develop distant metastses using quantitative image analysis and radiomics. We defined a new contrast based tumor habitat and analyzed textural kinetic features from this habitat for classification purposes. The proposed tumor habitat, which we call combined-habitat, is derived from the intersection of two individual tumor sub-regions: one that exhibits rapid initial contrast uptake and the other that exhibits rapid delayed contrast washout. Hence the combined-habitat represents the tumor sub-region within which the pixels undergo both rapid initial uptake and rapid delayed washout. We analyzed a dataset of twenty-seven representative two dimensional (2D) images from volumetric DCE-MRI of breast tumors, for classification of tumors with no lymph nodes from tumors with positive number of axillary lymph nodes. For this classification an accuracy of 88.9% was achieved. Twenty of the twenty-seven patients were analyzed for classification of distant metastatic tumors from indolent cancers (tumors with no lymph nodes), for which the accuracy was 84.3%.

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

Pullout strength of monocortical and bicortical screws in metaphyseal and diaphyseal regions of the canine humerus.

PubMed

Vaughn, Denty Paul; Syrcle, Jason Alan; Ball, John E; Elder, Steven H; Gambino, Jennifer Michele; Griffin, Russell L; McLaughlin, Ronald M

2016-11-23

Monocortical screws are commonly employed in locking plate fixation, but specific recommendations for their placement are lacking and use of short monocortical screws in metaphyseal bone may be contraindicated. Objectives of this study were to evaluate axial pullout strength of two different lengths of monocortical screws placed in various regions of the canine humerus compared to bicortical screws, and to derive cortical thickness and bone density values for those regions using quantitative computed tomography analysis (QCT). The QCT analysis was performed on 36 cadaveric canine humeri for six regions of interest (ROI). A bicortical, short monocortical, or 50% transcortical 3.5 mm screw was implanted in each ROI and axial pullout testing was performed. Bicortical screws were stronger than monocortical screws in all ROI except the lateral epicondylar crest. Short monocortical metaphyseal screws were weaker than those placed in other regions. The 50% transcortical screws were stronger than the short monocortical screws in the condyle. A linear relationship between screw length and pullout strength was observed. Cortical thickness and bone density measurements were obtained from multiple regions of the canine humerus using QCT. Use of short monocortical screws may contribute to failure of locking plate fixation of humeral fractures, especially when placed in the condyle. When bicortical screw placement is not possible, maximizing monocortical screw length may optimize fixation stability for distal humeral fractures.

SAR-aided method for rural soil evaluation

NASA Astrophysics Data System (ADS)

Lay-Ekuakille, Aime; Dellisanti, Carmelo; Pelillo, Vincenza; Tralli, Francesco

2003-03-01

The principal land characteristics that can be estimated by means of airphoto interpretation are bedrock type, landform, soil texture, site drainage conditions, susceptibility to flooding, and depth of unconsolidated materials over bedrock. In addition, the slope of the land surface can be estimated by airphoto interpretation and measured by phptpgrammetric methods. The aim of this paper is to show an experimental use of satellite images in determining soil quality affected by anthropic activities as rock crushing, or scarifying. Scarifying activities began, in Murgia area, Apulia Region, Italy), as land improvement for agriculture uses. Scarifying is defined as loosening (the surface of soil) by using an agricultural tool or a machine with prongs. This kind of activity is facilitated by the availability, on the market, of scarifying machines and the objective is to get a stratum of agriculture-useful loose material on the soil surface. Apulia Region Government has permitted calcareous stone scarifying with Regional Law n.54 (August 31, 1981) according to National Law n.984 (Dicember 27,1977), that provides for encouraging to transform grazing in sown land in order to create new possibility of forage production to increase zootecnical facilities. We have used ERS-2/SAR images as contribution in the process of soil characterization.The area we have considered is in Puglia Region and is subject to soil transformation due to rocks crushed on land for agricultural facilities. European Union, through the same Apulia Region Government, has renewed funds for the improvement of meadow and grazing for an overall surface of 2000 hectares. In this way it is clear to understand the importance of qualitative and quantitative evaluation of rock crushing or scarifying by using airphoto interpretation. We have evaluated the soil quality by introducing a multicriteria, analysis by using a qualitative and quantitative methodology, so that it will be possible to prevent damages on soil, sub-soil and hydrology. Decision analysis in Impact assessment is a set of procedures for analyzing complex decision problems. The strategy is to divide the decision problem into small, understandable parts; analyze each part; and integrate the parts in a logical manner to produce a meaningful solution. The terms multicriteria decision making (MCDM) and multicriteria decision analysis (MCDA) are used interchangeably.

Rockfall hazard and risk assessments along roads at a regional scale: example in Swiss Alps

NASA Astrophysics Data System (ADS)

Michoud, C.; Derron, M.-H.; Horton, P.; Jaboyedoff, M.; Baillifard, F.-J.; Loye, A.; Nicolet, P.; Pedrazzini, A.; Queyrel, A.

2012-03-01

Unlike fragmental rockfall runout assessments, there are only few robust methods to quantify rock-mass-failure susceptibilities at regional scale. A detailed slope angle analysis of recent Digital Elevation Models (DEM) can be used to detect potential rockfall source areas, thanks to the Slope Angle Distribution procedure. However, this method does not provide any information on block-release frequencies inside identified areas. The present paper adds to the Slope Angle Distribution of cliffs unit its normalized cumulative distribution function. This improvement is assimilated to a quantitative weighting of slope angles, introducing rock-mass-failure susceptibilities inside rockfall source areas previously detected. Then rockfall runout assessment is performed using the GIS- and process-based software Flow-R, providing relative frequencies for runout. Thus, taking into consideration both susceptibility results, this approach can be used to establish, after calibration, hazard and risk maps at regional scale. As an example, a risk analysis of vehicle traffic exposed to rockfalls is performed along the main roads of the Swiss alpine valley of Bagnes.

Reading in the brain of children and adults: a meta-analysis of 40 functional magnetic resonance imaging studies.

PubMed

Martin, Anna; Schurz, Matthias; Kronbichler, Martin; Richlan, Fabio

2015-05-01

We used quantitative, coordinate-based meta-analysis to objectively synthesize age-related commonalities and differences in brain activation patterns reported in 40 functional magnetic resonance imaging (fMRI) studies of reading in children and adults. Twenty fMRI studies with adults (age means: 23-34 years) were matched to 20 studies with children (age means: 7-12 years). The separate meta-analyses of these two sets showed a pattern of reading-related brain activation common to children and adults in left ventral occipito-temporal (OT), inferior frontal, and posterior parietal regions. The direct statistical comparison between the two meta-analytic maps of children and adults revealed higher convergence in studies with children in left superior temporal and bilateral supplementary motor regions. In contrast, higher convergence in studies with adults was identified in bilateral posterior OT/cerebellar and left dorsal precentral regions. The results are discussed in relation to current neuroanatomical models of reading and tentative functional interpretations of reading-related activation clusters in children and adults are provided. © 2015 Wiley Periodicals, Inc.

Are numbers grounded in a general magnitude processing system? A functional neuroimaging meta-analysis.

PubMed

Sokolowski, H Moriah; Fias, Wim; Bosah Ononye, Chuka; Ansari, Daniel

2017-10-01

It is currently debated whether numbers are processed using a number-specific system or a general magnitude processing system, also used for non-numerical magnitudes such as physical size, duration, or luminance. Activation likelihood estimation (ALE) was used to conduct the first quantitative meta-analysis of 93 empirical neuroimaging papers examining neural activation during numerical and non-numerical magnitude processing. Foci were compiled to generate probabilistic maps of activation for non-numerical magnitudes (e.g. physical size), symbolic numerical magnitudes (e.g. Arabic digits), and nonsymbolic numerical magnitudes (e.g. dot arrays). Conjunction analyses revealed overlapping activation for symbolic, nonsymbolic and non-numerical magnitudes in frontal and parietal lobes. Contrast analyses revealed specific activation in the left superior parietal lobule for symbolic numerical magnitudes. In contrast, small regions in the bilateral precuneus were specifically activated for nonsymbolic numerical magnitudes. No regions in the parietal lobes were activated for non-numerical magnitudes that were not also activated for numerical magnitudes. Therefore, numbers are processed using both a generalized magnitude system and format specific number regions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spatio-Temporal Simulation and Analysis of Regional Ecological Security Based on Lstm

NASA Astrophysics Data System (ADS)

Gong, C.; Qi, L.; Heming, L.; Karimian, H.; Yuqin, M.

2017-10-01

Region is a complicated system, where human, nature and society interact and influence. Quantitative modeling and simulation of ecology in the region are the key to realize the strategy of regional sustainable development. Traditional machine learning methods have made some achievements in the modeling of regional ecosystems, but it is difficult to determine the learning characteristics and to realize spatio-temporal simulation. Deep learning does not need prior identification of training characteristics, have excellent feature learning ability, can improve the accuracy of model prediction, so the use of deep learning model has a significant advantage. Therefore, we use net primary productivity (NPP), atmospheric optical depth (AOD), moderate-resolution imaging spectrometer (MODIS), Normalized Difference Vegetation Index (NDVI), landcover and population data, and use LSTM to do spatio-temporal simulation. We conduct spatial analysis and driving force analysis. The conclusions are as follows: the ecological deficit of northwestern Henan and urban communities such as Zhengzhou is higher. The reason of former lies in the weak land productivity of the Loess Plateau, the irrational crop cultivation mode. The latter lies in the high consumption of resources in the large urban agglomeration; The positive trend of Henan ecological development from 2013 is mainly due to the effective environmental protection policy in the 12th five-year plan; The main driver of the sustained ecological deficit growth of Henan in 2004-2013 is high-speed urbanization, increasing population and goods consumption. This article provides relevant basic scientific support and reference for the regional ecological scientific management and construction.

Mosaic organization of DNA nucleotides

NASA Technical Reports Server (NTRS)

Peng, C. K.; Buldyrev, S. V.; Havlin, S.; Simons, M.; Stanley, H. E.; Goldberger, A. L.

1994-01-01

Long-range power-law correlations have been reported recently for DNA sequences containing noncoding regions. We address the question of whether such correlations may be a trivial consequence of the known mosaic structure ("patchiness") of DNA. We analyze two classes of controls consisting of patchy nucleotide sequences generated by different algorithms--one without and one with long-range power-law correlations. Although both types of sequences are highly heterogenous, they are quantitatively distinguishable by an alternative fluctuation analysis method that differentiates local patchiness from long-range correlations. Application of this analysis to selected DNA sequences demonstrates that patchiness is not sufficient to account for long-range correlation properties.

Birefringence measurement of retinal nerve fiber layer using polarization-sensitive spectral domain optical coherence tomography with Jones matrix based analysis

NASA Astrophysics Data System (ADS)

Yamanari, Masahiro; Miura, Masahiro; Makita, Shuichi; Yatagai, Toyohiko; Yasuno, Yoshiaki

2007-02-01

Birefringence of retinal nerve fiber layer is measured by polarization-sensitive spectral domain optical coherence tomography using the B-scan-oriented polarization modulation method. Birefringence of the optical fiber and the cornea is compensated by Jones matrix based analysis. Three-dimensional phase retardation map around the optic nerve head and en-face phase retardation map of the retinal nerve fiber layer are shown. Unlike scanning laser polarimetry, our system can measure the phase retardation quantitatively without using bow-tie pattern of the birefringence in the macular region, which enables diagnosis of glaucoma even if the patients have macular disease.

A quantitative analysis of household energy consumption in rural west Java: with particular emphasis on socio-economic influences

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

Hadi, S.S.

1982-01-01

A survey was conducted to estimate per capita, per household, and total energy consumption by region, by level of development, and by fuel source in rural West Java. Socio-economic conditions were also measured by using parameters that included income, family size, husband education, wife education, biomass fuelstock, level of village development, and land size. These data are tabulated and used to develop a model that can predict probabilities of fuel use, consumption, and variety.