Detection of neovascularization based on fractal and texture analysis with interaction effects in diabetic retinopathy.

PubMed

Lee, Jack; Zee, Benny Chung Ying; Li, Qing

2013-01-01

Diabetic retinopathy is a major cause of blindness. Proliferative diabetic retinopathy is a result of severe vascular complication and is visible as neovascularization of the retina. Automatic detection of such new vessels would be useful for the severity grading of diabetic retinopathy, and it is an important part of screening process to identify those who may require immediate treatment for their diabetic retinopathy. We proposed a novel new vessels detection method including statistical texture analysis (STA), high order spectrum analysis (HOS), fractal analysis (FA), and most importantly we have shown that by incorporating their associated interactions the accuracy of new vessels detection can be greatly improved. To assess its performance, the sensitivity, specificity and accuracy (AUC) are obtained. They are 96.3%, 99.1% and 98.5% (99.3%), respectively. It is found that the proposed method can improve the accuracy of new vessels detection significantly over previous methods. The algorithm can be automated and is valuable to detect relatively severe cases of diabetic retinopathy among diabetes patients.

Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.

PubMed

Yang, Chao; He, Zengyou; Yu, Weichuan

2009-01-06

In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorithms is yet available. The main objective of this paper is to provide such a survey and to compare the performance of single spectrum based peak detection methods. In general, we can decompose a peak detection procedure into three consequent parts: smoothing, baseline correction and peak finding. We first categorize existing peak detection algorithms according to the techniques used in different phases. Such a categorization reveals the differences and similarities among existing peak detection algorithms. Then, we choose five typical peak detection algorithms to conduct a comprehensive experimental study using both simulation data and real MALDI MS data. The results of comparison show that the continuous wavelet-based algorithm provides the best average performance.

Analysis of copy number variants by three detection algorithms and their association with body size in horses.

PubMed

Metzger, Julia; Philipp, Ute; Lopes, Maria Susana; da Camara Machado, Artur; Felicetti, Michela; Silvestrelli, Maurizio; Distl, Ottmar

2013-07-18

Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height. Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.

Fast and objective detection and analysis of structures in downhole images

NASA Astrophysics Data System (ADS)

Wedge, Daniel; Holden, Eun-Jung; Dentith, Mike; Spadaccini, Nick

2017-09-01

Downhole acoustic and optical televiewer images, and formation microimager (FMI) logs are important datasets for structural and geotechnical analyses for the mineral and petroleum industries. Within these data, dipping planar structures appear as sinusoids, often in incomplete form and in abundance. Their detection is a labour intensive and hence expensive task and as such is a significant bottleneck in data processing as companies may have hundreds of kilometres of logs to process each year. We present an image analysis system that harnesses the power of automated image analysis and provides an interactive user interface to support the analysis of televiewer images by users with different objectives. Our algorithm rapidly produces repeatable, objective results. We have embedded it in an interactive workflow to complement geologists' intuition and experience in interpreting data to improve efficiency and assist, rather than replace the geologist. The main contributions include a new image quality assessment technique for highlighting image areas most suited to automated structure detection and for detecting boundaries of geological zones, and a novel sinusoid detection algorithm for detecting and selecting sinusoids with given confidence levels. Further tools are provided to perform rapid analysis of and further detection of structures e.g. as limited to specific orientations.

Prognostic value of bone marrow involvement by clonal immunoglobulin gene rearrangements in follicular lymphoma

PubMed Central

Berget, Ellen; Helgeland, Lars; Liseth, Knut; Løkeland, Turid; Molven, Anders; Vintermyr, Olav Karsten

2014-01-01

Aims We aimed to evaluate the prognostic value of routine use of PCR amplification of immunoglobulin gene rearrangements in bone marrow (BM) staging in patients with follicular lymphoma (FL). Methods Clonal rearrangements were assessed by immunoglobulin heavy and light-chain gene rearrangement analysis in BM aspirates from 96 patients diagnosed with FL and related to morphological detection of BM involvement in biopsies. In 71 patients, results were also compared with concurrent flow cytometry analysis. Results BM involvement was detected by PCR in 34.4% (33/96) of patients. The presence of clonal rearrangements by PCR was associated with advanced clinical stage (I–III vs IV; p<0.001), high FL International Prognostic Index (FLIPI) score (0–1, 2 vs ≥3; p=0.003), and detection of BM involvement by morphology and flow cytometry analysis (p<0.001 for both). PCR-positive patients had a significantly poorer survival than PCR-negative patients (p=0.001, log-rank test). Thirteen patients positive by PCR but without morphologically detectable BM involvement, had significantly poorer survival than patients with negative morphology and negative PCR result (p=0.002). The poor survival associated with BM involvement by PCR was independent of the FLIPI score (p=0.007, Cox regression). BM involvement by morphology or flow cytometry did not show a significant impact on survival. Conclusions Our results showed that routine use of PCR-based clonality analysis significantly improved the prognostic impact of BM staging in patients with FL. BM involvement by PCR was also an independent adverse prognostic factor. PMID:25233852

Validation of a next-generation sequencing assay for clinical molecular oncology.

PubMed

Cottrell, Catherine E; Al-Kateb, Hussam; Bredemeyer, Andrew J; Duncavage, Eric J; Spencer, David H; Abel, Haley J; Lockwood, Christina M; Hagemann, Ian S; O'Guin, Stephanie M; Burcea, Lauren C; Sawyer, Christopher S; Oschwald, Dayna M; Stratman, Jennifer L; Sher, Dorie A; Johnson, Mark R; Brown, Justin T; Cliften, Paul F; George, Bijoy; McIntosh, Leslie D; Shrivastava, Savita; Nguyen, Tudung T; Payton, Jacqueline E; Watson, Mark A; Crosby, Seth D; Head, Richard D; Mitra, Robi D; Nagarajan, Rakesh; Kulkarni, Shashikant; Seibert, Karen; Virgin, Herbert W; Milbrandt, Jeffrey; Pfeifer, John D

2014-01-01

Currently, oncology testing includes molecular studies and cytogenetic analysis to detect genetic aberrations of clinical significance. Next-generation sequencing (NGS) allows rapid analysis of multiple genes for clinically actionable somatic variants. The WUCaMP assay uses targeted capture for NGS analysis of 25 cancer-associated genes to detect mutations at actionable loci. We present clinical validation of the assay and a detailed framework for design and validation of similar clinical assays. Deep sequencing of 78 tumor specimens (≥ 1000× average unique coverage across the capture region) achieved high sensitivity for detecting somatic variants at low allele fraction (AF). Validation revealed sensitivities and specificities of 100% for detection of single-nucleotide variants (SNVs) within coding regions, compared with SNP array sequence data (95% CI = 83.4-100.0 for sensitivity and 94.2-100.0 for specificity) or whole-genome sequencing (95% CI = 89.1-100.0 for sensitivity and 99.9-100.0 for specificity) of HapMap samples. Sensitivity for detecting variants at an observed 10% AF was 100% (95% CI = 93.2-100.0) in HapMap mixes. Analysis of 15 masked specimens harboring clinically reported variants yielded concordant calls for 13/13 variants at AF of ≥ 15%. The WUCaMP assay is a robust and sensitive method to detect somatic variants of clinical significance in molecular oncology laboratories, with reduced time and cost of genetic analysis allowing for strategic patient management. Copyright © 2014 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Proteomics analysis of human breast milk to assess breast cancer risk.

PubMed

Aslebagh, Roshanak; Channaveerappa, Devika; Arcaro, Kathleen F; Darie, Costel C

2018-02-01

Detection of breast cancer (BC) in young women is challenging because mammography, the most common tool for detecting BC, is not effective on the dense breast tissue characteristic of young women. In addition to the limited means for detecting their BC, young women face a transient increased risk of pregnancy-associated BC. As a consequence, reproductively active women could benefit significantly from a tool that provides them with accurate risk assessment and early detection of BC. One potential method for detection of BC is biochemical monitoring of proteins and other molecules in bodily fluids such as serum, nipple aspirate, ductal lavage, tear, urine, saliva and breast milk. Of all these fluids, only breast milk provides access to a large volume of breast tissue, in the form of exfoliated epithelial cells, and to the local breast environment, in the form of molecules in the milk. Thus, analysis of breast milk is a non-invasive method with significant potential for assessing BC risk. Here we analyzed human breast milk by mass spectrometry (MS)-based proteomics to build a biomarker signature for early detection of BC. Ten milk samples from eight women provided five paired-groups (cancer versus control) for analysis of dysregulatedproteins: two within woman comparisons (milk from a diseased breast versus a healthy breast of the same woman) and three across women comparisons (milk from a woman with cancer versus a woman without cancer). Despite a wide range in the time between milk donation and cancer diagnosis (cancer diagnosis occurred from 1 month before to 24 months after milk donation), the levels of some proteins differed significantly between cancer and control in several of the five comparison groups. These pilot data are supportive of the idea that molecular analysis of breast milk will identify proteins informative for early detection and accurate assessment of BC risk, and warrant further research. Data are available via ProteomeXchange with identifier PXD007066. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface Management System Departure Event Data Analysis

NASA Technical Reports Server (NTRS)

Monroe, Gilena A.

2010-01-01

This paper presents a data analysis of the Surface Management System (SMS) performance of departure events, including push-back and runway departure events.The paper focuses on the detection performance, or the ability to detect departure events, as well as the prediction performance of SMS. The results detail a modest overall detection performance of push-back events and a significantly high overall detection performance of runway departure events. The overall detection performance of SMS for push-back events is approximately 55%.The overall detection performance of SMS for runway departure events nears 100%. This paper also presents the overall SMS prediction performance for runway departure events as well as the timeliness of the Aircraft Situation Display for Industry data source for SMS predictions.

The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid.

PubMed

Akata, Kentaro; Yatera, Kazuhiro; Yamasaki, Kei; Kawanami, Toshinori; Naito, Keisuke; Noguchi, Shingo; Fukuda, Kazumasa; Ishimoto, Hiroshi; Taniguchi, Hatsumi; Mukae, Hiroshi

2016-05-11

Aspiration pneumonia has been a growing interest in an aging population. Anaerobes are important pathogens, however, the etiology of aspiration pneumonia is not fully understood. In addition, the relationship between the patient clinical characteristics and the causative pathogens in pneumonia patients with aspiration risk factors are unclear. To evaluate the relationship between the patient clinical characteristics with risk factors for aspiration and bacterial flora in bronchoalveolar lavage fluid (BALF) in pneumonia patients, the bacterial floral analysis of 16S ribosomal RNA gene was applied in addition to cultivation methods in BALF samples. From April 2010 to February 2014, BALF samples were obtained from the affected lesions of pneumonia via bronchoscopy, and were evaluated by the bacterial floral analysis of 16S rRNA gene in addition to cultivation methods in patients with community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HCAP). Factors associated with aspiration risks in these patients were analyzed. A total of 177 (CAP 83, HCAP 94) patients were enrolled. According to the results of the bacterial floral analysis, detection rate of oral streptococci as the most detected bacterial phylotypes in BALF was significantly higher in patients with aspiration risks (31.0 %) than in patients without aspiration risks (14.7 %) (P = 0.009). In addition, the percentages of oral streptococci in each BALF sample were significantly higher in patients with aspiration risks (26.6 ± 32.0 %) than in patients without aspiration risks (13.8 ± 25.3 %) (P = 0.002). A multiple linear regression analysis showed that an Eastern Cooperative Oncology Group (ECOG) performance status (PS) of ≥3, the presence of comorbidities, and a history of pneumonia within a previous year were significantly associated with a detection of oral streptococci in BALF. The bacterial floral analysis of 16S rRNA gene revealed that oral streptococci were mostly detected as the most detected bacterial phylotypes in BALF samples in CAP and HCAP patients with aspiration risks, especially in those with a poor ECOG-PS or a history of pneumonia.

Evaluation of hemifield sector analysis protocol in multifocal visual evoked potential objective perimetry for the diagnosis and early detection of glaucomatous field defects.

PubMed

Mousa, Mohammad F; Cubbidge, Robert P; Al-Mansouri, Fatima; Bener, Abdulbari

2014-02-01

Multifocal visual evoked potential (mfVEP) is a newly introduced method used for objective visual field assessment. Several analysis protocols have been tested to identify early visual field losses in glaucoma patients using the mfVEP technique, some were successful in detection of field defects, which were comparable to the standard automated perimetry (SAP) visual field assessment, and others were not very informative and needed more adjustment and research work. In this study we implemented a novel analysis approach and evaluated its validity and whether it could be used effectively for early detection of visual field defects in glaucoma. Three groups were tested in this study; normal controls (38 eyes), glaucoma patients (36 eyes) and glaucoma suspect patients (38 eyes). All subjects had a two standard Humphrey field analyzer (HFA) test 24-2 and a single mfVEP test undertaken in one session. Analysis of the mfVEP results was done using the new analysis protocol; the hemifield sector analysis (HSA) protocol. Analysis of the HFA was done using the standard grading system. Analysis of mfVEP results showed that there was a statistically significant difference between the three groups in the mean signal to noise ratio (ANOVA test, p < 0.001 with a 95% confidence interval). The difference between superior and inferior hemispheres in all subjects were statistically significant in the glaucoma patient group in all 11 sectors (t-test, p < 0.001), partially significant in 5 / 11 (t-test, p < 0.01), and no statistical difference in most sectors of the normal group (1 / 11 sectors was significant, t-test, p < 0.9). Sensitivity and specificity of the HSA protocol in detecting glaucoma was 97% and 86%, respectively, and for glaucoma suspect patients the values were 89% and 79%, respectively. The new HSA protocol used in the mfVEP testing can be applied to detect glaucomatous visual field defects in both glaucoma and glaucoma suspect patients. Using this protocol can provide information about focal visual field differences across the horizontal midline, which can be utilized to differentiate between glaucoma and normal subjects. Sensitivity and specificity of the mfVEP test showed very promising results and correlated with other anatomical changes in glaucoma field loss.

Evaluation of Hemifield Sector Analysis Protocol in Multifocal Visual Evoked Potential Objective Perimetry for the Diagnosis and Early Detection of Glaucomatous Field Defects

PubMed Central

Mousa, Mohammad F.; Cubbidge, Robert P.; Al-Mansouri, Fatima

2014-01-01

Purpose Multifocal visual evoked potential (mfVEP) is a newly introduced method used for objective visual field assessment. Several analysis protocols have been tested to identify early visual field losses in glaucoma patients using the mfVEP technique, some were successful in detection of field defects, which were comparable to the standard automated perimetry (SAP) visual field assessment, and others were not very informative and needed more adjustment and research work. In this study we implemented a novel analysis approach and evaluated its validity and whether it could be used effectively for early detection of visual field defects in glaucoma. Methods Three groups were tested in this study; normal controls (38 eyes), glaucoma patients (36 eyes) and glaucoma suspect patients (38 eyes). All subjects had a two standard Humphrey field analyzer (HFA) test 24-2 and a single mfVEP test undertaken in one session. Analysis of the mfVEP results was done using the new analysis protocol; the hemifield sector analysis (HSA) protocol. Analysis of the HFA was done using the standard grading system. Results Analysis of mfVEP results showed that there was a statistically significant difference between the three groups in the mean signal to noise ratio (ANOVA test, p < 0.001 with a 95% confidence interval). The difference between superior and inferior hemispheres in all subjects were statistically significant in the glaucoma patient group in all 11 sectors (t-test, p < 0.001), partially significant in 5 / 11 (t-test, p < 0.01), and no statistical difference in most sectors of the normal group (1 / 11 sectors was significant, t-test, p < 0.9). Sensitivity and specificity of the HSA protocol in detecting glaucoma was 97% and 86%, respectively, and for glaucoma suspect patients the values were 89% and 79%, respectively. Conclusions The new HSA protocol used in the mfVEP testing can be applied to detect glaucomatous visual field defects in both glaucoma and glaucoma suspect patients. Using this protocol can provide information about focal visual field differences across the horizontal midline, which can be utilized to differentiate between glaucoma and normal subjects. Sensitivity and specificity of the mfVEP test showed very promising results and correlated with other anatomical changes in glaucoma field loss. PMID:24511212

Research on the strategy of underwater united detection fusion and communication using multi-sensor

NASA Astrophysics Data System (ADS)

Xu, Zhenhua; Huang, Jianguo; Huang, Hai; Zhang, Qunfei

2011-09-01

In order to solve the distributed detection fusion problem of underwater target detection, when the signal to noise ratio (SNR) of the acoustic channel is low, a new strategy for united detection fusion and communication using multiple sensors was proposed. The performance of detection fusion was studied and compared based on the Neyman-Pearson principle when the binary phase shift keying (BPSK) and on-off keying (OOK) modes were used by the local sensors. The comparative simulation and analysis between the optimal likelihood ratio test and the proposed strategy was completed, and both the theoretical analysis and simulation indicate that using the proposed new strategy could improve the detection performance effectively. In theory, the proposed strategy of united detection fusion and communication is of great significance to the establishment of an underwater target detection system.

Clinical Performance of an Ultrahigh Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders.

PubMed

Ho, Karen S; Twede, Hope; Vanzo, Rena; Harward, Erin; Hensel, Charles H; Martin, Megan M; Page, Stephanie; Peiffer, Andreas; Mowery-Rushton, Patricia; Serrano, Moises; Wassman, E Robert

2016-01-01

Copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) significantly contribute to the etiology of neurodevelopmental disorders, such as developmental delay (DD), intellectual disability (ID), and autism spectrum disorder (ASD). This study summarizes the results of 3.5 years of CMA testing by a CLIA-certified clinical testing laboratory 5487 patients with neurodevelopmental conditions were clinically evaluated for rare copy number variants using a 2.8-million probe custom CMA optimized for the detection of CNVs associated with neurodevelopmental disorders. We report an overall detection rate of 29.4% in our neurodevelopmental cohort, which rises to nearly 33% when cases with DD/ID and/or MCA only are considered. The detection rate for the ASD cohort is also significant, at 25%. Additionally, we find that detection rate and pathogenic yield of CMA vary significantly depending on the primary indications for testing, the age of the individuals tested, and the specialty of the ordering doctor. We also report a significant difference between the detection rate on the ultrahigh resolution optimized array in comparison to the array from which it originated. This increase in detection can significantly contribute to the efficient and effective medical management of neurodevelopmental conditions in the clinic.

EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units

PubMed Central

Kam-Thong, Tony; Czamara, Darina; Tsuda, Koji; Borgwardt, Karsten; Lewis, Cathryn M; Erhardt-Lehmann, Angelika; Hemmer, Bernhard; Rieckmann, Peter; Daake, Markus; Weber, Frank; Wolf, Christiane; Ziegler, Andreas; Pütz, Benno; Holsboer, Florian; Schölkopf, Bernhard; Müller-Myhsok, Bertram

2011-01-01

Detection of epistatic interaction between loci has been postulated to provide a more in-depth understanding of the complex biological and biochemical pathways underlying human diseases. Studying the interaction between two loci is the natural progression following traditional and well-established single locus analysis. However, the added costs and time duration required for the computation involved have thus far deterred researchers from pursuing a genome-wide analysis of epistasis. In this paper, we propose a method allowing such analysis to be conducted very rapidly. The method, dubbed EPIBLASTER, is applicable to case–control studies and consists of a two-step process in which the difference in Pearson's correlation coefficients is computed between controls and cases across all possible SNP pairs as an indication of significant interaction warranting further analysis. For the subset of interactions deemed potentially significant, a second-stage analysis is performed using the likelihood ratio test from the logistic regression to obtain the P-value for the estimated coefficients of the individual effects and the interaction term. The algorithm is implemented using the parallel computational capability of commercially available graphical processing units to greatly reduce the computation time involved. In the current setup and example data sets (211 cases, 222 controls, 299468 SNPs; and 601 cases, 825 controls, 291095 SNPs), this coefficient evaluation stage can be completed in roughly 1 day. Our method allows for exhaustive and rapid detection of significant SNP pair interactions without imposing significant marginal effects of the single loci involved in the pair. PMID:21150885

A hybrid symplectic principal component analysis and central tendency measure method for detection of determinism in noisy time series with application to mechanomyography

NASA Astrophysics Data System (ADS)

Xie, Hong-Bo; Dokos, Socrates

2013-06-01

We present a hybrid symplectic geometry and central tendency measure (CTM) method for detection of determinism in noisy time series. CTM is effective for detecting determinism in short time series and has been applied in many areas of nonlinear analysis. However, its performance significantly degrades in the presence of strong noise. In order to circumvent this difficulty, we propose to use symplectic principal component analysis (SPCA), a new chaotic signal de-noising method, as the first step to recover the system dynamics. CTM is then applied to determine whether the time series arises from a stochastic process or has a deterministic component. Results from numerical experiments, ranging from six benchmark deterministic models to 1/f noise, suggest that the hybrid method can significantly improve detection of determinism in noisy time series by about 20 dB when the data are contaminated by Gaussian noise. Furthermore, we apply our algorithm to study the mechanomyographic (MMG) signals arising from contraction of human skeletal muscle. Results obtained from the hybrid symplectic principal component analysis and central tendency measure demonstrate that the skeletal muscle motor unit dynamics can indeed be deterministic, in agreement with previous studies. However, the conventional CTM method was not able to definitely detect the underlying deterministic dynamics. This result on MMG signal analysis is helpful in understanding neuromuscular control mechanisms and developing MMG-based engineering control applications.

A hybrid symplectic principal component analysis and central tendency measure method for detection of determinism in noisy time series with application to mechanomyography.

PubMed

Xie, Hong-Bo; Dokos, Socrates

2013-06-01

We present a hybrid symplectic geometry and central tendency measure (CTM) method for detection of determinism in noisy time series. CTM is effective for detecting determinism in short time series and has been applied in many areas of nonlinear analysis. However, its performance significantly degrades in the presence of strong noise. In order to circumvent this difficulty, we propose to use symplectic principal component analysis (SPCA), a new chaotic signal de-noising method, as the first step to recover the system dynamics. CTM is then applied to determine whether the time series arises from a stochastic process or has a deterministic component. Results from numerical experiments, ranging from six benchmark deterministic models to 1/f noise, suggest that the hybrid method can significantly improve detection of determinism in noisy time series by about 20 dB when the data are contaminated by Gaussian noise. Furthermore, we apply our algorithm to study the mechanomyographic (MMG) signals arising from contraction of human skeletal muscle. Results obtained from the hybrid symplectic principal component analysis and central tendency measure demonstrate that the skeletal muscle motor unit dynamics can indeed be deterministic, in agreement with previous studies. However, the conventional CTM method was not able to definitely detect the underlying deterministic dynamics. This result on MMG signal analysis is helpful in understanding neuromuscular control mechanisms and developing MMG-based engineering control applications.

Detecting a periodic signal in the terrestrial cratering record

NASA Technical Reports Server (NTRS)

Grieve, Richard A. F.; Rupert, James D.; Goodacre, Alan K.; Sharpton, Virgil L.

1988-01-01

A time-series analysis of model periodic data, where the period and phase are known, has been performed in order to investigate whether a significant period can be detected consistently from a mix of random and periodic impacts. Special attention is given to the effect of age uncertainties and random ages in the detection of a periodic signal. An equivalent analysis is performed with observed data on crater ages and compared with the model data, and the effects of the temporal distribution of crater ages on the results from the time-series analysis are studied. Evidence for a consistent 30-m.y. period is found to be weak.

Improved computer-aided detection of small polyps in CT colonography using interpolation for curvature estimationa

PubMed Central

Liu, Jiamin; Kabadi, Suraj; Van Uitert, Robert; Petrick, Nicholas; Deriche, Rachid; Summers, Ronald M.

2011-01-01

Purpose: Surface curvatures are important geometric features for the computer-aided analysis and detection of polyps in CT colonography (CTC). However, the general kernel approach for curvature computation can yield erroneous results for small polyps and for polyps that lie on haustral folds. Those erroneous curvatures will reduce the performance of polyp detection. This paper presents an analysis of interpolation’s effect on curvature estimation for thin structures and its application on computer-aided detection of small polyps in CTC. Methods: The authors demonstrated that a simple technique, image interpolation, can improve the accuracy of curvature estimation for thin structures and thus significantly improve the sensitivity of small polyp detection in CTC. Results: Our experiments showed that the merits of interpolating included more accurate curvature values for simulated data, and isolation of polyps near folds for clinical data. After testing on a large clinical data set, it was observed that sensitivities with linear, quadratic B-spline and cubic B-spline interpolations significantly improved the sensitivity for small polyp detection. Conclusions: The image interpolation can improve the accuracy of curvature estimation for thin structures and thus improve the computer-aided detection of small polyps in CTC. PMID:21859029

Evaluation of Next-Generation Vision Testers for Aeromedical Certification of Aviation Personnel

DTIC Science & Technology

2009-07-01

measure distant, intermediate, and near acuity. The slides are essentially abbreviated versions of the Early Treatment for Diabetic Retinopathy Study...over, requiring intermediate vision testing and 12 were color deficient. Analysis was designed to detect statistically significant differences between...Vertical Phoria (Right & Left Hyperphoria) Test scores from each of the vision testers were collated and analyzed. Analysis was designed to detect

ATAC Autocuer Modeling Analysis.

DTIC Science & Technology

1981-01-01

the analysis of the simple rectangular scrnentation (1) is based on detection and estimation theory (2). This approach uses the concept of maximum ...continuous wave forms. In order to develop the principles of maximum likelihood, it is con- venient to develop the principles for the "classical...the concept of maximum likelihood is significant in that it provides the optimum performance of the detection/estimation problem. With a knowledge of

Esophageal cancer detection based on tissue surface-enhanced Raman spectroscopy and multivariate analysis

NASA Astrophysics Data System (ADS)

Feng, Shangyuan; Lin, Juqiang; Huang, Zufang; Chen, Guannan; Chen, Weisheng; Wang, Yue; Chen, Rong; Zeng, Haishan

2013-01-01

The capability of using silver nanoparticle based near-infrared surface enhanced Raman scattering (SERS) spectroscopy combined with principal component analysis (PCA) and linear discriminate analysis (LDA) to differentiate esophageal cancer tissue from normal tissue was presented. Significant differences in Raman intensities of prominent SERS bands were observed between normal and cancer tissues. PCA-LDA multivariate analysis of the measured tissue SERS spectra achieved diagnostic sensitivity of 90.9% and specificity of 97.8%. This exploratory study demonstrated great potential for developing label-free tissue SERS analysis into a clinical tool for esophageal cancer detection.

Influence analysis in quantitative trait loci detection.

PubMed

Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

2014-07-01

This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MPI Runtime Error Detection with MUST: Advances in Deadlock Detection

DOE PAGES

Hilbrich, Tobias; Protze, Joachim; Schulz, Martin; ...

2013-01-01

The widely used Message Passing Interface (MPI) is complex and rich. As a result, application developers require automated tools to avoid and to detect MPI programming errors. We present the Marmot Umpire Scalable Tool (MUST) that detects such errors with significantly increased scalability. We present improvements to our graph-based deadlock detection approach for MPI, which cover future MPI extensions. Our enhancements also check complex MPI constructs that no previous graph-based detection approach handled correctly. Finally, we present optimizations for the processing of MPI operations that reduce runtime deadlock detection overheads. Existing approaches often require ( p ) analysis time permore » MPI operation, for p processes. We empirically observe that our improvements lead to sub-linear or better analysis time per operation for a wide range of real world applications.« less

Drop coating deposition Raman spectroscopy of blood plasma for the detection of colorectal cancer

NASA Astrophysics Data System (ADS)

Li, Pengpeng; Chen, Changshui; Deng, Xiaoyuan; Mao, Hua; Jin, Shaoqin

2015-03-01

We have recently applied the technique of drop coating deposition Raman (DCDR) spectroscopy for colorectal cancer (CRC) detection using blood plasma. The aim of this study was to develop a more convenient and stable method based on blood plasma for noninvasive CRC detection. Significant differences are observed in DCDR spectra between healthy (n=105) and cancer (n=75) plasma from 15 CRC patients and 21 volunteers, particularly in the spectra that are related to proteins, nucleic acids, and β-carotene. The multivariate analysis principal components analysis and the linear discriminate analysis, together with leave-one-out, cross validation were used on DCDR spectra and yielded a sensitivity of 100% (75/75) and specificity of 98.1% (103/105) for detection of CRC. This study demonstrates that DCDR spectroscopy of blood plasma associated with multivariate statistical algorithms has the potential for the noninvasive detection of CRC.

JCDSA: a joint covariate detection tool for survival analysis on tumor expression profiles.

PubMed

Wu, Yiming; Liu, Yanan; Wang, Yueming; Shi, Yan; Zhao, Xudong

2018-05-29

Survival analysis on tumor expression profiles has always been a key issue for subsequent biological experimental validation. It is crucial how to select features which closely correspond to survival time. Furthermore, it is important how to select features which best discriminate between low-risk and high-risk group of patients. Common features derived from the two aspects may provide variable candidates for prognosis of cancer. Based on the provided two-step feature selection strategy, we develop a joint covariate detection tool for survival analysis on tumor expression profiles. Significant features, which are not only consistent with survival time but also associated with the categories of patients with different survival risks, are chosen. Using the miRNA expression data (Level 3) of 548 patients with glioblastoma multiforme (GBM) as an example, miRNA candidates for prognosis of cancer are selected. The reliability of selected miRNAs using this tool is demonstrated by 100 simulations. Furthermore, It is discovered that significant covariates are not directly composed of individually significant variables. Joint covariate detection provides a viewpoint for selecting variables which are not individually but jointly significant. Besides, it helps to select features which are not only consistent with survival time but also associated with prognosis risk. The software is available at http://bio-nefu.com/resource/jcdsa .

Elastic Versus Rigid Image Registration in Magnetic Resonance Imaging-transrectal Ultrasound Fusion Prostate Biopsy: A Systematic Review and Meta-analysis.

PubMed

Venderink, Wulphert; de Rooij, Maarten; Sedelaar, J P Michiel; Huisman, Henkjan J; Fütterer, Jurgen J

2016-07-29

The main difference between the available magnetic resonance imaging-transrectal ultrasound (MRI-TRUS) fusion platforms for prostate biopsy is the method of image registration being either rigid or elastic. As elastic registration compensates for possible deformation caused by the introduction of an ultrasound probe for example, it is expected that it would perform better than rigid registration. The aim of this meta-analysis is to compare rigid with elastic registration by calculating the detection odds ratio (OR) for both subgroups. The detection OR is defined as the ratio of the odds of detecting clinically significant prostate cancer (csPCa) by MRI-TRUS fusion biopsy compared with systematic TRUS biopsy. Secondary objectives were the OR for any PCa and the OR after pooling both registration techniques. The electronic databases PubMed, Embase, and Cochrane were systematically searched for relevant studies according to the Preferred Reporting Items for Systematic Review and Meta-analysis Statement. Studies comparing MRI-TRUS fusion and systematic TRUS-guided biopsies in the same patient were included. The quality assessment of included studies was performed using the Quality Assessment of Diagnostic Accuracy Studies version 2. Eleven papers describing elastic and 10 describing rigid registration were included. Meta-analysis showed an OR of csPCa for elastic and rigid registration of 1.45 (95% confidence interval [CI]: 1.21-1.73, p<0.0001) and 1.40 (95% CI: 1.13-1.75, p=0.002), respectively. No significant difference was seen between the subgroups (p=0.83). Pooling subgroups resulted in an OR of 1.43 (95% CI: 1.25-1.63, p<0.00001). No significant difference was identified between rigid and elastic registration for MRI-TRUS fusion-guided biopsy in the detection of csPCa; however, both techniques detected more csPCa than TRUS-guided biopsy alone. We did not identify any significant differences in prostate cancer detection between two distinct magnetic resonance imaging-transrectal ultrasound fusion systems which vary in their method of compensating for prostate deformation. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Polyp detection rate may predict adenoma detection rate: a meta-analysis.

PubMed

Niv, Yaron

2018-03-01

Adenoma detection rate (ADR) is defined as the number of colonoscopies with at least one adenoma, expressed as the ratio of the total number of colonoscopies performed. Recently, an application of a conversion factor to estimate the ADR from the polyp detection rate (PDR) was described. In this meta-analysis, we examined the correlation between ADR and PDR in the published studies and assessed the relative ratio of these ratios for a better and more accurate estimation. English Medical literature searches were performed for 'PDR' AND 'ADR'. A meta-analysis was carried out for papers that fulfilled the inclusion criteria using comprehensive meta-analysis software. Twenty-five studies and 42 sets of data, including 31 623 patients, from nine countries published till 31 August 2017, were found. Funnel plot did not indicate a significant publication bias. relative ratio for ADR calculated from PDR was 0.688, 95% confidence intervals: 0.680-0.695, P value of less than 0.0001 in the meta-analysis fixed model. Heterogeneity (the proportion of inconsistency in individual studies) between studies was significant, with Q=492.753, d.f. (Q) 41, P<0.0001, and I 91.679. We found the ratio of 0.688 can be used to calculate ADR from PDR for the individual endoscopist or for a group of endoscopists before receiving the formal results from the pathology department.

Diagnostic Performance of DNA Hypermethylation Markers in Peripheral Blood for the Detection of Colorectal Cancer: A Meta-Analysis and Systematic Review

PubMed Central

Li, Bingsheng; Gan, Aihua; Chen, Xiaolong; Wang, Xinying; He, Weifeng; Zhang, Xiaohui; Huang, Renxiang; Zhou, Shuzhu; Song, Xiaoxiao; Xu, Angao

2016-01-01

DNA hypermethylation in blood is becoming an attractive candidate marker for colorectal cancer (CRC) detection. To assess the diagnostic accuracy of blood hypermethylation markers for CRC in different clinical settings, we conducted a meta-analysis of published reports. Of 485 publications obtained in the initial literature search, 39 studies were included in the meta-analysis. Hypermethylation markers in peripheral blood showed a high degree of accuracy for the detection of CRC. The summary sensitivity was 0.62 [95% confidence interval (CI), 0.56–0.67] and specificity was 0.91 (95% CI, 0.89–0.93). Subgroup analysis showed significantly greater sensitivity for the methylated Septin 9 gene (SEPT9) subgroup (0.75; 95% CI, 0.67–0.81) than for the non-methylated SEPT9 subgroup (0.58; 95% CI, 0.52–0.64). Sensitivity and specificity were not affected significantly by target gene number, CRC staging, study region, or methylation analysis method. These findings show that hypermethylation markers in blood are highly sensitive and specific for CRC detection, with methylated SEPT9 being particularly robust. The diagnostic performance of hypermethylation markers, which have varied across different studies, can be improved by marker optimization. Future research should examine variation in diagnostic accuracy according to non-neoplastic factors. PMID:27158984

Is HPV DNA testing specificity comparable to that of cytological testing in primary cervical cancer screening? Results of a meta-analysis of randomized controlled trials.

PubMed

Pileggi, Claudia; Flotta, Domenico; Bianco, Aida; Nobile, Carmelo G A; Pavia, Maria

2014-07-01

Human-papillomavirus (HPV) DNA testing has been proposed as an alternative to primary cervical cancer screening using cytological testing. Review of the evidence shows that available data are conflicting for some aspects. The overall goal of the study is to update the performance of HPV DNA as stand-alone testing in primary cervical cancer screening, focusing particularly on the aspects related to the specificity profile of the HPV DNA testing in respect to cytology. We performed a meta-analysis of randomized controlled clinical trials. Eight articles were included in the meta-analysis. Three outcomes have been investigated: relative detection, relative specificity, and relative positive predictive value (PPV) of HPV DNA testing versus cytology. Overall evaluation of relative detection showed a significantly higher detection of CIN2+ and CIN3+ for HPV DNA testing versus cytology. Meta-analyses that considered all age groups showed a relative specificity that favored the cytology in detecting both CIN2+ and CIN3+ lesions whereas, in the ≥30 years' group, specificity of HPV DNA and cytology tests was similar in detecting both CIN2+ and CIN3+ lesions. Results of the pooled analysis on relative PPV showed a not significantly lower PPV of HPV DNA test over cytology. A main key finding of the study is that in women aged ≥30, has been found an almost overlapping specificity between the two screening tests in detecting CIN2 and above-grade lesions. Therefore, primary screening of cervical cancer by HPV DNA testing appears to offer the right balance between maximum detection of CIN2+ and adequate specificity, if performed in the age group ≥30 years. © 2013 UICC.

STATISTICAL METHOD FOR DETECTION OF A TREND IN ATMOSPHERIC SULFATE

EPA Science Inventory

Daily atmospheric concentrations of sulfate collected in northeastern Pennsylvania are regressed against meteorological factors, ozone, and time in order to determine if a significant trend in sulfate can be detected. he data used in this analysis were collected during the Sulfat...

On the Detectability of CO Molecules in the Interstellar Medium via X-Ray Spectroscopy

NASA Technical Reports Server (NTRS)

Joachimi, Katerine; Gatuzz, Efrain; Garcia, Javier; Kallman, Timothy R.

2016-01-01

We present a study of the detectability of CO molecules in the Galactic interstellar medium using high-resolution X-ray spectra obtained with the XMM-Newton Reflection Grating Spectrometer. We analysed 10 bright low mass X-ray binaries (LMXBs) to study the CO contribution in their line of sights. A total of 25 observations were fitted with the ISMabs X-ray absorption model which includes photoabsorption cross-sections for Oi, Oii, Oiii and CO. We performed a Monte Carlo (MC) simulation analysis of the goodness of fit in order to estimate the significance of the CO detection. We determine that the statistical analysis prevents a significant detection of CO molecular X-ray absorption features, except for the lines of sight towards XTE J1718-330 and 4U 1636-53. In the case of XTE J1817-330, this is the first report of the presence of CO along its line of sight. Our results reinforce the conclusion that molecules have a minor contribution to the absorption features in the O K-edge spectral region. We estimate a CO column density lower limit to perform a significant detection with XMM-Newton of N(CO) greater than 6 x 10(exp 16) per sq cm for typical exposure times.

Prenatal chromosomal microarray analysis in fetuses with congenital heart disease: a prospective cohort study.

PubMed

Wang, Yan; Cao, Li; Liang, Dong; Meng, Lulu; Wu, Yun; Qiao, Fengchang; Ji, Xiuqing; Luo, Chunyu; Zhang, Jingjing; Xu, Tianhui; Yu, Bin; Wang, Leilei; Wang, Ting; Pan, Qiong; Ma, Dingyuan; Hu, Ping; Xu, Zhengfeng

2018-02-01

Currently, chromosomal microarray analysis is considered the first-tier test in pediatric care and prenatal diagnosis. However, the diagnostic yield of chromosomal microarray analysis for prenatal diagnosis of congenital heart disease has not been evaluated based on a large cohort. Our aim was to evaluate the clinical utility of chromosomal microarray as the first-tier test for chromosomal abnormalities in fetuses with congenital heart disease. In this prospective study, 602 prenatal cases of congenital heart disease were investigated using single nucleotide polymorphism array over a 5-year period. Overall, pathogenic chromosomal abnormalities were identified in 125 (20.8%) of 602 prenatal cases of congenital heart disease, with 52.0% of them being numerical chromosomal abnormalities. The detection rates of likely pathogenic copy number variations and variants of uncertain significance were 1.3% and 6.0%, respectively. The detection rate of pathogenic chromosomal abnormalities in congenital heart disease plus additional structural anomalies (48.9% vs 14.3%, P < .0001) or intrauterine growth retardation group (50.0% vs 14.3%, P = .044) was significantly higher than that in isolated congenital heart disease group. Additionally, the detection rate in congenital heart disease with additional structural anomalies group was significantly higher than that in congenital heart disease with soft markers group (48.9% vs 19.8%, P < .0001). No significant difference was observed in the detection rates between congenital heart disease with additional structural anomalies and congenital heart disease with intrauterine growth retardation groups (48.9% vs 50.0%), congenital heart disease with soft markers and congenital heart disease with intrauterine growth retardation groups (19.8% vs 50.0%), or congenital heart disease with soft markers and isolated congenital heart disease groups (19.8% vs 14.3%). The detection rate in fetuses with congenital heart disease plus mild ventriculomegaly was significantly higher than in those with other types of soft markers (50.0% vs 15.6%, P < .05). Our study suggests chromosomal microarray analysis is a reliable and high-resolution technology and should be used as the first-tier test for prenatal diagnosis of congenital heart disease in clinical practice. Copyright © 2017 Elsevier Inc. All rights reserved.

Human papillomavirus in esophageal squamous cell carcinoma in Colombia and Chile

PubMed Central

Castillo, Andres; Aguayo, Francisco; Koriyama, Chihaya; Torres, Miyerlandi; Carrascal, Edwin; Corvalan, Alejandro; Roblero, Juan P; Naquira, Cecilia; Palma, Mariana; Backhouse, Claudia; Argandona, Jorge; Itoh, Tetsuhiko; Shuyama, Karem; Eizuru, Yoshito; Akiba, Suminori

2006-01-01

AIM: To examine the presence of human papillomavirus (HPV) in esophageal squamous cell carcinoma (ESCC) specimens collected from Colombia and Chile located in the northern and southern ends of the continent, respectively. METHODS: We examined 47 and 26 formalin-fixed and paraffin-embedded ESCC specimens from Colombia and Chile, respectively. HPV was detected using GP5+/GP6+ primer pair for PCR, and confirmed by Southern blot analysis. Sequencing analysis of L1 region fragment was used to identify HPV genotype. In addition, P16INK4A protein immunostaining of all the specimens was conducted. RESULTS: HPV was detected in 21 ESCC specimens (29%). Sequencing analysis of L1 region fragment identified HPV-16 genome in 6 Colombian cases (13%) and in 5 Chilean cases (19%). HPV-18 was detected in 10 cases (21%) in Colombia but not in any Chilean case. Since Chilean ESCC cases had a higher prevalence of HPV-16 (without statistical significance), but a significantly lower prevalence of HPV-18 than in Colombian cases (P = 0.011) even though the two countries have similar ESCC incidence rates, the frequency of HPV-related ESCC may not be strongly affected by risk factors affecting the incidence of ESCC. HPV-16 genome was more frequently detected in p16 positive carcinomas, although the difference was not statistically significant. HPV-18 detection rate did not show any association with p16 expression. Well-differentiated tumors tended to have either HPV-16 or HPV-18 but the association was not statistically significant. HPV genotypes other than HPV-16 or 18 were not detected in either country. CONCLUSION: HPV-16 and HPV-18 genotypes can be found in ESCC specimens collected from two South American countries. Further studies on the relationship between HPV-16 presence and p16 expression in ESCC would aid understanding of the mechanism underlying the presence of HPV in ESCC. PMID:17036393

Fast EEG spike detection via eigenvalue analysis and clustering of spatial amplitude distribution

NASA Astrophysics Data System (ADS)

Fukami, Tadanori; Shimada, Takamasa; Ishikawa, Bunnoshin

2018-06-01

Objective. In the current study, we tested a proposed method for fast spike detection in electroencephalography (EEG). Approach. We performed eigenvalue analysis in two-dimensional space spanned by gradients calculated from two neighboring samples to detect high-amplitude negative peaks. We extracted the spike candidates by imposing restrictions on parameters regarding spike shape and eigenvalues reflecting detection characteristics of individual medical doctors. We subsequently performed clustering, classifying detected peaks by considering the amplitude distribution at 19 scalp electrodes. Clusters with a small number of candidates were excluded. We then defined a score for eliminating spike candidates for which the pattern of detected electrodes differed from the overall pattern in a cluster. Spikes were detected by setting the score threshold. Main results. Based on visual inspection by a psychiatrist experienced in EEG, we evaluated the proposed method using two statistical measures of precision and recall with respect to detection performance. We found that precision and recall exhibited a trade-off relationship. The average recall value was 0.708 in eight subjects with the score threshold that maximized the F-measure, with 58.6  ±  36.2 spikes per subject. Under this condition, the average precision was 0.390, corresponding to a false positive rate 2.09 times higher than the true positive rate. Analysis of the required processing time revealed that, using a general-purpose computer, our method could be used to perform spike detection in 12.1% of the recording time. The process of narrowing down spike candidates based on shape occupied most of the processing time. Significance. Although the average recall value was comparable with that of other studies, the proposed method significantly shortened the processing time.

Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates.

PubMed

Schwämmle, Veit; León, Ileana Rodríguez; Jensen, Ole Nørregaard

2013-09-06

Large-scale quantitative analyses of biological systems are often performed with few replicate experiments, leading to multiple nonidentical data sets due to missing values. For example, mass spectrometry driven proteomics experiments are frequently performed with few biological or technical replicates due to sample-scarcity or due to duty-cycle or sensitivity constraints, or limited capacity of the available instrumentation, leading to incomplete results where detection of significant feature changes becomes a challenge. This problem is further exacerbated for the detection of significant changes on the peptide level, for example, in phospho-proteomics experiments. In order to assess the extent of this problem and the implications for large-scale proteome analysis, we investigated and optimized the performance of three statistical approaches by using simulated and experimental data sets with varying numbers of missing values. We applied three tools, including standard t test, moderated t test, also known as limma, and rank products for the detection of significantly changing features in simulated and experimental proteomics data sets with missing values. The rank product method was improved to work with data sets containing missing values. Extensive analysis of simulated and experimental data sets revealed that the performance of the statistical analysis tools depended on simple properties of the data sets. High-confidence results were obtained by using the limma and rank products methods for analyses of triplicate data sets that exhibited more than 1000 features and more than 50% missing values. The maximum number of differentially represented features was identified by using limma and rank products methods in a complementary manner. We therefore recommend combined usage of these methods as a novel and optimal way to detect significantly changing features in these data sets. This approach is suitable for large quantitative data sets from stable isotope labeling and mass spectrometry experiments and should be applicable to large data sets of any type. An R script that implements the improved rank products algorithm and the combined analysis is available.

The clinical evaluation of the CADence device in the acoustic detection of coronary artery disease.

PubMed

Thomas, Joseph L; Ridner, Michael; Cole, Jason H; Chambers, Jeffrey W; Bokhari, Sabahat; Yannopoulos, Demetris; Kern, Morton; Wilson, Robert F; Budoff, Matthew J

2018-06-23

The noninvasive detection of turbulent coronary flow may enable diagnosis of significant coronary artery disease (CAD) using novel sensor and analytic technology. Eligible patients (n = 1013) with chest pain and CAD risk factors undergoing nuclear stress testing were studied using the CADence (AUM Cardiovascular Inc., Northfield MN) acoustic detection (AD) system. The trial was designed to demonstrate non-inferiority of AD for diagnostic accuracy in detecting significant CAD as compared to an objective performance criteria (sensitivity 83% and specificity 80%, with 15% non-inferiority margins) for nuclear stress testing. AD analysis was blinded to clinical, core lab-adjudicated angiographic, and nuclear data. The presence of significant CAD was determined by computed tomographic (CCTA) or invasive angiography. A total of 1013 subjects without prior coronary revascularization or Q-wave myocardial infarction were enrolled. Primary analysis was performed on subjects with complete angiographic and AD data (n = 763) including 111 subjects (15%) with severe CAD based on CCTA (n = 34) and invasive angiography (n = 77). The sensitivity and specificity of AD were 78% (p = 0.012 for non-inferiority) and 35% (p < 0.001 for failure to demonstrate non-inferiority), respectively. AD results had a high 91% negative predictive value for the presence of significant CAD. AD testing failed to demonstrate non-inferior diagnostic accuracy as compared to the historical performance of a nuclear stress OPC due to low specificity. AD sensitivity was non-inferior in detecting significant CAD with a high negative predictive value supporting a potential value in excluding CAD.

Central sleep apnea detection from ECG-derived respiratory signals. Application of multivariate recurrence plot analysis.

PubMed

Maier, C; Dickhaus, H

2010-01-01

This study examines the suitability of recurrence plot analysis for the problem of central sleep apnea (CSA) detection and delineation from ECG-derived respiratory (EDR) signals. A parameter describing the average length of vertical line structures in recurrence plots is calculated at a time resolution of 1 s as 'instantaneous trapping time'. Threshold comparison of this parameter is used to detect ongoing CSA. In data from 26 patients (duration 208 h) we assessed sensitivity for detection of CSA and mixed apnea (MSA) events by comparing the results obtained from 8-channel Holter ECGs to the annotations (860 CSA, 480 MSA) of simultaneously registered polysomnograms. Multivariate combination of the EDR from different ECG leads improved the detection accuracy significantly. When all eight leads were considered, an average instantaneous vertical line length above 5 correctly identified 1126 of the 1340 events (sensitivity 84%) with a total number of 1881 positive detections. We conclude that recurrence plot analysis is a promising tool for detection and delineation of CSA epochs from EDR signals with high time resolution. Moreover, the approach is likewise applicable to directly measured respiratory signals.

Erythrocyte membrane analysis for type II diabetes detection using Raman spectroscopy in high-wavenumber region

NASA Astrophysics Data System (ADS)

Lin, Jinyong; Zeng, Yongyi; Lin, Juqiang; Wang, Jing; Li, Ling; Huang, Zufang; Li, Buhong; Zeng, Haishan; Chen, Rong

2014-03-01

Raman spectroscopy was employed to detect lipid variation occurring in type II diabetic erythrocyte membrane (EM) without using exogenous reagents. In high-wavenumber (HW) region, significant Raman spectral differences between diabetic and normal EM are observed at 2850, 2873, 2885, 2935, and 2965 cm-1, which are mainly related to lipid in EM. Based on principal component analysis, the diagnostic accuracy of HW region for diabetes detection is 98.8%, which is much higher than that of low-wavenumber region (82.9%). The results suggest that EM HW Raman region has great promise for the reagent-free and non-invasive detection of type II diabetes.

What drives high flow events in the Swiss Alps? Recent developments in wavelet spectral analysis and their application to hydrology

NASA Astrophysics Data System (ADS)

Schaefli, B.; Maraun, D.; Holschneider, M.

2007-12-01

Extreme hydrological events are often triggered by exceptional co-variations of the relevant hydrometeorological processes and in particular by exceptional co-oscillations at various temporal scales. Wavelet and cross wavelet spectral analysis offers promising time-scale resolved analysis methods to detect and analyze such exceptional co-oscillations. This paper presents the state-of-the-art methods of wavelet spectral analysis, discusses related subtleties, potential pitfalls and recently developed solutions to overcome them and shows how wavelet spectral analysis, if combined to a rigorous significance test, can lead to reliable new insights into hydrometeorological processes for real-world applications. The presented methods are applied to detect potentially flood triggering situations in a high Alpine catchment for which a recent re-estimation of design floods encountered significant problems simulating the observed high flows. For this case study, wavelet spectral analysis of precipitation, temperature and discharge offers a powerful tool to help detecting potentially flood producing meteorological situations and to distinguish between different types of floods with respect to the prevailing critical hydrometeorological conditions. This opens very new perspectives for the analysis of model performances focusing on the occurrence and non-occurrence of different types of high flow events. Based on the obtained results, the paper summarizes important recommendations for future applications of wavelet spectral analysis in hydrology.

Spatiotemporal Change Detection Using Landsat Imagery: the Case Study of Karacabey Flooded Forest, Bursa, Turkey

NASA Astrophysics Data System (ADS)

Akay, A. E.; Gencal, B.; Taş, İ.

2017-11-01

This short paper aims to detect spatiotemporal detection of land use/land cover change within Karacabey Flooded Forest region. Change detection analysis applied to Landsat 5 TM images representing July 2000 and a Landsat 8 OLI representing June 2017. Various image processing tools were implemented using ERDAS 9.2, ArcGIS 10.4.1, and ENVI programs to conduct spatiotemporal change detection over these two images such as band selection, corrections, subset, classification, recoding, accuracy assessment, and change detection analysis. Image classification revealed that there are five significant land use/land cover types, including forest, flooded forest, swamp, water, and other lands (i.e. agriculture, sand, roads, settlement, and open areas). The results indicated that there was increase in flooded forest, water, and other lands, while the cover of forest and swamp decreased.

Comparative elemental analysis of fine particulate matter (PM2.5) from industrial and residential areas in Greater Cairo-Egypt by means of a multi-secondary target energy dispersive X-ray fluorescence spectrometer

NASA Astrophysics Data System (ADS)

Shaltout, Abdallah A.; Hassan, Salwa K.; Karydas, Andreas G.; Zaki, Z. I.; Mostafa, Nasser Y.; Kregsamer, Peter; Wobrauschek, Peter; Streli, Christina

2018-07-01

Fine aerosol particles with aerodynamic diameter equal or <2.5 μm (PM2.5) have been collected from industrial and residential areas of Greater Cairo, Egypt during two different seasons namely; autumn 2014 and winter 2014/2015. Energy dispersive X-ray fluorescence (EDXRF) analysis utilizing polarization geometry and three different secondary targets (CaF2, Ge, and Mo) was employed for the quantitative analysis of eighteen (18) elements in PM2.5 samples. Light elements like Na and Mg was possible to be quantified, whereas detection limits in the range of few ng m-3 were attained for the most of the detected elements. Although, the average mass concentrations of the PM2.5 collected from the residential area (27 ± 7 μg m-3) is close to the annual mean limit value, a significant number of the collected samples (33%) presented higher average mass concentrations. For the industrial location, the average mass concentration is equal to 55 ± 19 μg m-3, exceeded twofold the annual mean limit value of the European Commission. Remarkably high elemental concentrations were determined for the most of the detected elements from the industrial area samples, clearly indicating the significant influence of anthropogenic activities. The present optimized EDXRF analysis offered significantly improved analytical range and limits of detection with respect to previous similar studies, thus enhancing our knowledge and understanding on the contribution of different pollution sources.

Investigation of the detection and monitoring of forest insect infestation in the Sierra Nevada Mountains of California

NASA Technical Reports Server (NTRS)

Hall, R. C. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Significant progress has been made in detecting insect outbreaks from ERTS-1 data during this period. It is possible to differentiate forested areas with heavy damage from those with little or no damage. The analysis is made with color infrared positive transparencies and prints. Enlargement of the transparencies makes it possible to detect and map areas of three degrees of tree mortality into heavy, medium, and light. It was also noted that shadows cast by massive rock domes closely resemble natural lakes.

Land use change detection with LANDSAT-2 data for monitoring and predicting regional water quality degradation. [Arkansas

NASA Technical Reports Server (NTRS)

Macdonald, H.; Steele, K. (Principal Investigator); Waite, W.; Rice, R.; Shinn, M.; Dillard, T.; Petersen, C.

1977-01-01

The author has identified the following significant results. Comparison between LANDSAT 1 and 2 imagery of Arkansas provided evidence of significant land use changes during the 1972-75 time period. Analysis of Arkansas historical water quality information has shown conclusively that whereas point source pollution generally can be detected by use of water quality data collected by state and federal agencies, sampling methodologies for nonpoint source contamination attributable to surface runoff are totally inadequate. The expensive undertaking of monitoring all nonpoint sources for numerous watersheds can be lessened by implementing LANDSAT change detection analyses.

Detecting coupled collective motions in protein by independent subspace analysis

NASA Astrophysics Data System (ADS)

Sakuraba, Shun; Joti, Yasumasa; Kitao, Akio

2010-11-01

Protein dynamics evolves in a high-dimensional space, comprising aharmonic, strongly correlated motional modes. Such correlation often plays an important role in analyzing protein function. In order to identify significantly correlated collective motions, here we employ independent subspace analysis based on the subspace joint approximate diagonalization of eigenmatrices algorithm for the analysis of molecular dynamics (MD) simulation trajectories. From the 100 ns MD simulation of T4 lysozyme, we extract several independent subspaces in each of which collective modes are significantly correlated, and identify the other modes as independent. This method successfully detects the modes along which long-tailed non-Gaussian probability distributions are obtained. Based on the time cross-correlation analysis, we identified a series of events among domain motions and more localized motions in the protein, indicating the connection between the functionally relevant phenomena which have been independently revealed by experiments.

Real-time detection of organic contamination events in water distribution systems by principal components analysis of ultraviolet spectral data.

PubMed

Zhang, Jian; Hou, Dibo; Wang, Ke; Huang, Pingjie; Zhang, Guangxin; Loáiciga, Hugo

2017-05-01

The detection of organic contaminants in water distribution systems is essential to protect public health from potential harmful compounds resulting from accidental spills or intentional releases. Existing methods for detecting organic contaminants are based on quantitative analyses such as chemical testing and gas/liquid chromatography, which are time- and reagent-consuming and involve costly maintenance. This study proposes a novel procedure based on discrete wavelet transform and principal component analysis for detecting organic contamination events from ultraviolet spectral data. Firstly, the spectrum of each observation is transformed using discrete wavelet with a coiflet mother wavelet to capture the abrupt change along the wavelength. Principal component analysis is then employed to approximate the spectra based on capture and fusion features. The significant value of Hotelling's T 2 statistics is calculated and used to detect outliers. An alarm of contamination event is triggered by sequential Bayesian analysis when the outliers appear continuously in several observations. The effectiveness of the proposed procedure is tested on-line using a pilot-scale setup and experimental data.

An Investigation of Document Partitions.

ERIC Educational Resources Information Center

Shaw, W. M., Jr.

1986-01-01

Empirical significance of document partitions is investigated as a function of index term-weight and similarity thresholds. Results show the same empirically preferred partitions can be detected by two independent strategies: an analysis of cluster-based retrieval analysis and an analysis of regularities in the underlying structure of the document…

Cardiac monitoring for detection of atrial fibrillation after TIA: A systematic review and meta-analysis.

PubMed

Korompoki, Eleni; Del Giudice, Angela; Hillmann, Steffi; Malzahn, Uwe; Gladstone, David J; Heuschmann, Peter; Veltkamp, Roland

2017-01-01

Background and purpose The detection rate of atrial fibrillation has not been studied specifically in transient ischemic attack (TIA) patients although extrapolation from ischemic stroke may be inadequate. We conducted a systematic review and meta-analysis to determine the rate of newly diagnosed atrial fibrillation using different methods of ECG monitoring in TIA. Methods A comprehensive literature search was performed following a pre-specified protocol the PRISMA statement. Prospective observational studies and randomized controlled trials were considered that included TIA patients who underwent cardiac monitoring for >12 h. Primary outcome was frequency of detection of atrial fibrillation ≥30 s. Analyses of subgroups and of duration and type of monitoring were performed. Results Seventeen studies enrolling 1163 patients were included. The pooled atrial fibrillation detection rate for all methods was 4% (95% CI: 2-7%). Yield of monitoring was higher in selected (higher age, more extensive testing for arrhythmias before enrolment, or presumed cardioembolic/cryptogenic cause) than in unselected cohorts (7% vs 3%). Pooled mean atrial fibrillation detection rates rose with duration of monitoring: 4% (24 h), 5% (24 h to 7 days) and 6% (>7 days), respectively. Yield of non-invasive was significantly lower than that of invasive monitoring (4% vs. 11%). Significant heterogeneity was observed among studies (I 2 =60.61%). Conclusion This first meta-analysis of atrial fibrillation detection in TIA patients finds a lower atrial fibrillation detection rate in TIA than reported for IS and TIA cohorts in previous meta-analyses. Prospective studies are needed to determine actual prevalence of atrial fibrillation and optimal diagnostic procedure for atrial fibrillation detection in TIA.

Genomic profiling of plasma cell disorders in a clinical setting: integration of microarray and FISH, after CD138 selection of bone marrow

PubMed Central

Berry, Nadine Kaye; Bain, Nicole L; Enjeti, Anoop K; Rowlings, Philip

2014-01-01

Aim To evaluate the role of whole genome comparative genomic hybridisation microarray (array-CGH) in detecting genomic imbalances as compared to conventional karyotype (GTG-analysis) or myeloma specific fluorescence in situ hybridisation (FISH) panel in a diagnostic setting for plasma cell dyscrasia (PCD). Methods A myeloma-specific interphase FISH (i-FISH) panel was carried out on CD138 PC-enriched bone marrow (BM) from 20 patients having BM biopsies for evaluation of PCD. Whole genome array-CGH was performed on reference (control) and neoplastic (test patient) genomic DNA extracted from CD138 PC-enriched BM and analysed. Results Comparison of techniques demonstrated a much higher detection rate of genomic imbalances using array-CGH. Genomic imbalances were detected in 1, 19 and 20 patients using GTG-analysis, i-FISH and array-CGH, respectively. Genomic rearrangements were detected in one patient using GTG-analysis and seven patients using i-FISH, while none were detected using array-CGH. I-FISH was the most sensitive method for detecting gene rearrangements and GTG-analysis was the least sensitive method overall. All copy number aberrations observed in GTG-analysis were detected using array-CGH and i-FISH. Conclusions We show that array-CGH performed on CD138-enriched PCs significantly improves the detection of clinically relevant and possibly novel genomic abnormalities in PCD, and thus could be considered as a standard diagnostic technique in combination with IGH rearrangement i-FISH. PMID:23969274

Genomic profiling of plasma cell disorders in a clinical setting: integration of microarray and FISH, after CD138 selection of bone marrow.

PubMed

Berry, Nadine Kaye; Bain, Nicole L; Enjeti, Anoop K; Rowlings, Philip

2014-01-01

To evaluate the role of whole genome comparative genomic hybridisation microarray (array-CGH) in detecting genomic imbalances as compared to conventional karyotype (GTG-analysis) or myeloma specific fluorescence in situ hybridisation (FISH) panel in a diagnostic setting for plasma cell dyscrasia (PCD). A myeloma-specific interphase FISH (i-FISH) panel was carried out on CD138 PC-enriched bone marrow (BM) from 20 patients having BM biopsies for evaluation of PCD. Whole genome array-CGH was performed on reference (control) and neoplastic (test patient) genomic DNA extracted from CD138 PC-enriched BM and analysed. Comparison of techniques demonstrated a much higher detection rate of genomic imbalances using array-CGH. Genomic imbalances were detected in 1, 19 and 20 patients using GTG-analysis, i-FISH and array-CGH, respectively. Genomic rearrangements were detected in one patient using GTG-analysis and seven patients using i-FISH, while none were detected using array-CGH. I-FISH was the most sensitive method for detecting gene rearrangements and GTG-analysis was the least sensitive method overall. All copy number aberrations observed in GTG-analysis were detected using array-CGH and i-FISH. We show that array-CGH performed on CD138-enriched PCs significantly improves the detection of clinically relevant and possibly novel genomic abnormalities in PCD, and thus could be considered as a standard diagnostic technique in combination with IGH rearrangement i-FISH.

Risk factors for human papillomavirus detection in urine samples of heterosexual men visiting urological clinics in Japan.

PubMed

Nakashima, Kazufumi; Shigehara, Kazuyoshi; Kitamura, Tadaichi; Yaegashi, Hiroshi; Shimamura, Masayoshi; Kawaguchi, Shohei; Izumi, Kouji; Kadono, Yoshifumi; Mizokami, Atsushi

2018-05-11

The present study aimed to investigate human papillomavirus (HPV) prevalence and identify risk factors for HPV detection in urine samples among heterosexual men attending urological clinics. Spot urine samples including initial stream were collected from 845 participants, and the cell pellets were preserved into liquid-based cytological solution. After DNA extraction from each sample, HPV-DNA amplification and genotyping were performed using Luminex multiplex polymerase chain reaction. Participants completed a questionnaire on their age, education, smoking status, sexuality, age of sexual debut, marital status, and present history of sexually transmitted infections. Data from 803 patients were included in the analysis. Overall HPV and high-risk (HR)HPV prevalence in urine samples were 6.2% and 3.1%, respectively. HPV and HR-HPV prevalences were the highest in men with urethritis, and were significantly higher than those without urethritis. HPV detection was the most common in men aged 40-49 years, although significant detection differences were not age-related. Urethritis was an independent risk factor for HPV detection from urine samples, with an odds ratio (OR) of 4.548 (95%CI; 1.802-11.476) (p = 0.001). On the other hand, a sub-analysis excluding men with urethritis demonstrated that prostate cancer was a significant risk factor for HPV detection, with OR of 2.844 (95%CI; 1.046-7.732) (p = 0.0410), whereas was not a significant risk for HR-HPV detection in urine samples. Prostate cancer may represent a risk factor for HPV detection in the urine of men without urethritis. The authors did not register to Clinical Trial because this is observational and cross-sectional study. Copyright © 2018 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

The Detection and Photometric Redshift Determination of Distant Galaxies using SIRTF's Infrared Array Camera

NASA Technical Reports Server (NTRS)

Simpson, C.; Eisenhardt, P.

1998-01-01

We investigate the ability of the Space Infrared Telescope Facility's Infrared Array Camera to detect distant (z3) galaxies and measure their photometric redshifts. Our analysis shows that changing the original long wavelength filter specifications provides significant improvements in performance in this and other areas.

Beta-Catenin and Epithelial Tumors: A Study Based on 374 Oropharyngeal Cancers

PubMed Central

Santoro, Angela; Pannone, Giuseppe; Papagerakis, Silvana; McGuff, H. Stan; Cafarelli, Barbara; Lepore, Silvia; De Maria, Salvatore; Rubini, Corrado; Mattoni, Marilena; Staibano, Stefania; Mezza, Ernesto; De Rosa, Gaetano; Aquino, Gabriella; Losito, Simona; Loreto, Carla; Crimi, Salvatore; Bufo, Pantaleo

2014-01-01

Introduction. Although altered regulation of the Wnt pathway via beta-catenin is a frequent event in several human cancers, its potential implications in oral/oropharyngeal squamous cell carcinomas (OSCC/OPSCC) are largely unexplored. Work purpose was to define association between beta-catenin expression and clinical-pathological parameters in 374 OSCCs/OP-SCCs by immunohistochemistry (IHC). Materials and Methods. Association between IHC detected patterns of protein expression and clinical-pathological parameters was assessed by statistical analysis and survival rates by Kaplan-Meier curves. Beta-catenin expression was also investigated in OSCC cell lines by Real-Time PCR. An additional analysis of the DNA content was performed on 22 representative OSCCs/OPSCCs by DNA-image-cytometric analysis. Results and Discussion. All carcinomas exhibited significant alterations of beta-catenin expression (P < 0.05). Beta-catenin protein was mainly detected in the cytoplasm of cancerous cells and only focal nuclear positivity was observed. Higher cytoplasmic expression correlated significantly with poor histological differentiation, advanced stage, and worst patient outcome (P < 0.05). By Real-Time PCR significant increase of beta-catenin mRNA was detected in OSCC cell lines and in 45% of surgical specimens. DNA ploidy study demonstrated high levels of aneuploidy in beta-catenin overexpressing carcinomas. Conclusions. This is the largest study reporting significant association between beta-catenin expression and clinical-pathological factors in patients with OSCCs/OPSCCs. PMID:24511551

Value of PAX1 Methylation Analysis by MS-HRM in the Triage of Atypical Squamous Cells of Undetermined Significance.

PubMed

Li, Shi-Rong; Wang, Zhen-Ming; Wang, Yu-Hui; Wang, Xi-Bo; Zhao, Jian-Qiang; Xue, Hai-Bin; Jiang, Fu-Guo

2015-01-01

Detection of cervical high grade lesions in patients with atypical squamous cells of undetermined significance (ASCUS) is still a challenge. Our study tested the efficacy of the paired boxed gene 1 (PAX1) methylation analysis by methylation-sensitive high-resolution melting (MS-HRM) in the detection of high grade lesions in ASCUS and compared performance with the hybrid capture 2 (HC2) human papillomavirus (HPV) test. A total of 463 consecutive ASCUS women from primary screening were selected. Their cervical scrapings were collected and assessed by PAX1 methylation analysis (MS-HRM) and high-risk HPV-DNA test (HC2). All patients with ASCUS were admitted to colposcopy and cervical biopsies. The Chi- square test was used to test the differences of PAX1 methylation or HPV infection between groups. The specificity, sensitivity, and accuracy for detecting CIN2 + lesions were: 95.6%, 82.4%, and 94.6%, respectively, for the PAX1 MS-HRM test; and 59.7%, 64.7%, and 60.0% for the HC2 HPV test. The PAX1 methylation analysis by MS-HRM demonstrated a better performance than the high-risk HPV-DNA test for the detection of high grade lesions (CIN2 +) in ASCUS cases. This approach could screen out the majority of low grade cases of ASCUS, and thus reduce the referral rate to colposcopy.

Prostate-specific membrane antigen PET/MRI validation of MR textural analysis for detection of transition zone prostate cancer.

PubMed

Bates, Anthony; Miles, Kenneth

2017-12-01

To validate MR textural analysis (MRTA) for detection of transition zone (TZ) prostate cancer through comparison with co-registered prostate-specific membrane antigen (PSMA) PET-MR. Retrospective analysis was performed for 30 men who underwent simultaneous PSMA PET-MR imaging for staging of prostate cancer. Thirty texture features were derived from each manually contoured T2-weighted, transaxial, prostatic TZ using texture analysis software that applies a spatial band-pass filter and quantifies texture through histogram analysis. Texture features of the TZ were compared to PSMA expression on the corresponding PET images. The Benjamini-Hochberg correction controlled the false discovery rate at <5%. Eighty-eight T2-weighted images in 18 patients demonstrated abnormal PSMA expression within the TZ on PET-MR. 123 images were PSMA negative. Based on the corrected p-value of 0.005, significant differences between PSMA positive and negative slices were found for 16 texture parameters: Standard deviation and mean of positive pixels for all spatial filters (p = <0.0001 for both at all spatial scaling factor (SSF) values) and mean intensity following filtration for SSF 3-6 mm (p = 0.0002-0.0018). Abnormal expression of PSMA within the TZ is associated with altered texture on T2-weighted MR, providing validation of MRTA for the detection of TZ prostate cancer. • Prostate transition zone (TZ) MR texture analysis may assist in prostate cancer detection. • Abnormal transition zone PSMA expression correlates with altered texture on T2-weighted MR. • TZ with abnormal PSMA expression demonstrates significantly reduced MI, SD and MPP.

[Comparative analysis of 6 kinds of bacteria in the subgingival plaque in different types of patients with periodontal diseases].

PubMed

Ma, Ying-ying; Zhang, Tao-wen; Jiang, Yu-xi; Liu, Shu-tai

2015-10-01

To detect the existence of Aa,Pg,Tf,Cr,Ec and Pn in the subgingival plaque, and determine their relationships among different types of periodontal diseases. Dental plaques from 120 subjects were sampled, including 40 volunteers with health periodontal status(Group A) , forty patients with dental plaque-induced gingival diseases(Group B) and 40 patients with moderate or severe chronic periodontitis (Group C) . These samples were detected based on bacterial composition using the terminal restriction fragment length polymorphism of 16S rRNA genes by multiple-polymerase chain reaction. The data was analysed with SPSS 13.0 software package for Chi-square test. The detection rate of Pn, Cr and Pg had significant differences between group A and B. The detection rate of Ec, Cr, Pg, Aa and Tf had significant differences between group C and B. The detection rate of Ec, Pn, Cr, Pg, Aa and Tf had significant differences between group A and C. The rate of Ec, Pn, Cr, Pg and Tf detected in moderate or patients with moderate or severe chronic periodontitis are significantly higher than that in healthy subjects, indicating that these bacteria have certain correlation with chronic periodontitis. The rate of Ec, Cr, Pg and Tf detected in severe chronic periodontitis are significantly higher than that in dental-induced gingivitis, suggesting their close relationship with the progress of periodontal disease.

Chromosomal Microarray Analysis of Consecutive Individuals with Autism Spectrum Disorders Using an Ultra-High Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders.

PubMed

Ho, Karen S; Wassman, E Robert; Baxter, Adrianne L; Hensel, Charles H; Martin, Megan M; Prasad, Aparna; Twede, Hope; Vanzo, Rena J; Butler, Merlin G

2016-12-09

Copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) significantly contribute to understanding the etiology of autism spectrum disorder (ASD) and other related conditions. In recognition of the value of CMA testing and its impact on medical management, CMA is in medical guidelines as a first-tier test in the evaluation of children with these disorders. As CMA becomes adopted into routine care for these patients, it becomes increasingly important to report these clinical findings. This study summarizes the results of over 4 years of CMA testing by a CLIA-certified clinical testing laboratory. Using a 2.8 million probe microarray optimized for the detection of CNVs associated with neurodevelopmental disorders, we report an overall CNV detection rate of 28.1% in 10,351 consecutive patients, which rises to nearly 33% in cases without ASD, with only developmental delay/intellectual disability (DD/ID) and/or multiple congenital anomalies (MCA). The overall detection rate for individuals with ASD is also significant at 24.4%. The detection rate and pathogenic yield of CMA vary significantly with the indications for testing, age, and gender, as well as the specialty of the ordering doctor. We note discrete differences in the most common recurrent CNVs found in individuals with or without a diagnosis of ASD.

Applying spatial analysis tools in public health: an example using SaTScan to detect geographic targets for colorectal cancer screening interventions.

PubMed

Sherman, Recinda L; Henry, Kevin A; Tannenbaum, Stacey L; Feaster, Daniel J; Kobetz, Erin; Lee, David J

2014-03-20

Epidemiologists are gradually incorporating spatial analysis into health-related research as geocoded cases of disease become widely available and health-focused geospatial computer applications are developed. One health-focused application of spatial analysis is cluster detection. Using cluster detection to identify geographic areas with high-risk populations and then screening those populations for disease can improve cancer control. SaTScan is a free cluster-detection software application used by epidemiologists around the world to describe spatial clusters of infectious and chronic disease, as well as disease vectors and risk factors. The objectives of this article are to describe how spatial analysis can be used in cancer control to detect geographic areas in need of colorectal cancer screening intervention, identify issues commonly encountered by SaTScan users, detail how to select the appropriate methods for using SaTScan, and explain how method selection can affect results. As an example, we used various methods to detect areas in Florida where the population is at high risk for late-stage diagnosis of colorectal cancer. We found that much of our analysis was underpowered and that no single method detected all clusters of statistical or public health significance. However, all methods detected 1 area as high risk; this area is potentially a priority area for a screening intervention. Cluster detection can be incorporated into routine public health operations, but the challenge is to identify areas in which the burden of disease can be alleviated through public health intervention. Reliance on SaTScan's default settings does not always produce pertinent results.

Prenatal Diagnosis of DNA Copy Number Variations by Genomic Single-Nucleotide Polymorphism Array in Fetuses with Congenital Heart Defects.

PubMed

Tang, Shaohua; Lv, Jiaojiao; Chen, Xiangnan; Bai, Lili; Li, Huanzheng; Chen, Chong; Wang, Ping; Xu, Xueqin; Lu, Jianxin

2016-01-01

To evaluate the usefulness of single-nucleotide polymorphism (SNP) array for prenatal genetic diagnosis of congenital heart defect (CHD), we used this approach to detect clinically significant copy number variants (CNVs) in fetuses with CHDs. A HumanCytoSNP-12 array was used to detect genomic samples obtained from 39 fetuses that exhibited cardiovascular abnormalities on ultrasound and had a normal karyotype. The relationship between CNVs and CHDs was identified by using genotype-phenotype comparisons and searching of chromosomal databases. All clinically significant CNVs were confirmed by real-time PCR. CNVs were detected in 38/39 (97.4%) fetuses: variants of unknown significance were detected in 2/39 (5.1%), and clinically significant CNVs were identified in 7/39 (17.9%). In 3 of the 7 fetuses with clinically significant CNVs, 3 rare and previously undescribed CNVs were detected, and these CNVs encompassed the CHD candidate genes FLNA (Xq28 dup), BCOR (Xp11.4 dup), and RBL2 (16q12.2 del). Compared with conventional cytogenetic genomics, SNP array analysis provides significantly improved detection of submicroscopic genomic aberrations in pregnancies with CHDs. Based on these results, we propose that genomic SNP array is an effective method which could be used in the prenatal diagnostic test to assist genetic counseling for pregnancies with CHDs. © 2015 S. Karger AG, Basel.

[Advances in automatic detection technology for images of thin blood film of malaria parasite].

PubMed

Juan-Sheng, Zhang; Di-Qiang, Zhang; Wei, Wang; Xiao-Guang, Wei; Zeng-Guo, Wang

2017-05-05

This paper reviews the computer vision and image analysis studies aiming at automated diagnosis or screening of malaria in microscope images of thin blood film smears. On the basis of introducing the background and significance of automatic detection technology, the existing detection technologies are summarized and divided into several steps, including image acquisition, pre-processing, morphological analysis, segmentation, count, and pattern classification components. Then, the principles and implementation methods of each step are given in detail. In addition, the promotion and application in automatic detection technology of thick blood film smears are put forwarded as questions worthy of study, and a perspective of the future work for realization of automated microscopy diagnosis of malaria is provided.

Shifted termination assay (STA) fragment analysis to detect BRAF V600 mutations in papillary thyroid carcinomas

PubMed Central

2013-01-01

Background BRAF mutation is an important diagnostic and prognostic marker in patients with papillary thyroid carcinoma (PTC). To be applicable in clinical laboratories with limited equipment, diverse testing methods are required to detect BRAF mutation. Methods A shifted termination assay (STA) fragment analysis was used to detect common V600 BRAF mutations in 159 PTCs with DNAs extracted from formalin-fixed paraffin-embedded tumor tissue. The results of STA fragment analysis were compared to those of direct sequencing. Serial dilutions of BRAF mutant cell line (SNU-790) were used to calculate limit of detection (LOD). Results BRAF mutations were detected in 119 (74.8%) PTCs by STA fragment analysis. In direct sequencing, BRAF mutations were observed in 118 (74.2%) cases. The results of STA fragment analysis had high correlation with those of direct sequencing (p < 0.00001, κ = 0.98). The LOD of STA fragment analysis and direct sequencing was 6% and 12.5%, respectively. In PTCs with pT3/T4 stages, BRAF mutation was observed in 83.8% of cases. In pT1/T2 carcinomas, BRAF mutation was detected in 65.9% and this difference was statistically significant (p = 0.007). Moreover, BRAF mutation was more frequent in PTCs with extrathyroidal invasion than tumors without extrathyroidal invasion (84.7% versus 62.2%, p = 0.001). To prepare and run the reactions, direct sequencing required 450 minutes while STA fragment analysis needed 290 minutes. Conclusions STA fragment analysis is a simple and sensitive method to detect BRAF V600 mutations in formalin-fixed paraffin-embedded clinical samples. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5684057089135749 PMID:23883275

Enhancing detection of steady-state visual evoked potentials using individual training data.

PubMed

Wang, Yijun; Nakanishi, Masaki; Wang, Yu-Te; Jung, Tzyy-Ping

2014-01-01

Although the performance of steady-state visual evoked potential (SSVEP)-based brain-computer interfaces (BCIs) has improved gradually in the past decades, it still does not meet the requirement of a high communication speed in many applications. A major challenge is the interference of spontaneous background EEG activities in discriminating SSVEPs. An SSVEP BCI using frequency coding typically does not have a calibration procedure since the frequency of SSVEPs can be recognized by power spectrum density analysis (PSDA). However, the detection rate can be deteriorated by the spontaneous EEG activities within the same frequency range because phase information of SSVEPs is ignored in frequency detection. To address this problem, this study proposed to incorporate individual SSVEP training data into canonical correlation analysis (CCA) to improve the frequency detection of SSVEPs. An eight-class SSVEP dataset recorded from 10 subjects in a simulated online BCI experiment was used for performance evaluation. Compared to the standard CCA method, the proposed method obtained significantly improved detection accuracy (95.2% vs. 88.4%, p<0.05) and information transfer rates (ITR) (104.6 bits/min vs. 89.1 bits/min, p<0.05). The results suggest that the employment of individual SSVEP training data can significantly improve the detection rate and thereby facilitate the implementation of a high-speed BCI.

Sonora exploratory study for the detection of wheat-leaf rust

NASA Technical Reports Server (NTRS)

Payne, R. W. (Principal Investigator)

1980-01-01

The applicability of LANDSAT remote sensing technology to the detection of a wheat-leaf-rust epidemic in Sonora, Mexico, during 1977 was investigated. LANDSAT data acquired during crop years 1975-76 and 1976-77 were clustered, classified, and analyzed in order to detect agricultural changes. Analysis of 1977 data indicates a significant proportion of the identified wheat is stressed (potentially rust-infected). Additional analyses show a significant increase in fallowing during the year, as well as a substantial decrease in reservoir levels in the Sonora agricultural region. Ground observations are required to substantiate these analyses. The possibility exists that heat-rust is not LANDSAT detectable and that the clusters identified as containing stressed signatures represent different varieties of wheat or perhaps nonwheat crops.

MO-FG-202-06: Improving the Performance of Gamma Analysis QA with Radiomics- Based Image Analysis

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

Wootton, L; Nyflot, M; Ford, E

2016-06-15

Purpose: The use of gamma analysis for IMRT quality assurance has well-known limitations. Traditionally, a simple thresholding technique is used to evaluated passing criteria. However, like any image the gamma distribution is rich in information which thresholding mostly discards. We therefore propose a novel method of analyzing gamma images that uses quantitative image features borrowed from radiomics, with the goal of improving error detection. Methods: 368 gamma images were generated from 184 clinical IMRT beams. For each beam the dose to a phantom was measured with EPID dosimetry and compared to the TPS dose calculated with and without normally distributedmore » (2mm sigma) errors in MLC positions. The magnitude of 17 intensity histogram and size-zone radiomic features were derived from each image. The features that differed most significantly between image sets were determined with ROC analysis. A linear machine-learning model was trained on these features to classify images as with or without errors on 180 gamma images.The model was then applied to an independent validation set of 188 additional gamma distributions, half with and half without errors. Results: The most significant features for detecting errors were histogram kurtosis (p=0.007) and three size-zone metrics (p<1e-6 for each). The sizezone metrics detected clusters of high gamma-value pixels under mispositioned MLCs. The model applied to the validation set had an AUC of 0.8, compared to 0.56 for traditional gamma analysis with the decision threshold restricted to 98% or less. Conclusion: A radiomics-based image analysis method was developed that is more effective in detecting error than traditional gamma analysis. Though the pilot study here considers only MLC position errors, radiomics-based methods for other error types are being developed, which may provide better error detection and useful information on the source of detected errors. This work was partially supported by a grant from the Agency for Healthcare Research and Quality, grant number R18 HS022244-01.« less

Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing.

PubMed

Li, Zibo; Guo, Xinwu; Tang, Lili; Peng, Limin; Chen, Ming; Luo, Xipeng; Wang, Shouman; Xiao, Zhi; Deng, Zhongping; Dai, Lizhong; Xia, Kun; Wang, Jun

2016-10-01

Circulating cell-free DNA (cfDNA) has been considered as a potential biomarker for non-invasive cancer detection. To evaluate the methylation levels of six candidate genes (EGFR, GREM1, PDGFRB, PPM1E, SOX17, and WRN) in plasma cfDNA as biomarkers for breast cancer early detection, quantitative analysis of the promoter methylation of these genes from 86 breast cancer patients and 67 healthy controls was performed by using microfluidic-PCR-based target enrichment and next-generation bisulfite sequencing technology. The predictive performance of different logistic models based on methylation status of candidate genes was investigated by means of the area under the ROC curve (AUC) and odds ratio (OR) analysis. Results revealed that EGFR, PPM1E, and 8 gene-specific CpG sites showed significantly hypermethylation in cancer patients' plasma and significantly associated with breast cancer (OR ranging from 2.51 to 9.88). The AUC values for these biomarkers were ranging from 0.66 to 0.75. Combinations of multiple hypermethylated genes or CpG sites substantially improved the predictive performance for breast cancer detection. Our study demonstrated the feasibility of quantitative measurement of candidate gene methylation in cfDNA by using microfluidic-PCR-based target enrichment and bisulfite next-generation sequencing, which is worthy of further validation and potentially benefits a broad range of applications in clinical oncology practice. Quantitative analysis of methylation pattern of plasma cfDNA by next-generation sequencing might be a valuable non-invasive tool for early detection of breast cancer.

High-throughput DNA microarray detection of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley, Nepal.

PubMed

Inoue, Daisuke; Hinoura, Takuji; Suzuki, Noriko; Pang, Junqin; Malla, Rabin; Shrestha, Sadhana; Chapagain, Saroj Kumar; Matsuzawa, Hiroaki; Nakamura, Takashi; Tanaka, Yasuhiro; Ike, Michihiko; Nishida, Kei; Sei, Kazunari

2015-01-01

Because of heavy dependence on groundwater for drinking water and other domestic use, microbial contamination of groundwater is a serious problem in the Kathmandu Valley, Nepal. This study investigated comprehensively the occurrence of pathogenic bacteria in shallow well groundwater in the Kathmandu Valley by applying DNA microarray analysis targeting 941 pathogenic bacterial species/groups. Water quality measurements found significant coliform (fecal) contamination in 10 of the 11 investigated groundwater samples and significant nitrogen contamination in some samples. The results of DNA microarray analysis revealed the presence of 1-37 pathogen species/groups, including 1-27 biosafety level 2 ones, in 9 of the 11 groundwater samples. While the detected pathogens included several feces- and animal-related ones, those belonging to Legionella and Arthrobacter, which were considered not to be directly associated with feces, were detected prevalently. This study could provide a rough picture of overall pathogenic bacterial contamination in the Kathmandu Valley, and demonstrated the usefulness of DNA microarray analysis as a comprehensive screening tool of a wide variety of pathogenic bacteria.

Identification and detection of anomalies through SSME data analysis

NASA Technical Reports Server (NTRS)

Pereira, Lisa; Ali, Moonis

1990-01-01

The goal of the ongoing research described in this paper is to analyze real-time ground test data in order to identify patterns associated with the anomalous engine behavior, and on the basis of this analysis to develop an expert system which detects anomalous engine behavior in the early stages of fault development. A prototype of the expert system has been developed and tested on the high frequency data of two SSME tests, namely Test #901-0516 and Test #904-044. The comparison of our results with the post-test analyses indicates that the expert system detected the presence of the anomalies in a significantly early stage of fault development.

Using health and demographic surveillance for the early detection of cholera outbreaks: analysis of community- and hospital-based data from Matlab, Bangladesh.

PubMed

Saulnier, Dell D; Persson, Lars-Åke; Streatfield, Peter Kim; Faruque, A S G; Rahman, Anisur

2016-01-01

Cholera outbreaks are a continuing problem in Bangladesh, and the timely detection of an outbreak is important for reducing morbidity and mortality. In Matlab, the ongoing Health and Demographic Surveillance System (HDSS) data records symptoms of diarrhea in children under the age of 5 years at the community level. Cholera surveillance in Matlab currently uses hospital-based data. The objective of this study is to determine whether increases in cholera in Matlab can be detected earlier by using HDSS diarrhea symptom data in a syndromic surveillance analysis, when compared to hospital admissions for cholera. HDSS diarrhea symptom data and hospital admissions for cholera in children under 5 years of age over a 2-year period were analyzed with the syndromic surveillance statistical program EARS (Early Aberration Reporting System). Dates when significant increases in either symptoms or cholera cases occurred were compared to one another. The analysis revealed that there were 43 days over 16 months when the cholera cases or diarrhea symptoms increased significantly. There were 8 months when both data sets detected days with significant increases. In 5 of the 8 months, increases in diarrheal symptoms occurred before increases of cholera cases. The increases in symptoms occurred between 1 and 15 days before the increases in cholera cases. The results suggest that the HDSS survey data may be able to detect an increase in cholera before an increase in hospital admissions is seen. However, there was no direct link between diarrheal symptom increases and cholera cases, and this, as well as other methodological weaknesses, should be taken into consideration.

A Population Study of Gaseous Exoplanets

NASA Astrophysics Data System (ADS)

Tsiaras, A.; Waldmann, I. P.; Zingales, T.; Rocchetto, M.; Morello, G.; Damiano, M.; Karpouzas, K.; Tinetti, G.; McKemmish, L. K.; Tennyson, J.; Yurchenko, S. N.

2018-04-01

We present here the analysis of 30 gaseous extrasolar planets, with temperatures between 600 and 2400 K and radii between 0.35 and 1.9 R Jup. The quality of the HST/WFC3 spatially scanned data combined with our specialized analysis tools allow us to study the largest and most self-consistent sample of exoplanetary transmission spectra to date and examine the collective behavior of warm and hot gaseous planets rather than isolated case studies. We define a new metric, the Atmospheric Detectability Index (ADI) to evaluate the statistical significance of an atmospheric detection and find statistically significant atmospheres in around 16 planets out of the 30 analyzed. For most of the Jupiters in our sample, we find the detectability of their atmospheres to be dependent on the planetary radius but not on the planetary mass. This indicates that planetary gravity plays a secondary role in the state of gaseous planetary atmospheres. We detect the presence of water vapour in all of the statistically detectable atmospheres, and we cannot rule out its presence in the atmospheres of the others. In addition, TiO and/or VO signatures are detected with 4σ confidence in WASP-76 b, and they are most likely present in WASP-121 b. We find no correlation between expected signal-to-noise and atmospheric detectability for most targets. This has important implications for future large-scale surveys.

Microbial community analysis of an Alabama coastal salt marsh impacted by the Deepwater Horizon Oil Spill

NASA Astrophysics Data System (ADS)

Beazley, M. J.; Martinez, R.; Rajan, S.; Powell, J.; Piceno, Y.; Tom, L.; Andersen, G. L.; Hazen, T. C.; Van Nostrand, J. D.; Zhou, J.; Mortazavi, B.; Sobecky, P. A.

2011-12-01

Microbial community responses of an Alabama coastal salt marsh environment to the Deepwater Horizon oil spill were studied by 16S rRNA (PhyloChip) and functional gene (GeoChip) microarray-based analysis. Oil and tar balls associated with the oil spill arrived along the Alabama coast in June 2010. Marsh and inlet sediment samples collected in June, July, and September 2010 from a salt marsh ecosystem at Point Aux Pines Alabama were analyzed to determine if bacterial community structure changed as a result of oil perturbation. Sediment total petroleum hydrocarbon (TPH) concentrations ranged from below detection to 189 mg kg-1 and were randomly dispersed throughout the salt marsh sediments. Total DNA extracted from sediment and particulates were used for PhyloChip and GeoChip hybridization. A total of 4000 to 8000 operational taxonomic units (OTUs) were detected in marsh and inlet samples. Distinctive changes in the number of detectable OTUs were observed between June, July, and September 2010. Surficial inlet sediments demonstrated a significant increase in the total number of OTUs between June and September that correlated with TPH concentrations. The most significant increases in bacterial abundance were observed in the phyla Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. Bacterial richness in marsh sediments also correlated with TPH concentrations with significant changes primarily in Acidobacteria, Actinobacteria, Firmicutes, Fusobacteria, Nitrospirae, and Proteobacteria. GeoChip microarray analysis detected 5000 to 8300 functional genes in marsh and inlet samples. Surficial inlet sediments demonstrated distinctive increases in the number of detectable genes and gene signal intensities in July samples compared to June. Signal intensities increased (> 1.5-fold) in genes associated with petroleum degradation. Genes related to metal resistance, stress, and carbon cycling also demonstrated increases in oiled sediments. This study demonstrates the value of applying phylogenetic and functional gene microarray technology to characterize the extensive microbial diversity of marsh environments. Moreover, this technology provides significant insight into bacterial community responses to anthropogenic oil events.

Dual-model automatic detection of nerve-fibres in corneal confocal microscopy images.

PubMed

Dabbah, M A; Graham, J; Petropoulos, I; Tavakoli, M; Malik, R A

2010-01-01

Corneal Confocal Microscopy (CCM) imaging is a non-invasive surrogate of detecting, quantifying and monitoring diabetic peripheral neuropathy. This paper presents an automated method for detecting nerve-fibres from CCM images using a dual-model detection algorithm and compares the performance to well-established texture and feature detection methods. The algorithm comprises two separate models, one for the background and another for the foreground (nerve-fibres), which work interactively. Our evaluation shows significant improvement (p approximately 0) in both error rate and signal-to-noise ratio of this model over the competitor methods. The automatic method is also evaluated in comparison with manual ground truth analysis in assessing diabetic neuropathy on the basis of nerve-fibre length, and shows a strong correlation (r = 0.92). Both analyses significantly separate diabetic patients from control subjects (p approximately 0).

Combining Trust and Behavioral Analysis to Detect Security Threats in Open Environments

DTIC Science & Technology

2010-11-01

behavioral feature values. This would provide a baseline notional object trust and is formally defined as follows: TO(1)[0, 1] = ∑ 0,n:νbt wtP (S) (8...TO(2)[0, 1] = ∑ wtP (S) · identity(O,P ) (9) 28- 12 RTO-MP-IST-091 Combining Trust and Behavioral Analysis to Detect Security Threats in Open...respectively. The wtP weight function determines the significance of a particular behavioral feature in the final trust calculation. Note that the weight

Medium-based noninvasive preimplantation genetic diagnosis for human α-thalassemias-SEA.

PubMed

Wu, Haitao; Ding, Chenhui; Shen, Xiaoting; Wang, Jing; Li, Rong; Cai, Bing; Xu, Yanwen; Zhong, Yiping; Zhou, Canquan

2015-03-01

To develop a noninvasive medium-based preimplantation genetic diagnosis (PGD) test for α-thalassemias-SEA. The embryos of α-thalassemia-SEA carriers undergoing in vitro fertilization (IVF) were cultured. Single cells were biopsied from blastomeres and subjected to fluorescent gap polymerase chain reaction (PCR) analysis; the spent culture media that contained embryo genomic DNA and corresponding blastocysts as verification were subjected to quantitative-PCR (Q-PCR) detection of α-thalassemia-SEA. The diagnosis efficiency and allele dropout (ADO) ratio were calculated, and the cell-free DNA concentration was quantitatively assessed in the culture medium. The diagnosis efficiency of medium-based α-thalassemias-SEA detection significantly increased compared with that of biopsy-based fluorescent gap PCR analysis (88.6% vs 82.1%, P < 0.05). There is no significant difference regarding ADO ratio between them. The optimal time for medium-based α-thalassemias-SEA detection is Day 5 (D5) following IVF. Medium-based α-thalassemias-SEA detection could represent a novel, quick, and noninvasive approach for carriers to undergo IVF and PGD.

Direct Detection and Identification of Prosthetic Joint Infection Pathogens in Synovial Fluid by Metagenomic Shotgun Sequencing.

PubMed

Ivy, Morgan I; Thoendel, Matthew J; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Hanssen, Arlen D; Abdel, Matthew P; Chia, Nicholas; Yao, Janet Z; Tande, Aaron J; Mandrekar, Jayawant N; Patel, Robin

2018-05-30

Background: Metagenomic shotgun sequencing has the potential to transform how serious infections are diagnosed by offering universal, culture-free pathogen detection. This may be especially advantageous for microbial diagnosis of prosthetic joint infection (PJI) by synovial fluid analysis, since synovial fluid cultures are not universally positive, and synovial fluid is easily obtained pre-operatively. We applied a metagenomics-based approach to synovial fluid in an attempt to detect microorganisms in 168 failed total knee arthroplasties. Results: Genus- and species-level analysis of metagenomic sequencing yielded the known pathogen in 74 (90%) and 68 (83%) of the 82 culture-positive PJIs analyzed, respectively, with testing of two (2%) and three (4%) samples, respectively, yielding additional pathogens not detected by culture. For the 25 culture-negative PJIs tested, genus- and species-level analysis yielded 19 (76%) and 21 (84%) samples with insignificant findings, respectively, and 6 (24%) and 4 (16%) with potential pathogens detected, respectively. Genus- and species-level analysis of the 60 culture-negative aseptic failure cases yielded 53 (88.3%) and 56 (93.3%) cases with insignificant findings, and 7 (11.7%) and 4 (6.7%) with potential clinically-significant organisms detected, respectively. There was one case of aseptic failure with synovial fluid culture growth; metagenomic analysis showed insignificant findings, suggesting possible synovial fluid culture contamination. Conclusion: Metagenomic shotgun sequencing can detect pathogens involved in PJI when applied to synovial fluid and may be particularly useful for culture-negative cases. Copyright © 2018 American Society for Microbiology.

Analysis of user characteristics related to drop-off detection with long cane

PubMed Central

Kim, Dae Shik; Emerson, Robert Wall; Curtis, Amy

2010-01-01

This study examined how user characteristics affect drop-off detection with the long cane. A mixed-measures design with block randomization was used for the study, in which 32 visually impaired adults attempted to detect the drop-offs using different cane techniques. Younger cane users detected drop-offs significantly more reliably (mean +/− standard deviation = 74.2% +/− 11.2% of the time) than older cane users (60.9% +/− 10.8%), p = 0.009. The drop-off detection threshold of the younger participants (5.2 +/− 2.1 cm) was also statistically significantly smaller than that of the older participants (7.9 +/− 2.2 cm), p = 0.007. Those with early-onset visual impairment (78.0% +/− 9.0%) also detected drop-offs significantly more reliably than those with later-onset visual impairment (67.3% +/− 12.4%), p = 0.01. No interaction occurred between examined user characteristics (age and age at onset of visual impairment) and the type of cane technique used in drop-off detection. The findings of the study may help orientation and mobility specialists select appropriate cane techniques in accordance with the cane user’s age and onset of visual impairment. PMID:20665349

Human papillomavirus detection with genotyping by the cobas and Aptima assays: Significant differences in HPV 16 detection?

PubMed

Chorny, Joseph A; Frye, Teresa C; Fisher, Beth L; Remmers, Carol L

2018-03-23

The primary high-risk human papillomavirus (hrHPV) assays in the United States are the cobas (Roche) and the Aptima (Hologic). The cobas assay detects hrHPV by DNA analysis while the Aptima detects messenger RNA (mRNA) oncogenic transcripts. As the Aptima assay identifies oncogenic expression, it should have a lower rate of hrHPV and genotype detection. The Kaiser Permanente Regional Reference Laboratory in Denver, Colorado changed its hrHPV assay from the cobas to the Aptima assay. The rates of hrHPV detection and genotyping were compared over successive six-month periods. The overall hrHPV detection rates by the two platforms were similar (9.5% versus 9.1%) and not statistically different. For genotyping, the HPV 16 rate by the cobas was 1.6% and by the Aptima it was 1.1%. These differences were statistically different with the Aptima detecting nearly one-third less HPV 16 infections. With the HPV 18 and HPV 18/45, there was a slightly higher detection rate of HPV 18/45 by the Aptima platform (0.5% versus 0.9%) and this was statistically significant. While HPV 16 represents a low percentage of hrHPV infections, it was detected significantly less by the Aptima assay compared to the cobas assay. This has been previously reported, although not highlighted. Given the test methodologies, one would expect the Aptima to detect less HPV 16. This difference appears to be mainly due to a significantly increased number of non-oncogenic HPV 16 infections detected by the cobas test as there were no differences in HPV 16 detection rates in the high-grade squamous intraepithelial lesions indicating that the two tests have similar sensitivities for oncogenic HPV 16. © 2018 Wiley Periodicals, Inc.

Multi-complexity ensemble measures for gait time series analysis: application to diagnostics, monitoring and biometrics.

PubMed

Gavrishchaka, Valeriy; Senyukova, Olga; Davis, Kristina

2015-01-01

Previously, we have proposed to use complementary complexity measures discovered by boosting-like ensemble learning for the enhancement of quantitative indicators dealing with necessarily short physiological time series. We have confirmed robustness of such multi-complexity measures for heart rate variability analysis with the emphasis on detection of emerging and intermittent cardiac abnormalities. Recently, we presented preliminary results suggesting that such ensemble-based approach could be also effective in discovering universal meta-indicators for early detection and convenient monitoring of neurological abnormalities using gait time series. Here, we argue and demonstrate that these multi-complexity ensemble measures for gait time series analysis could have significantly wider application scope ranging from diagnostics and early detection of physiological regime change to gait-based biometrics applications.

Efficacy of clinical and radiological methods to identify second mesiobuccal canals in maxillary first molars.

PubMed

Abuabara, Allan; Baratto-Filho, Flares; Aguiar Anele, Juliana; Leonardi, Denise Piotto; Sousa-Neto, Manoel Damião

2013-01-01

The success of endodontic treatment depends on the identification of all root canals. Technological advances have facilitated this process as well as the assessment of internal anatomical variations. The aim of this study was to compare the efficacy of clinical and radiological methods in locating second mesiobuccal canals (MB2) in maxillary first molars. Fifty patients referred for analysis; access and clinical analysis; cone-beam endodontic treatment of their maxillary first molars were submitted to the following assessments: analysis; access and clinical analysis; cone-beam computed tomography (CBCT); post-CBCT clinical analysis; clinical analysis using an operating microscope; and clinical analysis after Start X ultrasonic inserts in teeth with negative results in all previous analyses. Periapical radiographic analysis revealed the presence of MB2 in four (8%) teeth, clinical analysis in 25 (50%), CBCT analysis in 27 (54%) and clinical analysis following CBCT and using an operating microscope in 27 (54%) and 29 (58%) teeth, respectively. The use of Start X ultrasonic inserts allowed one to detect two additional teeth with MB2 (62%). According to Vertucci's classification 48% of the mesiobuccal canals found were type I, 28% type II, 18% type IV and 6% type V. Statistical analysis showed no significant differences (p > 0.5) in the ability of CBCT to detect MB2 canals when compared with clinical assessment with or without an operating microscope. A significant difference (p < 0.001)was found only between periapical radiography and clinical/CBCT evaluations. Combined use of different methods increased the detection ofthe second canal in MB roots, but without statistical difference among CBCT, operating microscope, Start X and clinical analysis.

Continuous ECG monitoring for tracking down atrial fibrillation after stroke: Holter or automated analysis strategy?

PubMed

Suissa, Laurent; Lachaud, Sylvain; Mahagne, Marie-Hélène

2014-01-01

Tracking down atrial fibrillation (AF) in the stroke unit is a relevant challenge for the prevention of recurrent AF-related stroke. The optimal terms of use of continuous ECG monitoring (CEM) are unknown. We compared 24-hour routine Holter ECG with two different CEM analysis strategies for AF detection. We prospectively enrolled consecutive ischemic stroke patients. All AF-naïve patients received CEM during hospitalization. Two methods for reading CEM data were compared: manual analysis using the Holter function (hCEM) and semiautomated analysis using software (aCEM). The McNemar test was used to compare AF detection rates. Of the 362 patients included, 58 (16.0%) were non-AF-naïve patients and 304 were AF-naïve patients. AF-Naïve patients underwent CEM with a median duration of 5.3 days (3.4-9.7). We detected 22 new AF cases (7.2%) with first-24-hour hCEM, 31 (10.2%) with aCEM, and 42 (13.8%) with hCEM. hCEM and aCEM both significantly increased the AF detection rate compared to first-24-hour hCEM. hCEM detected more new AF cases than aCEM (+3.6%, p = 0.003). In stroke patients, early and prolonged aCEM and hCEM both increase the AF detection rate compared to first-24-hour hCEM. hCEM gives the best AF detection rate. We suggest that in aCEM, detection based only on the ventricular rhythm analysis explains its lower specificity and sensitivity. © 2014 S. Karger AG, Basel.

"Textural analysis of multiparametric MRI detects transition zone prostate cancer".

PubMed

Sidhu, Harbir S; Benigno, Salvatore; Ganeshan, Balaji; Dikaios, Nikos; Johnston, Edward W; Allen, Clare; Kirkham, Alex; Groves, Ashley M; Ahmed, Hashim U; Emberton, Mark; Taylor, Stuart A; Halligan, Steve; Punwani, Shonit

2017-06-01

To evaluate multiparametric-MRI (mpMRI) derived histogram textural-analysis parameters for detection of transition zone (TZ) prostatic tumour. Sixty-seven consecutive men with suspected prostate cancer underwent 1.5T mpMRI prior to template-mapping-biopsy (TPM). Twenty-six men had 'significant' TZ tumour. Two radiologists in consensus matched TPM to the single axial slice best depicting tumour, or largest TZ diameter for those with benign histology, to define single-slice whole TZ-regions-of-interest (ROIs). Textural-parameter differences between single-slice whole TZ-ROI containing significant tumour versus benign/insignificant tumour were analysed using Mann Whitney U test. Diagnostic accuracy was assessed by receiver operating characteristic area under curve (ROC-AUC) analysis cross-validated with leave-one-out (LOO) analysis. ADC kurtosis was significantly lower (p < 0.001) in TZ containing significant tumour with ROC-AUC 0.80 (LOO-AUC 0.78); the difference became non-significant following exclusion of significant tumour from single-slice whole TZ-ROI (p = 0.23). T1-entropy was significantly lower (p = 0.004) in TZ containing significant tumour with ROC-AUC 0.70 (LOO-AUC 0.66) and was unaffected by excluding significant tumour from TZ-ROI (p = 0.004). Combining these parameters yielded ROC-AUC 0.86 (LOO-AUC 0.83). Textural features of the whole prostate TZ can discriminate significant prostatic cancer through reduced kurtosis of the ADC-histogram where significant tumour is included in TZ-ROI and reduced T1 entropy independent of tumour inclusion. • MR textural features of prostate transition zone may discriminate significant prostatic cancer. • Transition zone (TZ) containing significant tumour demonstrates a less peaked ADC histogram. • TZ containing significant tumour reveals higher post-contrast T1-weighted homogeneity. • The utility of MR texture analysis in prostate cancer merits further investigation.

The Effect of Right Colon Retroflexion on Adenoma Detection: A Systematic Review and Meta-analysis.

PubMed

Cohen, Jonah; Grunwald, Douglas; Grossberg, Laurie B; Sawhney, Mandeep S

2017-10-01

Although colonoscopy with polypectomy can prevent up to 80% of colorectal cancers, a significant adenoma miss rate still exists, particularly in the right colon. Previous studies addressing right colon retroflexion have revealed discordant evidence regarding the benefit of this maneuver on adenoma detection with concomitant concerns about safety and rates of maneuver success. In this meta-analysis, we sought to determine the effect of right colon retroflexion on improving adenoma detection compared with conventional colonoscopy without retroflexion, as well as determine the rates of retroflexion maneuver success and adverse events. Multiple databases including MEDLINE, Embase, and Web of Science were searched for studies on right colon retroflexion and its impact on adenoma detection compared with conventional colonoscopy. Pooled analyses of adenoma detection and retroflexion success were based on mixed-effects and random-effects models with heterogeneity analyses. Eight studies met the inclusion criteria (N=3660). The primary analysis comparing colonoscopy with right-sided retroflexion versus conventional colonoscopy to determine the per-adenoma miss rate in the right colon was 16.9% (95% confidence interval, 12.5%-22.5%). The overall rate of successful retroflexion was 91.9% (95% confidence interval, 86%-95%) and rate of adverse events was 0.03%. Colonoscopy with right-sided retroflexion significantly increases the detection of adenomas in the right colon compared with conventional colonoscopy with a high rate of maneuver success and small risk of adverse events. Thus, reexamination of the right colon in retroflexed view should be strongly considered in future standard of care colonoscopy guidelines for quality improvement in colon cancer prevention.

Highly sensitive fluorescence quantitative detection of specific DNA sequences with molecular beacons and nucleic acid dye SYBR Green I.

PubMed

Xiang, Dongshan; Zhai, Kun; Xiang, Wenjun; Wang, Lianzhi

2014-11-01

A highly sensitive fluorescence method of quantitative detection for specific DNA sequence is developed based on molecular beacon (MB) and nucleic acid dye SYBR Green I by synchronous fluorescence analysis. It is demonstrated by an oligonucleotide sequence of wild-type HBV (target DNA) as a model system. In this strategy, the fluorophore of MB is designed to be 6-carboxyfluorescein group (FAM), and the maximum excitation wavelength and maximum emission wavelength are both very close to that of SYBR Green I. In the presence of targets DNA, the MBs hybridize with the targets DNA and form double-strand DNA (dsDNA), the fluorophore FAM is separated from the quencher BHQ-1, thus the fluorophore emit fluorescence. At the same time, SYBR Green I binds to dsDNA, the fluorescence intensity of SYBR Green I is significantly enhanced. When targets DNA are detected by synchronous fluorescence analysis, the fluorescence peaks of FAM and SYBR Green I overlap completely, so the fluorescence signal of system will be significantly enhanced. Thus, highly sensitive fluorescence quantitative detection for DNA can be realized. Under the optimum conditions, the total fluorescence intensity of FAM and SYBR Green I exhibits good linear dependence on concentration of targets DNA in the range from 2×10(-11) to 2.5×10(-9)M. The detection limit of target DNA is estimated to be 9×10(-12)M (3σ). Compared with previously reported methods of detection DNA with MB, the proposed method can significantly enhance the detection sensitivity. Copyright © 2014 Elsevier B.V. All rights reserved.

MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

DOE PAGES

Chien, Chih-Yi; Chang, Ching-Wei; Tsai, Chen-An; ...

2014-01-01

Gene semore » t analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2) The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes the P values and FDR (false discovery rate) q -value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online.« less

AGILE detection of enhanced gamma-ray emission from the blazar 3C 279

NASA Astrophysics Data System (ADS)

Cardillo, M.; Verrecchia, F.; Pittori, C.; Lucarelli, F.; Ursi, A.; Piano, G.; Minervini, G.; Bulgarelli, A.; Fioretti, V.; Parmiggiani, N.; Tavani, M.; Munar-Adrover, P.; Donnarumma, I.; Vercellone, S.; Striani, E.; Cardillo, M.; Gianotti, F.; Trifoglio, M.; Giuliani, A.; Mereghetti, S.; Caraveo, P.; Perotti, F.; Chen, A.; Argan, A.; Costa, E.; Del Monte, E.; Evangelista, Y.; Feroci, M.; Lazzarotto, F.; Lapshov, I.; Pacciani, L.; Soffitta, P.; Sabatini, S.; Vittorini, V.; Pucella, G.; Rapisarda, M.; Di Cocco, G.; Fuschino, F.; Galli, M.; Labanti, C.; Marisaldi, M.; Pellizzoni, A.; Pilia, M.; Trois, A.; Barbiellini, G.; Vallazza, E.; Longo, F.; Morselli, A.; Picozza, P.; Prest, M.; Lipari, P.; Zanello, D.; Cattaneo, P. W.; Rappoldi, A.; Colafrancesco, S.; Ferrari, A.; Paoletti, F.; Antonelli, A.; Giommi, P.; Salotti, L.; Valentini, G.; D'Amico, F.

2018-06-01

AGILE is detecting enhanced gamma-ray emission above 100 MeV from the blazar 3C 279. Integrating from 2018-06-03 07:56:19 UT to 2018-06-05 07:56:19 UT, a preliminary maximum likelihood analysis yields a detection at a flux F(E > 100 MeV)=(7.0 +/- 1.5) x 10^-6 ph cm^-2 s^-1 and a significance greater than 7 sigma.

Cost-Effectiveness Analysis of Three Leprosy Case Detection Methods in Northern Nigeria

PubMed Central

Ezenduka, Charles; Post, Erik; John, Steven; Suraj, Abdulkarim; Namadi, Abdulahi; Onwujekwe, Obinna

2012-01-01

Background Despite several leprosy control measures in Nigeria, child proportion and disability grade 2 cases remain high while new cases have not significantly reduced, suggesting continuous spread of the disease. Hence, there is the need to review detection methods to enhance identification of early cases for effective control and prevention of permanent disability. This study evaluated the cost-effectiveness of three leprosy case detection methods in Northern Nigeria to identify the most cost-effective approach for detection of leprosy. Methods A cross-sectional study was carried out to evaluate the additional benefits of using several case detection methods in addition to routine practice in two north-eastern states of Nigeria. Primary and secondary data were collected from routine practice records and the Nigerian Tuberculosis and Leprosy Control Programme of 2009. The methods evaluated were Rapid Village Survey (RVS), Household Contact Examination (HCE) and Traditional Healers incentive method (TH). Effectiveness was measured as number of new leprosy cases detected and cost-effectiveness was expressed as cost per case detected. Costs were measured from both providers' and patients' perspectives. Additional costs and effects of each method were estimated by comparing each method against routine practise and expressed as incremental cost-effectiveness ratio (ICER). All costs were converted to the U.S. dollar at the 2010 exchange rate. Univariate sensitivity analysis was used to evaluate uncertainties around the ICER. Results The ICER for HCE was $142 per additional case detected at all contact levels and it was the most cost-effective method. At ICER of $194 per additional case detected, THs method detected more cases at a lower cost than the RVS, which was not cost-effective at $313 per additional case detected. Sensitivity analysis showed that varying the proportion of shared costs and subsistent wage for valuing unpaid time did not significantly change the results. Conclusion Complementing routine practice with household contact examination is the most cost-effective approach to identify new leprosy cases and we recommend that, depending on acceptability and feasibility, this intervention is introduced for improved case detection in Northern Nigeria. PMID:23029580

Edge detection and localization with edge pattern analysis and inflection characterization

NASA Astrophysics Data System (ADS)

Jiang, Bo

2012-05-01

In general edges are considered to be abrupt changes or discontinuities in two dimensional image signal intensity distributions. The accuracy of front-end edge detection methods in image processing impacts the eventual success of higher level pattern analysis downstream. To generalize edge detectors designed from a simple ideal step function model to real distortions in natural images, research on one dimensional edge pattern analysis to improve the accuracy of edge detection and localization proposes an edge detection algorithm, which is composed by three basic edge patterns, such as ramp, impulse, and step. After mathematical analysis, general rules for edge representation based upon the classification of edge types into three categories-ramp, impulse, and step (RIS) are developed to reduce detection and localization errors, especially reducing "double edge" effect that is one important drawback to the derivative method. But, when applying one dimensional edge pattern in two dimensional image processing, a new issue is naturally raised that the edge detector should correct marking inflections or junctions of edges. Research on human visual perception of objects and information theory pointed out that a pattern lexicon of "inflection micro-patterns" has larger information than a straight line. Also, research on scene perception gave an idea that contours have larger information are more important factor to determine the success of scene categorization. Therefore, inflections or junctions are extremely useful features, whose accurate description and reconstruction are significant in solving correspondence problems in computer vision. Therefore, aside from adoption of edge pattern analysis, inflection or junction characterization is also utilized to extend traditional derivative edge detection algorithm. Experiments were conducted to test my propositions about edge detection and localization accuracy improvements. The results support the idea that these edge detection method improvements are effective in enhancing the accuracy of edge detection and localization.

Deep learning on temporal-spectral data for anomaly detection

NASA Astrophysics Data System (ADS)

Ma, King; Leung, Henry; Jalilian, Ehsan; Huang, Daniel

2017-05-01

Detecting anomalies is important for continuous monitoring of sensor systems. One significant challenge is to use sensor data and autonomously detect changes that cause different conditions to occur. Using deep learning methods, we are able to monitor and detect changes as a result of some disturbance in the system. We utilize deep neural networks for sequence analysis of time series. We use a multi-step method for anomaly detection. We train the network to learn spectral and temporal features from the acoustic time series. We test our method using fiber-optic acoustic data from a pipeline.

Is High Resolution Melting Analysis (HRMA) Accurate for Detection of Human Disease-Associated Mutations? A Meta Analysis

PubMed Central

Ma, Feng-Li; Jiang, Bo; Song, Xiao-Xiao; Xu, An-Gao

2011-01-01

Background High Resolution Melting Analysis (HRMA) is becoming the preferred method for mutation detection. However, its accuracy in the individual clinical diagnostic setting is variable. To assess the diagnostic accuracy of HRMA for human mutations in comparison to DNA sequencing in different routine clinical settings, we have conducted a meta-analysis of published reports. Methodology/Principal Findings Out of 195 publications obtained from the initial search criteria, thirty-four studies assessing the accuracy of HRMA were included in the meta-analysis. We found that HRMA was a highly sensitive test for detecting disease-associated mutations in humans. Overall, the summary sensitivity was 97.5% (95% confidence interval (CI): 96.8–98.5; I2 = 27.0%). Subgroup analysis showed even higher sensitivity for non-HR-1 instruments (sensitivity 98.7% (95%CI: 97.7–99.3; I2 = 0.0%)) and an eligible sample size subgroup (sensitivity 99.3% (95%CI: 98.1–99.8; I2 = 0.0%)). HRMA specificity showed considerable heterogeneity between studies. Sensitivity of the techniques was influenced by sample size and instrument type but by not sample source or dye type. Conclusions/Significance These findings show that HRMA is a highly sensitive, simple and low-cost test to detect human disease-associated mutations, especially for samples with mutations of low incidence. The burden on DNA sequencing could be significantly reduced by the implementation of HRMA, but it should be recognized that its sensitivity varies according to the number of samples with/without mutations, and positive results require DNA sequencing for confirmation. PMID:22194806

Some findings on the applications of ERTS and Skylab imagery for metropolitan land use analysis

NASA Technical Reports Server (NTRS)

Alexander, R. H. (Principal Investigator); Milazzo, V. A.

1974-01-01

The author has identified the following significant results. Work undertaken on a three-sensor land use data evaluation for a portion of the Phoenix area is reported. Analyses between land use data generated from 1970 high altitude photography and that detectable from ERTS and Skylab, especially in terms of changes in land use indicate that ERTS and Skylab imagery can be used effectively to detect and identify areas of post-1970 land use change, especially those documenting urban expansion at the rural-urban fringe. Significant preliminary findings on the utility of ERTS and Skylab data for metropolitan land use analysis, substantiated by evaluation with 1970 and 1972 ground control land use data are reported.

Integrating drivers influencing the detection of plant pests carried in the international cut flower trade.

PubMed

Areal, F J; Touza, J; MacLeod, A; Dehnen-Schmutz, K; Perrings, C; Palmieri, M G; Spence, N J

2008-12-01

This paper analyses the cut flower market as an example of an invasion pathway along which species of non-indigenous plant pests can travel to reach new areas. The paper examines the probability of pest detection by assessing information on pest detection and detection effort associated with the import of cut flowers. We test the link between the probability of plant pest arrivals, as a precursor to potential invasion, and volume of traded flowers using count data regression models. The analysis is applied to the UK import of specific genera of cut flowers from Kenya between 1996 and 2004. There is a link between pest detection and the Genus of cut flower imported. Hence, pest detection efforts should focus on identifying and targeting those imported plants with a high risk of carrying pest species. For most of the plants studied, efforts allocated to inspection have a significant influence on the probability of pest detection. However, by better targeting inspection efforts, it is shown that plant inspection effort could be reduced without increasing the risk of pest entry. Similarly, for most of the plants analysed, an increase in volume traded will not necessarily lead to an increase in the number of pests entering the UK. For some species, such as Carthamus and Veronica, the volume of flowers traded has a significant and positive impact on the likelihood of pest detection. We conclude that analysis at the rank of plant Genus is important both to understand the effectiveness of plant pest detection efforts and consequently to manage the risk of introduction of non-indigenous species.

Differences in Looking at Own- and Other-Race Faces Are Subtle and Analysis-Dependent: An Account of Discrepant Reports.

PubMed

Arizpe, Joseph; Kravitz, Dwight J; Walsh, Vincent; Yovel, Galit; Baker, Chris I

2016-01-01

The Other-Race Effect (ORE) is the robust and well-established finding that people are generally poorer at facial recognition of individuals of another race than of their own race. Over the past four decades, much research has focused on the ORE because understanding this phenomenon is expected to elucidate fundamental face processing mechanisms and the influence of experience on such mechanisms. Several recent studies of the ORE in which the eye-movements of participants viewing own- and other-race faces were tracked have, however, reported highly conflicting results regarding the presence or absence of differential patterns of eye-movements to own- versus other-race faces. This discrepancy, of course, leads to conflicting theoretical interpretations of the perceptual basis for the ORE. Here we investigate fixation patterns to own- versus other-race (African and Chinese) faces for Caucasian participants using different analysis methods. While we detect statistically significant, though subtle, differences in fixation pattern using an Area of Interest (AOI) approach, we fail to detect significant differences when applying a spatial density map approach. Though there were no significant differences in the spatial density maps, the qualitative patterns matched the results from the AOI analyses reflecting how, in certain contexts, Area of Interest (AOI) analyses can be more sensitive in detecting the differential fixation patterns than spatial density analyses, due to spatial pooling of data with AOIs. AOI analyses, however, also come with the limitation of requiring a priori specification. These findings provide evidence that the conflicting reports in the prior literature may be at least partially accounted for by the differences in the statistical sensitivity associated with the different analysis methods employed across studies. Overall, our results suggest that detection of differences in eye-movement patterns can be analysis-dependent and rests on the assumptions inherent in the given analysis.

Differences in Looking at Own- and Other-Race Faces Are Subtle and Analysis-Dependent: An Account of Discrepant Reports

PubMed Central

Arizpe, Joseph; Kravitz, Dwight J.; Walsh, Vincent; Yovel, Galit; Baker, Chris I.

2016-01-01

The Other-Race Effect (ORE) is the robust and well-established finding that people are generally poorer at facial recognition of individuals of another race than of their own race. Over the past four decades, much research has focused on the ORE because understanding this phenomenon is expected to elucidate fundamental face processing mechanisms and the influence of experience on such mechanisms. Several recent studies of the ORE in which the eye-movements of participants viewing own- and other-race faces were tracked have, however, reported highly conflicting results regarding the presence or absence of differential patterns of eye-movements to own- versus other-race faces. This discrepancy, of course, leads to conflicting theoretical interpretations of the perceptual basis for the ORE. Here we investigate fixation patterns to own- versus other-race (African and Chinese) faces for Caucasian participants using different analysis methods. While we detect statistically significant, though subtle, differences in fixation pattern using an Area of Interest (AOI) approach, we fail to detect significant differences when applying a spatial density map approach. Though there were no significant differences in the spatial density maps, the qualitative patterns matched the results from the AOI analyses reflecting how, in certain contexts, Area of Interest (AOI) analyses can be more sensitive in detecting the differential fixation patterns than spatial density analyses, due to spatial pooling of data with AOIs. AOI analyses, however, also come with the limitation of requiring a priori specification. These findings provide evidence that the conflicting reports in the prior literature may be at least partially accounted for by the differences in the statistical sensitivity associated with the different analysis methods employed across studies. Overall, our results suggest that detection of differences in eye-movement patterns can be analysis-dependent and rests on the assumptions inherent in the given analysis. PMID:26849447

Detection of glycosylation abnormality in rheumatoid IgG using N-acetylglucosamine-specific Psathyrella velutina lectin.

PubMed

Tsuchiya, N; Endo, T; Matsuta, K; Yoshinoya, S; Takeuchi, F; Nagano, Y; Shiota, M; Furukawa, K; Kochibe, N; Ito, K

1993-07-15

Although the galactose deficiency in the Asn297-linked sugar chains of serum IgG from patients with rheumatoid arthritis (RA) has been established, structural analysis of sugar chains has not been readily available. Psathyrella velutina lectin (PVL) preferentially interacts with the N-acetylglucosamine beta 1-->2Man group, exposed at the termini of sugar chains in agalacto IgG. Biotinylated PVL reacted strongly in Western blotting with H chains of IgG derived from patients with RA. An ELISA-based assay for the detection of agalacto IgG was developed using recombinant protein G and biotinylated PVL in combination, and the screening of patients' sera was performed. PVL binding of serum IgG significantly correlated with percentage of galactose-deficient IgG determined by the structural analysis. Age-related slight increase in PVL binding was observed among normal controls. Patients with RA showed significantly higher PVL binding (37.90 +/- 42.25 U/ml, n = 93) as compared with normal controls (5.75 +/- 2.92 U/ml, n = 112) (p = 0.0001). Patients with SLE showed lower but still significant PVL binding (17.86 +/- 5.18 U/ml, n = 10, p = 0.0001). PVL binding correlated with C-reactive protein level in serial analysis of individual RA patients, and was significantly higher in the synovial fluid compared with paired serum samples. PVL binding assay may provide an ideal tool for the simple and sensitive detection of agalacto IgG.

Three-dimensional images contribute to the diagnosis of mucous retention cyst in maxillary sinus.

PubMed

Donizeth-Rodrigues, Cleomar; Fonseca-Da Silveira, Márcia; Gonçalves-De Alencar, Ana-Helena; Garcia-Santos-Silva, Maria-Alves; Francisco-De-Mendonça, Elismauro; Estrela, Carlos

2013-01-01

To evaluate the detection of mucous retention cyst of maxillary sinus (MRCMS) using panoramic radiography and cone beam computed tomography (CBCT). A digital database with 6,000 panoramic radiographs was reviewed for MRCMS. Suggestive images of MRCMS were detected on 185 radiographs, and patients were located and invited to return for follow-up. Thirty patients returned, and control panoramic radiographs were obtained 6 to 46 months after the initial radiograph. When MRCMS was found on control radiographs, CBCT scans were obtained. Cysts were measured and compared on radiographs and scans. The Wilcoxon, Spearman and Kolmorogov-Smirnov tests were used for statistical analysis. The level of significance was set at 5%. There were statistically significant differences between the two methods (p<0.05): 23 MRCMS detected on panoramic radiographs were confirmed by CBCT, but 5 MRCMS detected on CBCT images had not been identified by panoramic radiography. Eight MRCMS detected on control radiographs were not confirmed by CBCT. MRCMS size differences from initial to control panoramic radiographs and CBCT scans were not statistically significant (p= 0.617 and p= 0.626). The correlation between time and MRCMS size differences was not significant (r = -0.16, p = 0.381). CBCT scanning detect MRCMS more accurately than panoramic radiography.

Aliphatic long chain quaternary ammonium compounds analysis by ion-pair chromatography coupled with suppressed conductivity and UV detection in lysing reagents for blood cell analysers.

PubMed

Giovannelli, D; Abballe, F

2005-08-26

A method has been developed which allows simultaneous determination of three linear alkyl trimethylammonium salts. Dodecyltrimethylammonium chloride, tetradecyltrimethylammonium bromide and hexadecyltrimethylammonium chloride are widely used as main active ingredients of lysing reagents for blood cell analyzers which perform white blood cells differential determination into two or more sub-populations by impedance analysis. The ion-pair on styrene-divinyl benzene chromatographic phase looks like a suitable, reliable and long term stable tool for separation of such quaternary compounds. The detection based on suppressed conductivity was chosen because of the lack of significance chromophores. A micromembrane suppressor device compatible with high solvent concentration (up to 80%) was used in order to minimize the conductivity background before the detection. In the present work we show how the chemical post column derivatization makes the alkyl chain detectable also by UV direct detection at 210 nm.

Trend analysis of long-term temperature time series in the Greater Toronto Area (GTA)

NASA Astrophysics Data System (ADS)

Mohsin, Tanzina; Gough, William A.

2010-08-01

As the majority of the world’s population is living in urban environments, there is growing interest in studying local urban climates. In this paper, for the first time, the long-term trends (31-162 years) of temperature change have been analyzed for the Greater Toronto Area (GTA). Annual and seasonal time series for a number of urban, suburban, and rural weather stations are considered. Non-parametric statistical techniques such as Mann-Kendall test and Theil-Sen slope estimation are used primarily for the assessing of the significance and detection of trends, and the sequential Mann test is used to detect any abrupt climate change. Statistically significant trends for annual mean and minimum temperatures are detected for almost all stations in the GTA. Winter is found to be the most coherent season contributing substantially to the increase in annual minimum temperature. The analyses of the abrupt changes in temperature suggest that the beginning of the increasing trend in Toronto started after the 1920s and then continued to increase to the 1960s. For all stations, there is a significant increase of annual and seasonal (particularly winter) temperatures after the 1980s. In terms of the linkage between urbanization and spatiotemporal thermal patterns, significant linear trends in annual mean and minimum temperature are detected for the period of 1878-1978 for the urban station, Toronto, while for the rural counterparts, the trends are not significant. Also, for all stations in the GTA that are situated in all directions except south of Toronto, substantial temperature change is detected for the periods of 1970-2000 and 1989-2000. It is concluded that the urbanization in the GTA has significantly contributed to the increase of the annual mean temperatures during the past three decades. In addition to urbanization, the influence of local climate, topography, and larger scale warming are incorporated in the analysis of the trends.

Use of power analysis to develop detectable significance criteria for sea urchin toxicity tests

USGS Publications Warehouse

Carr, R.S.; Biedenbach, J.M.

1999-01-01

When sufficient data are available, the statistical power of a test can be determined using power analysis procedures. The term “detectable significance” has been coined to refer to this criterion based on power analysis and past performance of a test. This power analysis procedure has been performed with sea urchin (Arbacia punctulata) fertilization and embryological development data from sediment porewater toxicity tests. Data from 3100 and 2295 tests for the fertilization and embryological development tests, respectively, were used to calculate the criteria and regression equations describing the power curves. Using Dunnett's test, a minimum significant difference (MSD) (β = 0.05) of 15.5% and 19% for the fertilization test, and 16.4% and 20.6% for the embryological development test, for α ≤ 0.05 and α ≤ 0.01, respectively, were determined. The use of this second criterion reduces type I (false positive) errors and helps to establish a critical level of difference based on the past performance of the test.

Monitoring environmental pollutants by microchip capillary electrophoresis with electrochemical detection

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

Chen, Gang; Lin, Yuehe; Wang, Joseph

2006-01-15

This is a review article. During the past decade, significant progress in the development of miniaturized microfluidic systems has Occurred due to the numerous advantages of microchip analysis. This review focuses on recent advances and the key strategies in microchip capillary electrophoresis (CE) with electrochemical detection (ECD) for separating and detecting a variety of environmental pollutants. The subjects covered include the fabrication of microfluidic chips, ECD, typical applications of microchip CE with ECD in environmental analysis, and future prospects. It is expected that microchip CE-ECD will become a powerful tool in the environmental field and will lead to the creationmore » of truly portable devices.« less

Early Oscillation Detection for Hybrid DC/DC Converter Fault Diagnosis

NASA Technical Reports Server (NTRS)

Wang, Bright L.

2011-01-01

This paper describes a novel fault detection technique for hybrid DC/DC converter oscillation diagnosis. The technique is based on principles of feedback control loop oscillation and RF signal modulations, and Is realized by using signal spectral analysis. Real-circuit simulation and analytical study reveal critical factors of the oscillation and indicate significant correlations between the spectral analysis method and the gain/phase margin method. A stability diagnosis index (SDI) is developed as a quantitative measure to accurately assign a degree of stability to the DC/DC converter. This technique Is capable of detecting oscillation at an early stage without interfering with DC/DC converter's normal operation and without limitations of probing to the converter.

Stereometric parameters change vs. Topographic Change Analysis (TCA) agreement in Heidelberg Retina Tomography III (HRT-3) early detection of clinical significant glaucoma progression.

PubMed

Dascalu, A M; Cherecheanu, A P; Stana, D; Voinea, L; Ciuluvica, R; Savlovschi, C; Serban, D

2014-01-01

to investigate the sensitivity and specificity of the stereometric parameters change analysis vs. Topographic Change Analysis in early detection of glaucoma progression. 81 patients with POAG were monitored for 4 years (GAT monthly, SAP at every 6 months, optic disc photographs and HRT3 yearly). The exclusion criteria were other optic disc or retinal pathology; topographic standard deviation (TSD>30; inter-test variation of reference height>25 μm. The criterion for structural progression was the following: at least 20 adjacent super-pixels with a clinically significant decrease in height (>5%). 16 patients of the total 81 presented structural progression on TCA. The most useful stereometric parameters for the early detection of glaucoma progression were the following: Rim Area change (sensitivity 100%, specificity 74.2% for a "cut-off " value of -0.05), C/D Area change (sensitivity 85.7%, specificity 71.5% for a "cut off " value of 0.02), C/D linear change (sensitivity 85.7%, specificity 71.5% for a "cut-off " value of 0.02), Rim Volume change (sensitivity 71.4%, specificity 88.8% for a "cut-off " value of -0.04). RNFL Thickness change (<0) was highly sensitive (82%), but less specific for glaucoma progression (45,2%). Changes of the other stereometric parameters have a limited diagnostic value for the early detection of glaucoma progression. TCA is a valuable tool for the assessment of the structural progression in glaucoma patients and its inter-test variability is low. On long-term, the quantitative analysis according to stereometric parameters change is also very important. The most relevant parameters to detect progression are RA, C/D Area, Linear C/D and RV.

Pathological changes in Alzheimer"s brain evaluated with fluorescence emission analysis (FEA)

NASA Astrophysics Data System (ADS)

Christov, Alexander; Ottman, Todd; Grammas, Paula

2004-07-01

Development of AD is associated with cerebrovascular deposition of amyloid beta (Aβ) as well as a progressive increase in vasular collagen content. Both AΒ and collagen are naturally fluorescent compounds when exposed to UV light. We analyzed autofluorescence emitted from brain tissue samples and isolated brain resistance vessels harvested postmortem from patients with Alzheimer's disease (AD) and age-matched controls. Fluorescence emission, excited at 355 nm with an Nd:YAG laser, was measured using a fiber-optic based fluorescence spectroscopic system for tissue analysis. Significantly higher values of fluorescence emission intensity (P<0.001) in the spectral region from 465 to 490 nm were detected in brain resistance vessel samples from AD patients compared to the normal individuals. Results from western blot analysis showed elevated levels of type I and type III collagen, and reduced levels of type IV collagen in resistance vessels from AD patients, compared to control samples. In addition, using direct scanning of the cortical suface for fluoresxcence emission by the laser-induced fluorescence spectroscopy system we detected a significantly (P<0.05) higher level of apoptosis in AD brain tissue compared to age-matched controls. Fluorescence emission analysis (FEA) appears to be a sensitive technique for detecting structural changes in AD brain tissue.

Vision-based method for detecting driver drowsiness and distraction in driver monitoring system

NASA Astrophysics Data System (ADS)

Jo, Jaeik; Lee, Sung Joo; Jung, Ho Gi; Park, Kang Ryoung; Kim, Jaihie

2011-12-01

Most driver-monitoring systems have attempted to detect either driver drowsiness or distraction, although both factors should be considered for accident prevention. Therefore, we propose a new driver-monitoring method considering both factors. We make the following contributions. First, if the driver is looking ahead, drowsiness detection is performed; otherwise, distraction detection is performed. Thus, the computational cost and eye-detection error can be reduced. Second, we propose a new eye-detection algorithm that combines adaptive boosting, adaptive template matching, and blob detection with eye validation, thereby reducing the eye-detection error and processing time significantly, which is hardly achievable using a single method. Third, to enhance eye-detection accuracy, eye validation is applied after initial eye detection, using a support vector machine based on appearance features obtained by principal component analysis (PCA) and linear discriminant analysis (LDA). Fourth, we propose a novel eye state-detection algorithm that combines appearance features obtained using PCA and LDA, with statistical features such as the sparseness and kurtosis of the histogram from the horizontal edge image of the eye. Experimental results showed that the detection accuracies of the eye region and eye states were 99 and 97%, respectively. Both driver drowsiness and distraction were detected with a success rate of 98%.

Identification of stable QTLs causing chalk in rice grains in nine environments.

PubMed

Zhao, Xiangqian; Daygon, Venea D; McNally, Kenneth L; Hamilton, Ruaraidh Sackville; Xie, Fangming; Reinke, Russell F; Fitzgerald, Melissa A

2016-01-01

A novel QTL cluster for chalkiness on Chr04 was identified using single environment analysis and joint mapping across 9 environments in Asia and South American. QTL NILs showed that each had a significant effect on chalk. Chalk in rice grains leads to a significant loss in the proportion of marketable grains in a harvested crop, leading to a significant financial loss to rice farmers and traders. To identify the genetic basis of chalkiness, two sets of recombinant inbred lines (RILs) derived from reciprocal crosses between Lemont and Teqing were used to find stable QTLs for chalkiness. The RILs were grown in seven locations in Asia and Latin American and in two controlled environments in phytotrons. A total of 32 (21) and 46 (22) QTLs for DEC and PGWC, most of them explaining more than 10% of phenotypic variation, were detected based on single environment analysis in T/L (L/T) population, respectively. Seven (2) and 7 (3) QTLs for DEC and PGWC were identified in the T/L (L/T) population using joined analysis across all environments, respectively. Six major QTLs clusters were found on five chromosomes: 1, 2, 4, 5 and 11. The biggest cluster at id4007289-RM252 on Chr04 was a novelty, including 16 and 4 QTLs detected by single environment analysis and joint mapping across all environments, respectively. The detected digenic epistatic QTLs explained up to 13% of phenotypic variation, suggesting that epistasis play an important role in the genetic control of chalkiness in rice. QTL NILs showed that each QTL cluster had a significant effect on chalk. These chromosomal regions could be targets for MAS, fine mapping and map-based cloning for low chalkiness breeding.

A Vibration-Based Approach for Stator Winding Fault Diagnosis of Induction Motors: Application of Envelope Analysis

DTIC Science & Technology

2014-10-02

takes it either as auxiliary to magnetic flux, or is not able to detect the winding faults unless severity is already quite significant. This paper...different loads, speeds and severity levels. The experimental results show that the proposed method was able to detect inter-turn faults in the...maintenance strategy requires the technologies of: (a) on- line condition monitoring, (b) fault detection and diagnosis, and (c) prognostics. Figure 1

Energy-Dispersive X-Ray Fluorescence Spectrometry: A Long Overdue Addition to the Chemistry Curriculum

ERIC Educational Resources Information Center

Palmer, Peter T.

2011-01-01

Portable Energy-Dispersive X-Ray Fluorescence (XRF) analyzers have undergone significant improvements over the past decade. Salient advantages of XRF for elemental analysis include minimal sample preparation, multielement analysis capabilities, detection limits in the low parts per million (ppm) range, and analysis times on the order of 1 min.…

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

Verrecchia, F.; Pittori, C.; Lucarelli, F.

The LIGO/Virgo Collaboration (LVC) detected on 2017 January 4 a significant gravitational-wave (GW) event (now named GW170104). We report in this Letter the main results obtained from the analysis of hard X-ray and gamma-ray data of the AGILE mission that repeatedly observed the GW170104 localization region (LR). At the LVC detection time T {sub 0} AGILE observed about 36% of the LR. The gamma-ray imaging detector did not reveal any significant emission in the energy range 50 MeV–30 GeV. Furthermore, no significant gamma-ray transients were detected in the LR that was repeatedly exposed over timescales of minutes, hours, and days.more » We also searched for transient emission using data near T {sub 0} of the omnidirectional detector MCAL operating in the energy band 0.4–100 MeV. A refined analysis of MCAL data shows the existence of a weak event (that we call “E2”) with a signal-to-noise ratio of 4.4 σ lasting about 32 ms and occurring 0.46 ± 0.05 s before T {sub 0}. A study of the MCAL background and of the false-alarm rate of E2 leads to the determination of a post-trial significance between 2.4σ and 2.7σ for a temporal coincidence with GW170104. We note that E2 has characteristics similar to those detected from the weak precursor of GRB 090510. The candidate event E2 is worth consideration for simultaneous detection by other satellites. If associated with GW170104, it shows emission in the MeV band of a short burst preceding the final coalescence by 0.46 s and involving ∼10{sup −7} of the total rest mass energy of the system.« less

Detection and Evaluation of Spatio-Temporal Spike Patterns in Massively Parallel Spike Train Data with SPADE.

PubMed

Quaglio, Pietro; Yegenoglu, Alper; Torre, Emiliano; Endres, Dominik M; Grün, Sonja

2017-01-01

Repeated, precise sequences of spikes are largely considered a signature of activation of cell assemblies. These repeated sequences are commonly known under the name of spatio-temporal patterns (STPs). STPs are hypothesized to play a role in the communication of information in the computational process operated by the cerebral cortex. A variety of statistical methods for the detection of STPs have been developed and applied to electrophysiological recordings, but such methods scale poorly with the current size of available parallel spike train recordings (more than 100 neurons). In this work, we introduce a novel method capable of overcoming the computational and statistical limits of existing analysis techniques in detecting repeating STPs within massively parallel spike trains (MPST). We employ advanced data mining techniques to efficiently extract repeating sequences of spikes from the data. Then, we introduce and compare two alternative approaches to distinguish statistically significant patterns from chance sequences. The first approach uses a measure known as conceptual stability, of which we investigate a computationally cheap approximation for applications to such large data sets. The second approach is based on the evaluation of pattern statistical significance. In particular, we provide an extension to STPs of a method we recently introduced for the evaluation of statistical significance of synchronous spike patterns. The performance of the two approaches is evaluated in terms of computational load and statistical power on a variety of artificial data sets that replicate specific features of experimental data. Both methods provide an effective and robust procedure for detection of STPs in MPST data. The method based on significance evaluation shows the best overall performance, although at a higher computational cost. We name the novel procedure the spatio-temporal Spike PAttern Detection and Evaluation (SPADE) analysis.

Detection and Evaluation of Spatio-Temporal Spike Patterns in Massively Parallel Spike Train Data with SPADE

PubMed Central

Quaglio, Pietro; Yegenoglu, Alper; Torre, Emiliano; Endres, Dominik M.; Grün, Sonja

2017-01-01

Repeated, precise sequences of spikes are largely considered a signature of activation of cell assemblies. These repeated sequences are commonly known under the name of spatio-temporal patterns (STPs). STPs are hypothesized to play a role in the communication of information in the computational process operated by the cerebral cortex. A variety of statistical methods for the detection of STPs have been developed and applied to electrophysiological recordings, but such methods scale poorly with the current size of available parallel spike train recordings (more than 100 neurons). In this work, we introduce a novel method capable of overcoming the computational and statistical limits of existing analysis techniques in detecting repeating STPs within massively parallel spike trains (MPST). We employ advanced data mining techniques to efficiently extract repeating sequences of spikes from the data. Then, we introduce and compare two alternative approaches to distinguish statistically significant patterns from chance sequences. The first approach uses a measure known as conceptual stability, of which we investigate a computationally cheap approximation for applications to such large data sets. The second approach is based on the evaluation of pattern statistical significance. In particular, we provide an extension to STPs of a method we recently introduced for the evaluation of statistical significance of synchronous spike patterns. The performance of the two approaches is evaluated in terms of computational load and statistical power on a variety of artificial data sets that replicate specific features of experimental data. Both methods provide an effective and robust procedure for detection of STPs in MPST data. The method based on significance evaluation shows the best overall performance, although at a higher computational cost. We name the novel procedure the spatio-temporal Spike PAttern Detection and Evaluation (SPADE) analysis. PMID:28596729

Search for gamma-ray emission from Galactic novae with the Fermi -LAT

NASA Astrophysics Data System (ADS)

Franckowiak, A.; Jean, P.; Wood, M.; Cheung, C. C.; Buson, S.

2018-02-01

Context. A number of novae have been found to emit high-energy gamma rays (>100 MeV). However, the origin of this emission is not yet understood. We report on the search for gamma-ray emission from 75 optically detected Galactic novae in the first 7.4 years of operation of the Fermi Large Area Telescope using the Pass 8 data set. Aims: We compile an optical nova catalog including light curves from various resources and estimate the optical peak time and optical peak magnitude in order to search for gamma-ray emission to determine whether all novae are gamma-ray emitters. Methods: We repeated the analysis of the six novae previously identified as gamma-ray sources and developed a unified analysis strategy that we then applied to all novae in our catalog. We searched for emission in a 15 day time window in two-day steps ranging from 20 days before to 20 days after the optical peak time. We performed a population study with Monte Carlo simulations to set constraints on the properties of the gamma-ray emission of novae. Results: Two new novae candidates have been found at 2σ global significance. Although these two novae candidates were not detected at a significant level individually, taking them together with the other non-detected novae, we found a sub-threshold nova population with a cumulative 3σ significance. We report the measured gamma-ray flux for detected sources and flux upper limits for novae without significant detection. Our results can be reproduced by several gamma-ray emissivity models (e.g., a power-law distribution with a slope of 2), while a constant emissivity model (i.e., assuming novae are standard candles) can be rejected.

Search for gamma-ray emission from Galactic novae with the Fermi-LAT

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

Franckowiak, A.; Jean, P.; Wood, M.

Context. A number of novae have been found to emit high-energy gamma rays (>100 MeV). However, the origin of this emission is not yet understood. We report on the search for gamma-ray emission from 75 optically detected Galactic novae in the first 7.4 years of operation of the Fermi Large Area Telescope using the Pass 8 data set. Aims. We compile an optical nova catalog including light curves from various resources and estimate the optical peak time and optical peak magnitude in order to search for gamma-ray emission to determine whether all novae are gamma-ray emitters. Methods. We repeated themore » analysis of the six novae previously identified as gamma-ray sources and developed a unified analysis strategy that we then applied to all novae in our catalog. We searched for emission in a 15 day time window in two-day steps ranging from 20 days before to 20 days after the optical peak time. We performed a population study with Monte Carlo simulations to set constraints on the properties of the gamma-ray emission of novae. Results. Two new novae candidates have been found at ~ 2σ global significance. Although these two novae candidates were not detected at a significant level individually, taking them together with the other non-detected novae, we found a sub-threshold nova population with a cumulative 3σ significance. We report the measured gamma-ray flux for detected sources and flux upper limits for novae without significant detection. Lastly, our results can be reproduced by several gamma-ray emissivity models (e.g., a power-law distribution with a slope of 2), while a constant emissivity model (i.e., assuming novae are standard candles) can be rejected.« less

Search for gamma-ray emission from Galactic novae with the Fermi-LAT

DOE PAGES

Franckowiak, A.; Jean, P.; Wood, M.; ...

2018-02-05

Context. A number of novae have been found to emit high-energy gamma rays (>100 MeV). However, the origin of this emission is not yet understood. We report on the search for gamma-ray emission from 75 optically detected Galactic novae in the first 7.4 years of operation of the Fermi Large Area Telescope using the Pass 8 data set. Aims. We compile an optical nova catalog including light curves from various resources and estimate the optical peak time and optical peak magnitude in order to search for gamma-ray emission to determine whether all novae are gamma-ray emitters. Methods. We repeated themore » analysis of the six novae previously identified as gamma-ray sources and developed a unified analysis strategy that we then applied to all novae in our catalog. We searched for emission in a 15 day time window in two-day steps ranging from 20 days before to 20 days after the optical peak time. We performed a population study with Monte Carlo simulations to set constraints on the properties of the gamma-ray emission of novae. Results. Two new novae candidates have been found at ~ 2σ global significance. Although these two novae candidates were not detected at a significant level individually, taking them together with the other non-detected novae, we found a sub-threshold nova population with a cumulative 3σ significance. We report the measured gamma-ray flux for detected sources and flux upper limits for novae without significant detection. Lastly, our results can be reproduced by several gamma-ray emissivity models (e.g., a power-law distribution with a slope of 2), while a constant emissivity model (i.e., assuming novae are standard candles) can be rejected.« less

Theoretical detection limit of PIXE analysis using 20 MeV proton beams

NASA Astrophysics Data System (ADS)

Ishii, Keizo; Hitomi, Keitaro

2018-02-01

Particle-induced X-ray emission (PIXE) analysis is usually performed using proton beams with energies in the range 2∼3 MeV because at these energies, the detection limit is low. The detection limit of PIXE analysis depends on the X-ray production cross-section, the continuous background of the PIXE spectrum and the experimental parameters such as the beam currents and the solid angle and detector efficiency of X-ray detector. Though the continuous background increases as the projectile energy increases, the cross-section of the X-ray increases as well. Therefore, the detection limit of high energy proton PIXE is not expected to increase significantly. We calculated the cross sections of continuous X-rays produced in several bremsstrahlung processes and estimated the detection limit of a 20 MeV proton PIXE analysis by modelling the Compton tail of the γ-rays produced in the nuclear reactions, and the escape effect on the secondary electron bremsstrahlung. We found that the Compton tail does not affect the detection limit when a thin X-ray detector is used, but the secondary electron bremsstrahlung escape effect does have an impact. We also confirmed that the detection limit of the PIXE analysis, when used with 4 μm polyethylene backing film and an integrated beam current of 1 μC, is 0.4∼2.0 ppm for proton energies in the range 10∼30 MeV and elements with Z = 16-90. This result demonstrates the usefulness of several 10 MeV cyclotrons for performing PIXE analysis. Cyclotrons with these properties are currently installed in positron emission tomography (PET) centers.

Real-time Supervised Detection of Pink Areas in Dermoscopic Images of Melanoma: Importance of Color Shades, Texture and Location

PubMed Central

Kaur, Ravneet; Albano, Peter P.; Cole, Justin G.; Hagerty, Jason; LeAnder, Robert W.; Moss, Randy H.; Stoecker, William V.

2015-01-01

Background/Purpose Early detection of malignant melanoma is an important public health challenge. In the USA, dermatologists are seeing more melanomas at an early stage, before classic melanoma features have become apparent. Pink color is a feature of these early melanomas. If rapid and accurate automatic detection of pink color in these melanomas could be accomplished, there could be significant public health benefits. Methods Detection of three shades of pink (light pink, dark pink, and orange pink) was accomplished using color analysis techniques in five color planes (red, green, blue, hue and saturation). Color shade analysis was performed using a logistic regression model trained with an image set of 60 dermoscopic images of melanoma that contained pink areas. Detected pink shade areas were further analyzed with regard to the location within the lesion, average color parameters over the detected areas, and histogram texture features. Results Logistic regression analysis of a separate set of 128 melanomas and 128 benign images resulted in up to 87.9% accuracy in discriminating melanoma from benign lesions measured using area under the receiver operating characteristic curve. The accuracy in this model decreased when parameters for individual shades, texture, or shade location within the lesion were omitted. Conclusion Texture, color, and lesion location analysis applied to multiple shades of pink can assist in melanoma detection. When any of these three details: color location, shade analysis, or texture analysis were omitted from the model, accuracy in separating melanoma from benign lesions was lowered. Separation of colors into shades and further details that enhance the characterization of these color shades are needed for optimal discrimination of melanoma from benign lesions. PMID:25809473

Real-time supervised detection of pink areas in dermoscopic images of melanoma: importance of color shades, texture and location.

PubMed

Kaur, R; Albano, P P; Cole, J G; Hagerty, J; LeAnder, R W; Moss, R H; Stoecker, W V

2015-11-01

Early detection of malignant melanoma is an important public health challenge. In the USA, dermatologists are seeing more melanomas at an early stage, before classic melanoma features have become apparent. Pink color is a feature of these early melanomas. If rapid and accurate automatic detection of pink color in these melanomas could be accomplished, there could be significant public health benefits. Detection of three shades of pink (light pink, dark pink, and orange pink) was accomplished using color analysis techniques in five color planes (red, green, blue, hue, and saturation). Color shade analysis was performed using a logistic regression model trained with an image set of 60 dermoscopic images of melanoma that contained pink areas. Detected pink shade areas were further analyzed with regard to the location within the lesion, average color parameters over the detected areas, and histogram texture features. Logistic regression analysis of a separate set of 128 melanomas and 128 benign images resulted in up to 87.9% accuracy in discriminating melanoma from benign lesions measured using area under the receiver operating characteristic curve. The accuracy in this model decreased when parameters for individual shades, texture, or shade location within the lesion were omitted. Texture, color, and lesion location analysis applied to multiple shades of pink can assist in melanoma detection. When any of these three details: color location, shade analysis, or texture analysis were omitted from the model, accuracy in separating melanoma from benign lesions was lowered. Separation of colors into shades and further details that enhance the characterization of these color shades are needed for optimal discrimination of melanoma from benign lesions. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Damage detection of engine bladed-disks using multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Fang, X.; Tang, J.

2006-03-01

The timely detection of damage in aero-engine bladed-disks is an extremely important and challenging research topic. Bladed-disks have high modal density and, particularly, their vibration responses are subject to significant uncertainties due to manufacturing tolerance (blade-to-blade difference or mistuning), operating condition change and sensor noise. In this study, we present a new methodology for the on-line damage detection of engine bladed-disks using their vibratory responses during spin-up or spin-down operations which can be measured by blade-tip-timing sensing technique. We apply a principle component analysis (PCA)-based approach for data compression, feature extraction, and denoising. The non-model based damage detection is achieved by analyzing the change between response features of the healthy structure and of the damaged one. We facilitate such comparison by incorporating the Hotelling's statistic T2 analysis, which yields damage declaration with a given confidence level. The effectiveness of the method is demonstrated by case studies.

Detection of proximal caries using digital radiographic systems with different resolutions.

PubMed

Nikneshan, Sima; Abbas, Fatemeh Mashhadi; Sabbagh, Sedigheh

2015-01-01

Dental radiography is an important tool for detection of caries and digital radiography is the latest advancement in this regard. Spatial resolution is a characteristic of digital receptors used for describing the quality of images. This study was aimed to compare the diagnostic accuracy of two digital radiographic systems with three different resolutions for detection of noncavitated proximal caries. Diagnostic accuracy. Seventy premolar teeth were mounted in 14 gypsum blocks. Digora; Optime and RVG Access were used for obtaining digital radiographs. Six observers evaluated the proximal surfaces in radiographs for each resolution in order to determine the depth of caries based on a 4-point scale. The teeth were then histologically sectioned, and the results of histologic analysis were considered as the gold standard. Data were entered using SPSS version 18 software and the Kruskal-Wallis test was used for data analysis. P <0.05 was considered as statistically significant. No significant difference was found between different resolutions for detection of proximal caries (P > 0.05). RVG access system had the highest specificity (87.7%) and Digora; Optime at high resolution had the lowest specificity (84.2%). Furthermore, Digora; Optime had higher sensitivity for detection of caries exceeding outer half of enamel. Judgment of oral radiologists for detection of the depth of caries had higher reliability than that of restorative dentistry specialists. The three resolutions of Digora; Optime and RVG access had similar accuracy in detection of noncavitated proximal caries.

Robust detection of multiple sclerosis lesions from intensity-normalized multi-channel MRI

NASA Astrophysics Data System (ADS)

Karpate, Yogesh; Commowick, Olivier; Barillot, Christian

2015-03-01

Multiple sclerosis (MS) is a disease with heterogeneous evolution among the patients. Quantitative analysis of longitudinal Magnetic Resonance Images (MRI) provides a spatial analysis of the brain tissues which may lead to the discovery of biomarkers of disease evolution. Better understanding of the disease will lead to a better discovery of pathogenic mechanisms, allowing for patient-adapted therapeutic strategies. To characterize MS lesions, we propose a novel paradigm to detect white matter lesions based on a statistical framework. It aims at studying the benefits of using multi-channel MRI to detect statistically significant differences between each individual MS patient and a database of control subjects. This framework consists in two components. First, intensity standardization is conducted to minimize the inter-subject intensity difference arising from variability of the acquisition process and different scanners. The intensity normalization maps parameters obtained using a robust Gaussian Mixture Model (GMM) estimation not affected by the presence of MS lesions. The second part studies the comparison of multi-channel MRI of MS patients with respect to an atlas built from the control subjects, thereby allowing us to look for differences in normal appearing white matter, in and around the lesions of each patient. Experimental results demonstrate that our technique accurately detects significant differences in lesions consequently improving the results of MS lesion detection.

DNA nanomechanics allows direct digital detection of complementary DNA and microRNA targets.

PubMed

Husale, Sudhir; Persson, Henrik H J; Sahin, Ozgur

2009-12-24

Techniques to detect and quantify DNA and RNA molecules in biological samples have had a central role in genomics research. Over the past decade, several techniques have been developed to improve detection performance and reduce the cost of genetic analysis. In particular, significant advances in label-free methods have been reported. Yet detection of DNA molecules at concentrations below the femtomolar level requires amplified detection schemes. Here we report a unique nanomechanical response of hybridized DNA and RNA molecules that serves as an intrinsic molecular label. Nanomechanical measurements on a microarray surface have sufficient background signal rejection to allow direct detection and counting of hybridized molecules. The digital response of the sensor provides a large dynamic range that is critical for gene expression profiling. We have measured differential expressions of microRNAs in tumour samples; such measurements have been shown to help discriminate between the tissue origins of metastatic tumours. Two hundred picograms of total RNA is found to be sufficient for this analysis. In addition, the limit of detection in pure samples is found to be one attomolar. These results suggest that nanomechanical read-out of microarrays promises attomolar-level sensitivity and large dynamic range for the analysis of gene expression, while eliminating biochemical manipulations, amplification and labelling.

Analysis of surface EMG baseline for detection of hidden muscle activity

NASA Astrophysics Data System (ADS)

Zhang, Xu; Zhou, Ping

2014-02-01

Objective. This study explored the feasibility of detecting hidden muscle activity in surface electromyogram (EMG) baseline. Approach. Power spectral density (PSD) analysis and multi-scale entropy (MSE) analysis were used. Both analyses were applied to computer simulations of surface EMG baseline with the presence (representing activity data) or absence (representing reference data) of hidden muscle activity, as well as surface electrode array EMG baseline recordings of healthy control and amyotrophic lateral sclerosis (ALS) subjects. Main results. Although the simulated reference data and the activity data yielded no distinguishable difference in the time domain, they demonstrated a significant difference in the frequency and signal complexity domains with the PSD and MSE analyses. For a comparison using pooled data, such a difference was also observed when the PSD and MSE analyses were applied to surface electrode array EMG baseline recordings of healthy control and ALS subjects, which demonstrated no distinguishable difference in the time domain. Compared with the PSD analysis, the MSE analysis appeared to be more sensitive for detecting the difference in surface EMG baselines between the two groups. Significance. The findings implied the presence of a hidden muscle activity in surface EMG baseline recordings from the ALS subjects. To promote the presented analysis as a useful diagnostic or investigatory tool, future studies are necessary to assess the pathophysiological nature or origins of the hidden muscle activity, as well as the baseline difference at the individual subject level.

Analysis of Surface EMG Baseline for Detection of Hidden Muscle Activity

PubMed Central

Zhang, Xu; Zhou, Ping

2014-01-01

Objective This study explored the feasibility of detecting hidden muscle activity in surface electromyogram (EMG) baseline. Approach Power spectral density (PSD) analysis and multi-scale entropy (MSE) analysis were used respectively. Both analyses were applied to computer simulations of surface EMG baseline with presence (representing activity data) or absence (representing reference data) of hidden muscle activity, as well as surface electrode array EMG baseline recordings of healthy control and amyotrophic lateral sclerosis (ALS) subjects. Main results Although the simulated reference data and the activity data yielded no distinguishable difference in the time domain, they demonstrated a significant difference in the frequency and signal complexity domains with the PSD and MSE analyses. For a comparison using pooled data, such a difference was also observed when the PSD and MSE analyses were applied to surface electrode array EMG baseline recordings of healthy control and ALS subjects, which demonstrated no distinguishable difference in the time domain. Compared with the PSD analysis, the MSE analysis appeared to be more sensitive for detecting the difference in surface EMG baselines between the two groups. Significance The findings implied presence of hidden muscle activity in surface EMG baseline recordings from the ALS subjects. To promote the presented analysis as a useful diagnostic or investigatory tool, future studies are necessary to assess the pathophysiological nature or origins of the hidden muscle activity, as well as the baseline difference at the individual subject level. PMID:24445526

The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer.

PubMed

Aghdam, Rosa; Baghfalaki, Taban; Khosravi, Pegah; Saberi Ansari, Elnaz

2017-12-01

Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM) method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/. Copyright © 2017. Production and hosting by Elsevier B.V.

The echo Doppler spectrum of valvular abnormalities in the hospitalized octogenarian.

PubMed

Zavitsanos, J P; Goldman, A P; Kotler, M N; Maze, S S; Kochar, G; Parry, W

1988-10-01

Cardiac valves thicken and become more opaque with advancing age. As more individuals live longer and as more treatment modalities such as valvuloplasty evolve, the presence and significance of these valvular abnormalities become important. We retrospectively studied 628 octogenarian patients to try and define further the presence and significance of these abnormalities detected by Doppler echocardiography. A group of 547 patients were suitable for analysis. Age ranged from 80 to 96 years (mean 84.4). The female:male ratio was 1.9:1. Mitral, aortic, and tricuspid regurgitation (MR, AR, and TR) were significant if the jet moved greater than 2 cm from the plane of the valve away or toward the transducer, depending on transducer position. Mitral regurgitation was detected in 331 patients (60.5%) and was significant in 82 patients (15%). Aortic regurgitation was detected in 276 patients (50.5%) and was significant in 70 patients (12.8%). Tricuspid regurgitation was detected in 131 patients (23.9%) and was significant in 30 patients (5.5%). Regurgitant lesions were detected in two valves in 150 patients (27.4%) three valves in 57 patients (10.4%), in all four valves in 17 patients (3.1%). Aortic stenosis was detected in 160 patients (29.3%). The gradient range was 16-156 mmHg (mean 47.8). Significant aortic stenosis was present in 70 patients (12.8%) (gradient greater than 50 mmHg), of whom 54 had isolated pure aortic stenosis and 16 had mixed lesion. In 40% of these patients, significant aortic stenosis was an unexpected finding at two-dimensional echocardiography. Valvular pathology is common in the octogenarian population.(ABSTRACT TRUNCATED AT 250 WORDS)

Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method.

PubMed

Karain, Wael I

2017-11-28

Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis. We start from the assumption that a protein has a "baseline" recurrence structure over a given period of time. Any statistically significant deviation from this recurrence structure, as inferred from complexity measures provided by recurrence quantification analysis, is considered a transition in the dynamics of the protein. We apply this technique to a 132 ns long molecular dynamics simulation of the β-Lactamase Inhibitory Protein BLIP. We are able to detect conformational transitions in the nanosecond range in the recurrence dynamics of the BLIP protein during the simulation. The results compare favorably to those extracted using the principal component analysis technique. The recurrence quantification analysis based bootstrap technique is able to detect transitions between different dynamics states for a protein over different time scales. It is not limited to linear dynamics regimes, and can be generalized to any time scale. It also has the potential to be used to cluster frames in molecular dynamics trajectories according to the nature of their recurrence dynamics. One shortcoming for this method is the need to have large enough time windows to insure good statistical quality for the recurrence complexity measures needed to detect the transitions.

Rapid detection of Escherichia coli and enterococci in recreational water using an immunomagnetic separation/adenosine triphosphate technique

USGS Publications Warehouse

Bushon, R.N.; Brady, A.M.; Likirdopulos, C.A.; Cireddu, J.V.

2009-01-01

Aims: The aim of this study was to examine a rapid method for detecting Escherichia coli and enterococci in recreational water. Methods and Results: Water samples were assayed for E. coli and enterococci by traditional and immunomagnetic separation/adenosine triphosphate (IMS/ATP) methods. Three sample treatments were evaluated for the IMS/ATP method: double filtration, single filtration, and direct analysis. Pearson's correlation analysis showed strong, significant, linear relations between IMS/ATP and traditional methods for all sample treatments; strongest linear correlations were with the direct analysis (r = 0.62 and 0.77 for E. coli and enterococci, respectively). Additionally, simple linear regression was used to estimate bacteria concentrations as a function of IMS/ATP results. The correct classification of water-quality criteria was 67% for E. coli and 80% for enterococci. Conclusions: The IMS/ATP method is a viable alternative to traditional methods for faecal-indicator bacteria. Significance and Impact of the Study: The IMS/ATP method addresses critical public health needs for the rapid detection of faecal-indicator contamination and has potential for satisfying US legislative mandates requiring methods to detect bathing water contamination in 2 h or less. Moreover, IMS/ATP equipment is considerably less costly and more portable than that for molecular methods, making the method suitable for field applications. ?? 2009 The Authors.

Asynchronous detection of kinesthetic attention during mobilization of lower limbs using EEG measurements

NASA Astrophysics Data System (ADS)

Melinscak, Filip; Montesano, Luis; Minguez, Javier

2016-02-01

Objective. Attention is known to modulate the plasticity of the motor cortex, and plasticity is crucial for recovery in motor rehabilitation. This study addresses the possibility of using an EEG-based brain-computer interface (BCI) to detect kinesthetic attention to movement. Approach. A novel experiment emulating physical rehabilitation was designed to study kinesthetic attention. The protocol involved continuous mobilization of lower limbs during which participants reported levels of attention to movement—from focused kinesthetic attention to mind wandering. For this protocol an asynchronous BCI detector of kinesthetic attention and deliberate mind wandering was designed. Main results. EEG analysis showed significant differences in theta, alpha, and beta bands, related to the attentional state. These changes were further pinpointed to bands relative to the frequency of the individual alpha peak. The accuracy of the designed BCI ranged between 60.8% and 68.4% (significantly above chance level), depending on the used analysis window length, i.e. acceptable detection delay. Significance. This study shows it is possible to use self-reporting to study attention-related changes in EEG during continuous mobilization. Such a protocol is used to develop an asynchronous BCI detector of kinesthetic attention, with potential applications to motor rehabilitation.

Robust Cell Detection of Histopathological Brain Tumor Images Using Sparse Reconstruction and Adaptive Dictionary Selection

PubMed Central

Su, Hai; Xing, Fuyong; Yang, Lin

2016-01-01

Successful diagnostic and prognostic stratification, treatment outcome prediction, and therapy planning depend on reproducible and accurate pathology analysis. Computer aided diagnosis (CAD) is a useful tool to help doctors make better decisions in cancer diagnosis and treatment. Accurate cell detection is often an essential prerequisite for subsequent cellular analysis. The major challenge of robust brain tumor nuclei/cell detection is to handle significant variations in cell appearance and to split touching cells. In this paper, we present an automatic cell detection framework using sparse reconstruction and adaptive dictionary learning. The main contributions of our method are: 1) A sparse reconstruction based approach to split touching cells; 2) An adaptive dictionary learning method used to handle cell appearance variations. The proposed method has been extensively tested on a data set with more than 2000 cells extracted from 32 whole slide scanned images. The automatic cell detection results are compared with the manually annotated ground truth and other state-of-the-art cell detection algorithms. The proposed method achieves the best cell detection accuracy with a F1 score = 0.96. PMID:26812706

Thirty Years of Vegetation Change in the Coastal Santa Cruz Mountains of Northern California Detected Using Landsat Satellite Image Analysis

NASA Technical Reports Server (NTRS)

Potter, Christopher

2015-01-01

Results from Landsat satellite image times series analysis since 1983 of this study area showed gradual, statistically significant increases in the normalized difference vegetation index (NDVI) in more than 90% of the (predominantly second-growth) evergreen forest locations sampled.

Clinical evaluation of a novel population-based regression analysis for detecting glaucomatous visual field progression.

PubMed

Kovalska, M P; Bürki, E; Schoetzau, A; Orguel, S F; Orguel, S; Grieshaber, M C

2011-04-01

The distinction of real progression from test variability in visual field (VF) series may be based on clinical judgment, on trend analysis based on follow-up of test parameters over time, or on identification of a significant change related to the mean of baseline exams (event analysis). The aim of this study was to compare a new population-based method (Octopus field analysis, OFA) with classic regression analyses and clinical judgment for detecting glaucomatous VF changes. 240 VF series of 240 patients with at least 9 consecutive examinations available were included into this study. They were independently classified by two experienced investigators. The results of such a classification served as a reference for comparison for the following statistical tests: (a) t-test global, (b) r-test global, (c) regression analysis of 10 VF clusters and (d) point-wise linear regression analysis. 32.5 % of the VF series were classified as progressive by the investigators. The sensitivity and specificity were 89.7 % and 92.0 % for r-test, and 73.1 % and 93.8 % for the t-test, respectively. In the point-wise linear regression analysis, the specificity was comparable (89.5 % versus 92 %), but the sensitivity was clearly lower than in the r-test (22.4 % versus 89.7 %) at a significance level of p = 0.01. A regression analysis for the 10 VF clusters showed a markedly higher sensitivity for the r-test (37.7 %) than the t-test (14.1 %) at a similar specificity (88.3 % versus 93.8 %) for a significant trend (p = 0.005). In regard to the cluster distribution, the paracentral clusters and the superior nasal hemifield progressed most frequently. The population-based regression analysis seems to be superior to the trend analysis in detecting VF progression in glaucoma, and may eliminate the drawbacks of the event analysis. Further, it may assist the clinician in the evaluation of VF series and may allow better visualization of the correlation between function and structure owing to VF clusters. © Georg Thieme Verlag KG Stuttgart · New York.

Detection of major climatic and environmental predictors of liver fluke exposure risk in Ireland using spatial cluster analysis.

PubMed

Selemetas, Nikolaos; de Waal, Theo

2015-04-30

Fasciolosis caused by Fasciola hepatica (liver fluke) can cause significant economic and production losses in dairy cow farms. The aim of the current study was to identify important weather and environmental predictors of the exposure risk to liver fluke by detecting clusters of fasciolosis in Ireland. During autumn 2012, bulk-tank milk samples from 4365 dairy farms were collected throughout Ireland. Using an in-house antibody-detection ELISA, the analysis of BTM samples showed that 83% (n=3602) of dairy farms had been exposed to liver fluke. The Getis-Ord Gi* statistic identified 74 high-risk and 130 low-risk significant (P<0.01) clusters of fasciolosis. The low-risk clusters were mostly located in the southern regions of Ireland, whereas the high-risk clusters were mainly situated in the western part. Several climatic variables (monthly and seasonal mean rainfall and temperatures, total wet days and rain days) and environmental datasets (soil types, enhanced vegetation index and normalised difference vegetation index) were used to investigate dissimilarities in the exposure to liver fluke between clusters. Rainfall, total wet days and rain days, and soil type were the significant classes of climatic and environmental variables explaining the differences between significant clusters. A discriminant function analysis was used to predict the exposure risk to liver fluke using 80% of data for modelling and the remaining subset of 20% for post hoc model validation. The most significant predictors of the model risk function were total rainfall in August and September and total wet days. The risk model presented 100% sensitivity and 91% specificity and an accuracy of 95% correctly classified cases. A risk map of exposure to liver fluke was constructed with higher probability of exposure in western and north-western regions. The results of this study identified differences between clusters of fasciolosis in Ireland regarding climatic and environmental variables and detected significant predictors of the exposure risk to liver fluke. Copyright © 2015 Elsevier B.V. All rights reserved.

Cadmium toxicity at low concentration on rabbit spermatozoa motility, morphology and membrane integrity in vitro.

PubMed

Roychoudhury, Shubhadeep; Massanyi, Peter; Bulla, Jozef; Choudhury, Manabendra Dutta; Lukac, Norbert; Filipejova, Terezia; Trandzik, Jozef; Toman, Robert; Almasiova, Viera

2010-09-01

In this study the effect of cadmium on various parameters of spermatozoa motility, morphology as well as on the spermatozoa membrane integrity in rabbits was analyzed in vitro, experimental concentrations ranging from 0.62 to 0.98 micro g CdCl(2)/mL. Pooled rabbit (n = 5) semen was cultured in vitro with cadmium and subsequently diluted to various experimental concentrations apart from control which received no cadmium exposure. Using computer assisted semen analysis method (CASA) we detected decrease of total motility with in the higher concentration range at Time 0. However, with increasing time (after 1 and 2 h of culture), cadmium exerted deleterious effect leading to significant motility reduction in comparison to control. A similar trend was exhibited in case of progressive motility, too. Most of the spermatozoa distance and velocity parameters detected no significant change in comparison to control at the beginning of culture (Time 0), although the toxic effect became significant (P < 0.05) with the passage of culture time (Times 1 and 2 h) in all concentrations. Analysis of spermatozoa morphology detected significant (P < 0.05) alterations at higher concentrations. At higher concentrations acrosomal changes, head without flagellum/separated flagellum, broken flagellum and other abnormalities were significantly higher (P < 0.05), while knob-twisted flagellum and small heads differed significantly (P < 0.05) in comparison to control at all concentrations. In regards to flagellum torso, flagellum ball and retention of cytoplasmic drop statistically higher values (P < 0.05) were noted at the maxium experimental concentration only. Annexin analysis for detection of spermatozoa with disordered membranes revealed higher occurrence of positive spermatozoa in cadmium exposed groups. Annexin-positive reactions suggested alterations in anterior part of head (acrosome) and in flagellum (mitochondrial segment) of spermatozoa. This paper underlines that cadmium is highly toxic for rabbit spermatozoa, as visualized by the toxic effects on parameters of spermatozoa motility, morphology and membrane integrity. The toxic effect is more drastic at higher concentrations. This study also indicates that cadmium requires a minimum one hour incubation time to exert its deletorious effects on various parameters of spermatozoa, particularly at low concentrations.

Method for combined biometric and chemical analysis of human fingerprints.

PubMed

Staymates, Jessica L; Orandi, Shahram; Staymates, Matthew E; Gillen, Greg

This paper describes a method for combining direct chemical analysis of latent fingerprints with subsequent biometric analysis within a single sample. The method described here uses ion mobility spectrometry (IMS) as a chemical detection method for explosives and narcotics trace contamination. A collection swab coated with a high-temperature adhesive has been developed to lift latent fingerprints from various surfaces. The swab is then directly inserted into an IMS instrument for a quick chemical analysis. After the IMS analysis, the lifted print remains intact for subsequent biometric scanning and analysis using matching algorithms. Several samples of explosive-laden fingerprints were successfully lifted and the explosives detected with IMS. Following explosive detection, the lifted fingerprints remained of sufficient quality for positive match scores using a prepared gallery consisting of 60 fingerprints. Based on our results ( n  = 1200), there was no significant decrease in the quality of the lifted print post IMS analysis. In fact, for a small subset of lifted prints, the quality was improved after IMS analysis. The described method can be readily applied to domestic criminal investigations, transportation security, terrorist and bombing threats, and military in-theatre settings.

Early diagnosis of orthopedic implant failure using macromolecular imaging agents.

PubMed

Ren, Ke; Dusad, Anand; Zhang, Yijia; Purdue, P Edward; Fehringer, Edward V; Garvin, Kevin L; Goldring, Steven R; Wang, Dong

2014-08-01

To develop and evaluate diagnostic tools for early detection of wear particle-induced orthopaedic implant loosening. N-(2-Hydroxypropyl)methacrylamide (HPMA) copolymer was tagged with a near infrared dye and used to detect the inflammation induced by polymethylmethacrylate (PMMA) particles in a murine peri-implant osteolysis model. It was established by inserting an implant into the distal femur and challenging with routine PMMA particles infusion. The osteolysis was evaluated by micro-CT and histological analysis at different time points. Significant peri-implant osteolysis was found 3-month post PMMA particle challenge by micro-CT and histological analysis. At 1-month post challenge, when there was no significant peri-implant bone loss, the HPMA copolymer-near infrared dye conjugate was found to specifically target the femur with PMMA particles deposition, but not the contralateral control femur with phosphate buffered saline (PBS) infusion. The results from this study demonstrate the feasibility of utilizing the macromolecular diagnostic agent to detect particle-induced peri-implant inflammation prior to the development of detectable osteolysis. Recognition of this early pathological event would provide the window of opportunity for prevention of peri-implant osteolysis and subsequent orthopaedic implant failure.

Landsat change detection can aid in water quality monitoring

NASA Technical Reports Server (NTRS)

Macdonald, H. C.; Steele, K. F.; Waite, W. P.; Shinn, M. R.

1977-01-01

Comparison between Landsat-1 and -2 imagery of Arkansas provided evidence of significant land use changes during the 1972-75 time period. Analysis of Arkansas historical water quality information has shown conclusively that whereas point source pollution generally can be detected by use of water quality data collected by state and federal agencies, sampling methodologies for nonpoint source contamination attributable to surface runoff are totally inadequate. The expensive undertaking of monitoring all nonpoint sources for numerous watersheds can be lessened by implementing Landsat change detection analyses.

Linear-array EUS improves detection of pancreatic lesions in high-risk individuals: a randomized tandem study

PubMed Central

Shin, Eun Ji; Topazian, Mark; Goggins, Michael G.; Syngal, Sapna; Saltzman, John R.; Lee, Jeffrey H.; Farrell, James J.; Canto, Marcia I.

2015-01-01

Background Studies comparing linear and radial EUS for the detection of pancreatic lesions in an asymptomatic population with increased risk for pancreatic cancer are lacking. Objectives To compare pancreatic lesion detection rates between radial and linear EUS and to determine the incremental diagnostic yield of a second EUS examination. Design Randomized controlled tandem study. Setting Five academic centers in the United States. Patients Asymptomatic high-risk individuals (HRIs) for pancreatic cancer undergoing screening EUS. Interventions Linear and radial EUS performed in randomized order. Main Outcome Measurements Pancreatic lesion detection rate by type of EUS, miss rate of 1 EUS examination, and incremental diagnostic yield of a second EUS examination (second-pass effect). Results Two hundred seventy-eight HRIs were enrolled, mean age 56 years (43.2%), and 90% were familial pancreatic cancer relatives. Two hundred twenty-four HRIs underwent tandem radial and linear EUS. When we used per-patient analysis, the overall prevalence of any pancreatic lesion was 45%. Overall, 16 of 224 HRIs (7.1%) had lesions missed during the initial EUS that were detected by the second EUS examination. The per-patient lesion miss rate was significantly greater for radial followed by linear EUS (9.8%) than for linear followed by radial EUS (4.5%) (P = .03). When we used per-lesion analysis, 73 of 109 lesions (67%) were detected by radial EUS and 99 of 120 lesions (82%) were detected by linear EUS (P < .001) during the first examination. The overall miss rate for a pancreatic lesion after 1 EUS examination was 47 of 229 (25%). The miss rate was significantly lower for linear EUS compared with radial EUS (17.5% vs 33.0%, P = .007). Limitations Most detected pancreatic lesions were not confirmed by pathology. Conclusion Linear EUS detects more pancreatic lesions than radial EUS. There was a “second-pass effect” with additional lesions detected with a second EUS examination. This effect was significantly greater when linear EUS was used after an initial radial EUS examination. PMID:25930097

Linear-array EUS improves detection of pancreatic lesions in high-risk individuals: a randomized tandem study.

PubMed

Shin, Eun Ji; Topazian, Mark; Goggins, Michael G; Syngal, Sapna; Saltzman, John R; Lee, Jeffrey H; Farrell, James J; Canto, Marcia I

2015-11-01

Studies comparing linear and radial EUS for the detection of pancreatic lesions in an asymptomatic population with increased risk for pancreatic cancer are lacking. To compare pancreatic lesion detection rates between radial and linear EUS and to determine the incremental diagnostic yield of a second EUS examination. Randomized controlled tandem study. Five academic centers in the United States. Asymptomatic high-risk individuals (HRIs) for pancreatic cancer undergoing screening EUS. Linear and radial EUS performed in randomized order. Pancreatic lesion detection rate by type of EUS, miss rate of 1 EUS examination, and incremental diagnostic yield of a second EUS examination (second-pass effect). Two hundred seventy-eight HRIs were enrolled, mean age 56 years (43.2%), and 90% were familial pancreatic cancer relatives. Two hundred twenty-four HRIs underwent tandem radial and linear EUS. When we used per-patient analysis, the overall prevalence of any pancreatic lesion was 45%. Overall, 16 of 224 HRIs (7.1%) had lesions missed during the initial EUS that were detected by the second EUS examination. The per-patient lesion miss rate was significantly greater for radial followed by linear EUS (9.8%) than for linear followed by radial EUS (4.5%) (P = .03). When we used per-lesion analysis, 73 of 109 lesions (67%) were detected by radial EUS and 99 of 120 lesions (82%) were detected by linear EUS (P < .001) during the first examination. The overall miss rate for a pancreatic lesion after 1 EUS examination was 47 of 229 (25%). The miss rate was significantly lower for linear EUS compared with radial EUS (17.5% vs 33.0%, P = .007). Most detected pancreatic lesions were not confirmed by pathology. Linear EUS detects more pancreatic lesions than radial EUS. There was a "second-pass effect" with additional lesions detected with a second EUS examination. This effect was significantly greater when linear EUS was used after an initial radial EUS examination. Copyright © 2015 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: Sources and avoidance of false-positive detection.

PubMed

Owa, Chie; Poulin, Matthew; Yan, Liying; Shioda, Toshi

2018-01-01

The existence of cytosine methylation in mammalian mitochondrial DNA (mtDNA) is a controversial subject. Because detection of DNA methylation depends on resistance of 5'-modified cytosines to bisulfite-catalyzed conversion to uracil, examined parameters that affect technical adequacy of mtDNA methylation analysis. Negative control amplicons (NCAs) devoid of cytosine methylation were amplified to cover the entire human or mouse mtDNA by long-range PCR. When the pyrosequencing template amplicons were gel-purified after bisulfite conversion, bisulfite pyrosequencing of NCAs did not detect significant levels of bisulfite-resistant cytosines (brCs) at ND1 (7 CpG sites) or CYTB (8 CpG sites) genes (CI95 = 0%-0.94%); without gel-purification, significant false-positive brCs were detected from NCAs (CI95 = 4.2%-6.8%). Bisulfite pyrosequencing of highly purified, linearized mtDNA isolated from human iPS cells or mouse liver detected significant brCs (~30%) in human ND1 gene when the sequencing primer was not selective in bisulfite-converted and unconverted templates. However, repeated experiments using a sequencing primer selective in bisulfite-converted templates almost completely (< 0.8%) suppressed brC detection, supporting the false-positive nature of brCs detected using the non-selective primer. Bisulfite-seq deep sequencing of linearized, gel-purified human mtDNA detected 9.4%-14.8% brCs for 9 CpG sites in ND1 gene. However, because all these brCs were associated with adjacent non-CpG brCs showing the same degrees of bisulfite resistance, DNA methylation in this mtDNA-encoded gene was not confirmed. Without linearization, data generated by bisulfite pyrosequencing or deep sequencing of purified mtDNA templates did not pass the quality control criteria. Shotgun bisulfite sequencing of human mtDNA detected extremely low levels of CpG methylation (<0.65%) over non-CpG methylation (<0.55%). Taken together, our study demonstrates that adequacy of mtDNA methylation analysis using methods dependent on bisulfite conversion needs to be established for each experiment, taking effects of incomplete bisulfite conversion and template impurity or topology into consideration.

Use of next-generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia[S

PubMed Central

Iacocca, Michael A.; Wang, Jian; Dron, Jacqueline S.; Robinson, John F.; McIntyre, Adam D.; Cao, Henian

2017-01-01

Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene (LDLR). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories. PMID:28874442

Simultaneous analysis of six aldehyde-DNA adducts in salivary DNA of nonsmokers and smokers using stable isotope dilution liquid chromatography electrospray ionization-tandem mass spectrometry.

PubMed

Li, Xiangyu; Liu, Lujuan; Wang, Hongjuan; Chen, Jian; Zhu, Beibei; Chen, Huan; Hou, Hongwei; Hu, Qingyuan

2017-08-15

A stable method, using isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS), to simultaneously determine six aldehyde-DNA adducts was developed and applied to the analysis of human salivary DNA samples. The detection limit of these six DNA adducts was in the range of 0.006-0.014ng/mL and that of the quantification limit was 0.017-0.026ng/mL. The intra-day and inter-day precision of all aldehyde-DNA adducts was <10%. The analysis was completed within 25min. Additionally, a noninvasive technique was used to collect the DNA samples from human saliva. The new method was successfully applied for the analysis of salivary DNA of nonsmokers and smokers. Five aldehyde-DNA adducts were detected in both smoker and nonsmoker salivary DNA, while α-Acr-dG was not detected in all the samples. Among these detected DNA adducts, no significant differences were found between smoker and nonsmoker (p>0.05). This may due to the individual detoxifying differences or environmental and endogenous exposure. Our study provides a rapid and selective method to simultaneously detect six aldehyde-DNA adducts and to assess potential DNA damage induced by aldehydes. Copyright © 2017 Elsevier B.V. All rights reserved.

A comparison of two follow-up analyses after multiple analysis of variance, analysis of variance, and descriptive discriminant analysis: A case study of the program effects on education-abroad programs

Treesearch

Alvin H. Yu; Garry Chick

2010-01-01

This study compared the utility of two different post-hoc tests after detecting significant differences within factors on multiple dependent variables using multivariate analysis of variance (MANOVA). We compared the univariate F test (the Scheffé method) to descriptive discriminant analysis (DDA) using an educational-tour survey of university study-...

Scientific fraud in 20 falsified anesthesia papers : detection using financial auditing methods.

PubMed

Hein, J; Zobrist, R; Konrad, C; Schuepfer, G

2012-06-01

Data from natural sources show counter-intuitive distribution patterns for the leading digits to the left of the decimal point and the digit 1 is observed more frequently than all other numbers. This pattern, which was first described by Newcomb and later confirmed by Benford, is used in financial and tax auditing to detect fraud. Deviations from the pattern indicate possible falsifications. Anesthesiology journals are affected not only by ghostwriting and plagiarism but also by counterfeiting. In the present study 20 publications in anesthesiology known to be falsified by an author were investigated for irregularities with respect to Benford's law using the χ(2)-test and the Z-test. In the 20 retracted publications an average first-digit frequency of 243.1 (standard deviation SD ± 118.2, range: 30-592) and an average second-digit frequency of 132.3 (SD ± 72.2, range: 15-383) were found. The observed distribution of the first and second digits to the left of the decimal point differed significantly (p< 0.01) from the expected distribution described by Benford. Only the observed absolute frequencies for digits 3, 4 and 5 did not differ significantly from the expected values. In an analysis of each paper 17 out of 20 studies differed significantly from the expected value for the first digit and 18 out of 20 studies varied significantly from the expected value of the second digit. Only one paper did not vary significantly from expected values for the digits to the left of the decimal. For comparison, a meta-analysis using complex mathematical procedures was chosen as a control. The analysis showed a first-digit distribution consistent with the Benford distribution. Thus, the method used in the present study seems to be sensitive for detecting fraud. Additional statements of specificity cannot yet be made as this requires further analysis of data that is definitely not falsified. Future studies exploring conformity might help prevent falsified studies from being published.

Video content analysis of surgical procedures.

PubMed

Loukas, Constantinos

2018-02-01

In addition to its therapeutic benefits, minimally invasive surgery offers the potential for video recording of the operation. The videos may be archived and used later for reasons such as cognitive training, skills assessment, and workflow analysis. Methods from the major field of video content analysis and representation are increasingly applied in the surgical domain. In this paper, we review recent developments and analyze future directions in the field of content-based video analysis of surgical operations. The review was obtained from PubMed and Google Scholar search on combinations of the following keywords: 'surgery', 'video', 'phase', 'task', 'skills', 'event', 'shot', 'analysis', 'retrieval', 'detection', 'classification', and 'recognition'. The collected articles were categorized and reviewed based on the technical goal sought, type of surgery performed, and structure of the operation. A total of 81 articles were included. The publication activity is constantly increasing; more than 50% of these articles were published in the last 3 years. Significant research has been performed for video task detection and retrieval in eye surgery. In endoscopic surgery, the research activity is more diverse: gesture/task classification, skills assessment, tool type recognition, shot/event detection and retrieval. Recent works employ deep neural networks for phase and tool recognition as well as shot detection. Content-based video analysis of surgical operations is a rapidly expanding field. Several future prospects for research exist including, inter alia, shot boundary detection, keyframe extraction, video summarization, pattern discovery, and video annotation. The development of publicly available benchmark datasets to evaluate and compare task-specific algorithms is essential.

Three-dimensional images contribute to the diagnosis of mucous retention cyst in maxillary sinus

PubMed Central

Donizeth-Rodrigues, Cleomar; Fonseca-Da Silveira, Márcia; Gonçalves-De Alencar, Ana H.; Garcia-Santos-Silva, Maria A.; Francisco-De-Mendonça, Elismauro

2013-01-01

Objective: To evaluate the detection of mucous retention cyst of maxillary sinus (MRCMS) using panoramic radiography and cone beam computed tomography (CBCT). Study Design: A digital database with 6,000 panoramic radiographs was reviewed for MRCMS. Suggestive images of MRCMS were detected on 185 radiographs, and patients were located and invited to return for follow-up. Thirty patients returned, and control panoramic radiographs were obtained 6 to 46 months after the initial radiograph. When MRCMS was found on control radiographs, CBCT scans were obtained. Cysts were measured and compared on radiographs and scans. The Wilcoxon, Spearman and Kolmorogov-Smirnov tests were used for statistical analysis. The level of significance was set at 5%. Results: There were statistically significant differences between the two methods (p<0.05): 23 MRCMS detected on panoramic radiographs were confirmed by CBCT, but 5 MRCMS detected on CBCT images had not been identified by panoramic radiography. Eight MRCMS detected on control radiographs were not confirmed by CBCT. MRCMS size differences from initial to control panoramic radiographs and CBCT scans were not statistically significant (p= 0.617 and p= 0.626). The correlation between time and MRCMS size differences was not significant (r = -0.16, p = 0.381). Conclusion: CBCT scanning detect MRCMS more accurately than panoramic radiography. Key words:Mucous cyst, maxillary sinus, panoramic radiograph, cone beam computed tomography. PMID:23229251

Application of PCR-LDR-nucleic acid detection strip in detection of YMDD mutation in hepatitis B patients treated with lamivudine.

PubMed

Xu, Gaolian; You, Qimin; Pickerill, Sam; Zhong, Huayan; Wang, Hongying; Shi, Jian; Luo, Ying; You, Paul; Kong, Huimin; Lu, Fengmin; Hu, Lin

2010-07-01

Chronic hepatitis B virus (CHBV) infection causes cirrhosis and hepatocellular carcinoma. Lamivudine (LAM) has been successfully used to treat CHBV infections but prolonged use leads to the emergence of drug-resistant variants. This is primarily linked to a mutation in the tyrosine-methionine-aspartate-aspartate (YMDD) motif of the HBV polymerase gene at position 204. Rapid diagnosis of drug-resistant HBV is necessary for a prompt treatment response. Common diagnostic methods such as sequencing and restriction fragment length polymorphism (RFLP) analysis lack sensitivity and require significant processing. The aim of this study was to demonstrate the usefulness of a novel diagnostic method that combines polymerase chain reaction (PCR), ligase detection reaction (LDR) and a nucleic acid detection strip (NADS) in detecting site-specific mutations related to HBV LAM resistance. We compared this method (PLNA) to direct sequencing and RFLP analysis in 50 clinical samples from HBV infected patients. There was 90% concordance between all three results. PLNA detected more samples containing mutant variants than both sequencing and RFLP analysis and was more sensitive in detecting mixed variant populations. Plasmid standards indicated that the sensitivity of PLNA is at or below 3,000 copies per ml and that it can detect a minor variant at 5% of the total viral population. This warrants its further development and suggests that the PLNA method could be a useful tool in detecting LAM resistance. (c) 2010 Wiley-Liss, Inc.

Real-time detection of deoxyribonucleic acid bases via their negative differential conductance signature.

PubMed

Dragoman, D; Dragoman, M

2009-08-01

In this Brief Report, we present a method for the real-time detection of the bases of the deoxyribonucleic acid using their signatures in negative differential conductance measurements. The present methods of electronic detection of deoxyribonucleic acid bases are based on a statistical analysis because the electrical currents of the four bases are weak and do not differ significantly from one base to another. In contrast, we analyze a device that combines the accumulated knowledge in nanopore and scanning tunneling detection and which is able to provide very distinctive electronic signatures for the four bases.

A gas ionisation detector in the axial (Bragg) geometry used for the time-of-flight elastic recoil detection analysis

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

Siketić, Zdravko; Skukan, Natko; Bogdanović Radović, Iva

2015-08-15

In this paper, time-of-flight elastic recoil detection analysis spectrometer with a newly constructed gas ionization detector for energy detection is presented. The detector is designed in the axial (Bragg) geometry with a 3 × 3 array of 50 nm thick Si{sub 3}N{sub 4} membranes as an entrance window. 40 mbar isobutane gas was sufficient to stop a 30 MeV primary iodine beam as well as all recoils in the detector volume. Spectrometer and detector performances were determined showing significant improvement in the mass and energy resolution, respectively, comparing to the spectrometer with a standard silicon particle detector for an energymore » measurement.« less

Accuracy of MSCT Coronary Angiography with 64 Row CT Scanner—Facing the Facts

PubMed Central

Wehrschuetz, M.; Wehrschuetz, E.; Schuchlenz, H.; Schaffler, G.

2010-01-01

Improvements in multislice computed tomography (MSCT) angiography of the coronary vessels have enabled the minimally invasive detection of coronary artery stenoses, while quantitative coronary angiography (QCA) is the accepted reference standard for evaluation thereof. Sixteen-slice MSCT showed promising diagnostic accuracy in detecting coronary artery stenoses haemodynamically and the subsequent introduction of 64-slice scanners promised excellent and fast results for coronary artery studies. This prompted us to evaluate the diagnostic accuracy, sensitivity, specificity, and the negative und positive predictive value of 64-slice MSCT in the detection of haemodynamically significant coronary artery stenoses. Thirty-seven consecutive subjects with suspected coronary artery disease were evaluated with MSCT angiography and the results compared with QCA. All vessels were considered for the assessment of significant coronary artery stenosis (diameter reduction ≥ 50%). Thirteen patients (35%) were identified as having significant coronary artery stenoses on QCA with 6.3% (35/555) affected segments. None of the coronary segments were excluded from analysis. Overall sensitivity for classifying stenoses of 64-slice MSCT was 69%, specificity was 92%, positive predictive value was 38% and negative predictive value was 98%. The interobserver variability for detection of significant lesions had a k-value of 0.43. Sixty-four-slice MSCT offers the diagnostic potential to detect coronary artery disease, to quantify haemodynamically significant coronary artery stenoses and to avoid unnecessary invasive coronary artery examinations. PMID:20567636

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

PubMed

Dessimoz, Christophe; Boeckmann, Brigitte; Roth, Alexander C J; Gonnet, Gaston H

2006-01-01

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.

Detection of a gravitropism phenotype in glutamate receptor-like 3.3 mutants of Arabidopsis thaliana using machine vision and computation.

PubMed

Miller, Nathan D; Durham Brooks, Tessa L; Assadi, Amir H; Spalding, Edgar P

2010-10-01

Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca(2+)-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function.

Detection of a Gravitropism Phenotype in glutamate receptor-like 3.3 Mutants of Arabidopsis thaliana Using Machine Vision and Computation

PubMed Central

Miller, Nathan D.; Durham Brooks, Tessa L.; Assadi, Amir H.; Spalding, Edgar P.

2010-01-01

Gene disruption frequently produces no phenotype in the model plant Arabidopsis thaliana, complicating studies of gene function. Functional redundancy between gene family members is one common explanation but inadequate detection methods could also be responsible. Here, newly developed methods for automated capture and processing of time series of images, followed by computational analysis employing modified linear discriminant analysis (LDA) and wavelet-based differentiation, were employed in a study of mutants lacking the Glutamate Receptor-Like 3.3 gene. Root gravitropism was selected as the process to study with high spatiotemporal resolution because the ligand-gated Ca2+-permeable channel encoded by GLR3.3 may contribute to the ion fluxes associated with gravity signal transduction in roots. Time series of root tip angles were collected from wild type and two different glr3.3 mutants across a grid of seed-size and seedling-age conditions previously found to be important to gravitropism. Statistical tests of average responses detected no significant difference between populations, but LDA separated both mutant alleles from the wild type. After projecting the data onto LDA solution vectors, glr3.3 mutants displayed greater population variance than the wild type in all four conditions. In three conditions the projection means also differed significantly between mutant and wild type. Wavelet analysis of the raw response curves showed that the LDA-detected phenotypes related to an early deceleration and subsequent slower-bending phase in glr3.3 mutants. These statistically significant, heritable, computation-based phenotypes generated insight into functions of GLR3.3 in gravitropism. The methods could be generally applicable to the study of phenotypes and therefore gene function. PMID:20647506

Computer-aided detection of breast masses: Four-view strategy for screening mammography

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

Wei Jun; Chan Heangping; Zhou Chuan

2011-04-15

Purpose: To improve the performance of a computer-aided detection (CAD) system for mass detection by using four-view information in screening mammography. Methods: The authors developed a four-view CAD system that emulates radiologists' reading by using the craniocaudal and mediolateral oblique views of the ipsilateral breast to reduce false positives (FPs) and the corresponding views of the contralateral breast to detect asymmetry. The CAD system consists of four major components: (1) Initial detection of breast masses on individual views, (2) information fusion of the ipsilateral views of the breast (referred to as two-view analysis), (3) information fusion of the corresponding viewsmore » of the contralateral breast (referred to as bilateral analysis), and (4) fusion of the four-view information with a decision tree. The authors collected two data sets for training and testing of the CAD system: A mass set containing 389 patients with 389 biopsy-proven masses and a normal set containing 200 normal subjects. All cases had four-view mammograms. The true locations of the masses on the mammograms were identified by an experienced MQSA radiologist. The authors randomly divided the mass set into two independent sets for cross validation training and testing. The overall test performance was assessed by averaging the free response receiver operating characteristic (FROC) curves of the two test subsets. The FP rates during the FROC analysis were estimated by using the normal set only. The jackknife free-response ROC (JAFROC) method was used to estimate the statistical significance of the difference between the test FROC curves obtained with the single-view and the four-view CAD systems. Results: Using the single-view CAD system, the breast-based test sensitivities were 58% and 77% at the FP rates of 0.5 and 1.0 per image, respectively. With the four-view CAD system, the breast-based test sensitivities were improved to 76% and 87% at the corresponding FP rates, respectively. The improvement was found to be statistically significant (p<0.0001) by JAFROC analysis. Conclusions: The four-view information fusion approach that emulates radiologists' reading strategy significantly improves the performance of breast mass detection of the CAD system in comparison with the single-view approach.« less

Oral bacteria influenced by the functional status of the elderly people and the type and quality of facilities for the bedridden.

PubMed

Tada, A; Watanabe, T; Yokoe, H; Hanada, N; Tanzawa, H

2002-01-01

To analyse the relationship between oral bacteria and the health and functional status of the elderly. The bacteria species in the oral cavity of the elderly were examined. It was found that the bedridden subjects staying at two hospitals for long-term (HOBR) showed significantly lower detection rates of commensal bacteria species and significantly higher detection rates of Pseudomonas aeruginosa, of methicillin-resistant Staphylococcus aureus (MRSA) and of coagulase(-) Staph. aureus than those living independently (the independent). In addition, the detection rate of Haemophilus parainfluenzae in NUBR was discovered to be higher than that found in the independent. In HOBR, the detection rate of Ps. aeruginosa was significantly higher among in-patients who required continual care than those in need of partial care, while the detection rate of MRSA was significantly higher among in-patients with low serum albumin than those with normal serum albumin. Oral bacteria examination analysis proved that the risks of infection of some pathogenic bacteria species were correlated with functional status, physical function and nutritional state. Our study suggests that the oral bacteria, especially pathogenic bacteria were influenced by the functional status of the elderly and the type and quality of the facilities for the bedridden, physical function and nutritional state.

Acoustic Analysis and Electroglottography in Elite Vocal Performers.

PubMed

Villafuerte-Gonzalez, Rocio; Valadez-Jimenez, Victor M; Sierra-Ramirez, Jose A; Ysunza, Pablo Antonio; Chavarria-Villafuerte, Karen; Hernandez-Lopez, Xochiquetzal

2017-05-01

Acoustic analysis of voice (AAV) and electroglottography (EGG) have been used for assessing vocal quality in patients with voice disorders. The effectiveness of these procedures for detecting mild disturbances in vocal quality in elite vocal performers has been controversial. To compare acoustic parameters obtained by AAV and EGG before and after vocal training to determine the effectiveness of these procedures for detecting vocal improvements in elite vocal performers. Thirty-three elite vocal performers were studied. The study group included 14 males and 19 females, ages 18-40 years, without a history of voice disorders. Acoustic parameters were obtained through AAV and EGG before and after vocal training using the Linklater method. Nonsignificant differences (P > 0.05) were found between values of fundamental frequency (F 0 ), shimmer, and jitter obtained by both procedures before vocal training. Mean F 0 was similar after vocal training. Jitter percentage as measured by AAV showed nonsignificant differences (P > 0.05) before and after vocal training. Shimmer percentage as measured by AAV demonstrated a significant reduction (P < 0.05) after vocal training. As measured by EGG after vocal training, shimmer and jitter were significantly reduced (P < 0.05); open quotient was significantly increased (P < 0.05); and irregularity was significantly reduced (P < 0.05). AAV and EGG were effective for detecting improvements in vocal function after vocal training in male and female elite vocal performers undergoing vocal training. EGG demonstrated better efficacy for detecting improvements and provided additional parameters as compared to AAV. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Botulinum neurotoxin: where are we with detection technologies?

PubMed

Singh, Ajay K; Stanker, Larry H; Sharma, Shashi K

2013-02-01

Because of its high toxicity, botulinum neurotoxin (BoNT) poses a significant risk to humans and it represents a possible biological warfare agent. Nevertheless, BoNT serotypes A and B are considered an effective treatment for a variety of neurological disorders. The growing applicability of BoNT as a drug, and its potential use as a biological threat agent, highlight the urgent need to develop sensitive detection assays and therapeutic counter measures. In the last decade, significant progress has been made in BoNT detection technologies but none have fully replaced the mouse lethality assay, the current "gold standard". Recently, new advances in robotics and the availability of new reagents have allowed development of methods for rapid toxin analysis. These technologies while promising need further refinement.

A hybrid correlation analysis with application to imaging genetics

NASA Astrophysics Data System (ADS)

Hu, Wenxing; Fang, Jian; Calhoun, Vince D.; Wang, Yu-Ping

2018-03-01

Investigating the association between brain regions and genes continues to be a challenging topic in imaging genetics. Current brain region of interest (ROI)-gene association studies normally reduce data dimension by averaging the value of voxels in each ROI. This averaging may lead to a loss of information due to the existence of functional sub-regions. Pearson correlation is widely used for association analysis. However, it only detects linear correlation whereas nonlinear correlation may exist among ROIs. In this work, we introduced distance correlation to ROI-gene association analysis, which can detect both linear and nonlinear correlations and overcome the limitation of averaging operations by taking advantage of the information at each voxel. Nevertheless, distance correlation usually has a much lower value than Pearson correlation. To address this problem, we proposed a hybrid correlation analysis approach, by applying canonical correlation analysis (CCA) to the distance covariance matrix instead of directly computing distance correlation. Incorporating CCA into distance correlation approach may be more suitable for complex disease study because it can detect highly associated pairs of ROI and gene groups, and may improve the distance correlation level and statistical power. In addition, we developed a novel nonlinear CCA, called distance kernel CCA, which seeks the optimal combination of features with the most significant dependence. This approach was applied to imaging genetic data from the Philadelphia Neurodevelopmental Cohort (PNC). Experiments showed that our hybrid approach produced more consistent results than conventional CCA across resampling and both the correlation and statistical significance were increased compared to distance correlation analysis. Further gene enrichment analysis and region of interest (ROI) analysis confirmed the associations of the identified genes with brain ROIs. Therefore, our approach provides a powerful tool for finding the correlation between brain imaging and genomic data.

Nonlinear, non-stationary image processing technique for eddy current NDE

NASA Astrophysics Data System (ADS)

Yang, Guang; Dib, Gerges; Kim, Jaejoon; Zhang, Lu; Xin, Junjun; Udpa, Lalita

2012-05-01

Automatic analysis of eddy current (EC) data has facilitated the analysis of large volumes of data generated in the inspection of steam generator tubes in nuclear power plants. The traditional procedure for analysis of EC data includes data calibration, pre-processing, region of interest (ROI) detection, feature extraction and classification. Accurate ROI detection has been enhanced by pre-processing, which involves reducing noise and other undesirable components as well as enhancing defect indications in the raw measurement. This paper presents the Hilbert-Huang Transform (HHT) for feature extraction and support vector machine (SVM) for classification. The performance is shown to significantly better than the existing rule based classification approach used in industry.

Evaluation of BACTEC 9240 blood culture system by using high-volume aerobic resin media.

PubMed Central

Schwabe, L D; Thomson, R B; Flint, K K; Koontz, F P

1995-01-01

The BACTEC 9240 blood culture system (Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) is one of three automated, continuous-monitoring systems that is widely used in clinical laboratories. The BACTEC 9240 was compared with the BACTEC NR 660 for the detection of organisms and bacteremic episodes; time to detection of positive cultures; number of false-positive and false-negative cultures; and time needed to load, process, and perform quality control functions by using high-volume aerobic media. Blood specimens (5,282) were inoculated in equal volumes (5 to 10 ml per bottle) into BACTEC Plus Aerobic/F (9240 system) and BACTEC Plus NR26 (660 system) bottles. Clinically significant isolates were detected in 6.6% of cultures, representing 348 microorganisms and 216 bacteremic episodes. Two hundred forty-eight microorganisms were detected by both systems, 48 by the 9240 only and 52 by the 660 only (P = not significant). Of the bacteremic episodes, 158 were detected by both systems, 27 by the 9240 only and 31 by the 660 only (P = not significant). Analysis of data by month revealed equivalent recovery rates for both systems, with the exception of a 30-day period at one study site during which the 660 system detected significantly more microorganisms. Following a proprietary hardware design retrofit of the 9240 instrument, detection rates were again equivalent for the remaining three months at this study site. Positive cultures detected by both systems were detected an average of 4.3 h faster by the 9240 system (21 versus 25.3 h). The numbers of false-positive cultures for the 9240 and 660 systems were 40 (1.0%) and 9 ( < 1.0%), respectively.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7494044

Comparing GWAS Results of Complex Traits Using Full Genetic Model and Additive Models for Revealing Genetic Architecture

PubMed Central

Monir, Md. Mamun; Zhu, Jun

2017-01-01

Most of the genome-wide association studies (GWASs) for human complex diseases have ignored dominance, epistasis and ethnic interactions. We conducted comparative GWASs for total cholesterol using full model and additive models, which illustrate the impacts of the ignoring genetic variants on analysis results and demonstrate how genetic effects of multiple loci could differ across different ethnic groups. There were 15 quantitative trait loci with 13 individual loci and 3 pairs of epistasis loci identified by full model, whereas only 14 loci (9 common loci and 5 different loci) identified by multi-loci additive model. Again, 4 full model detected loci were not detected using multi-loci additive model. PLINK-analysis identified two loci and GCTA-analysis detected only one locus with genome-wide significance. Full model identified three previously reported genes as well as several new genes. Bioinformatics analysis showed some new genes are related with cholesterol related chemicals and/or diseases. Analyses of cholesterol data and simulation studies revealed that the full model performs were better than the additive-model performs in terms of detecting power and unbiased estimations of genetic variants of complex traits. PMID:28079101

Preliminary analysis for trends in selected water-quality characteristics, Powder River, Montana and Wyoming, water years 1952-85

USGS Publications Warehouse

Cary, L.E.

1989-01-01

Selected water-quality data from two streamflow-gaging stations on the Powder River, Montana and Wyoming, were statistically analyzed for trends using the seasonal Kendall test. Data for water years 1952-63 and 1975-85 from the Powder River near Locate, Montana, and water years 1967-68 and 1976-85 from the Powder River at Sussex, Wyoming, were analyzed. Data for the earlier period near Locate were discharge-weighted monthly mean values, whereas data for the late period near Locate and at Sussex were from periodic samples. For data from water years 1952-63 near Locate, increasing trends were detected in sodium and sodium-adsorption ratio; no trends were detected in specific conductance, hardness, non-carbonate hardness, alkalinity, dissolved solids, or sulfate. For data from water years 1975-85 near Locate, increasing trends were detected in specific conductance, sodium, sodium-adsorption ratio, and chloride; no trends were detected in hardness, noncarbonate hardness, alkalinity, dissolved solids, calcium, magnesium, potassium, or sulfate. At Sussex (water years 1967-68 and 1976-85), increasing trends were detected in sodium, sodium-adsorption ratio, and chloride, and a decreasing trend was detected in sulfate. No trends were detected in specific conductance, alkalinity, or dissolved solids. When the 1967-68 data were deleted and the analysis repeated for the 1976-85 data, only sodium-adsorption ratio displayed a significant (increasing) trend. Because the study was exploratory, causes and effects were not considered. The results might have been affected by sample size, number of seasons, heterogeneity, significance level, serial correlation, and data adjustment for changes in discharge. (USGS)

Analytical methods for determination of mycotoxins: a review.

PubMed

Turner, Nicholas W; Subrahmanyam, Sreenath; Piletsky, Sergey A

2009-01-26

Mycotoxins are small (MW approximately 700), toxic chemical products formed as secondary metabolites by a few fungal species that readily colonise crops and contaminate them with toxins in the field or after harvest. Ochratoxins and Aflatoxins are mycotoxins of major significance and hence there has been significant research on broad range of analytical and detection techniques that could be useful and practical. Due to the variety of structures of these toxins, it is impossible to use one standard technique for analysis and/or detection. Practical requirements for high-sensitivity analysis and the need for a specialist laboratory setting create challenges for routine analysis. Several existing analytical techniques, which offer flexible and broad-based methods of analysis and in some cases detection, have been discussed in this manuscript. There are a number of methods used, of which many are lab-based, but to our knowledge there seems to be no single technique that stands out above the rest, although analytical liquid chromatography, commonly linked with mass spectroscopy is likely to be popular. This review manuscript discusses (a) sample pre-treatment methods such as liquid-liquid extraction (LLE), supercritical fluid extraction (SFE), solid phase extraction (SPE), (b) separation methods such as (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC), and capillary electrophoresis (CE) and (c) others such as ELISA. Further currents trends, advantages and disadvantages and future prospects of these methods have been discussed.

The fabrication of magnetic particle-based chemiluminescence immunoassay for human epididymis protein-4 detection in ovarian cancer.

PubMed

Fu, Xiaoling; Liu, Yangyang; Qiu, Ruiyun; Foda, Mohamed F; Zhang, Yong; Wang, Tao; Li, Jinshan

2018-03-01

The magnetic particles have a significant influence on the immunoassay detection and cancer therapy. Herein, the chemiluminescence immunoassay combined with the magnetic particles (MPCLIA) was presented for the clinical determination and analysis of human epididymis protein 4 (HE4) in the human serum. Under the optimized experiment conditions, the secure MPCLIA method can detect HE4 in the broader range of 0-1000 pmol/L, with a lower detection limit of 1.35 pmol/L. The satisfactory recovery rate of the method in the serum ranged from 83.62% to 105.10%, which was well within the requirement of clinical analysis. Moreover, the results showed the good correlation with enzyme-linked immunosorbent assay (ELISA), with the correlation coefficient of 0.9589. This proposed method has been successfully applied to the clinical determination of HE4 in the human serum.

Rapid detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV) by real-time, isothermal recombinase polymerase amplification assay.

PubMed

Xia, Xiaoming; Yu, Yongxin; Hu, Linghao; Weidmann, Manfred; Pan, Yingjie; Yan, Shuling; Wang, Yongjie

2015-04-01

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) causes mortality or runt deformity syndrome in penaeid shrimps and is responsible for significant economic losses in the shrimp aquaculture industry. Here, we describe a novel real-time isothermal recombinase polymerase amplification (RPA) assay developed for IHHNV detection. Using IHHNV plasmid standards and DNA samples from a variety of organisms, we evaluated the ability of the IHHNV-RPA assay to detect IHHNV based on analysis of its sensitivity, specificity, rapidity, and reproducibility. Probit analysis of eight independent experimental replicates indicated satisfactory performance of the RPA assay, which is sufficiently sensitive to detect as few as 4 copies of the IHHNV genome within 7 min at 39 °C with 95 % reliability. Therefore, this rapid RPA method has great potential for applications, either in field use or as a point of care diagnostic technique.

Facial arthralgia and myalgia: can they be differentiated by trigeminal sensory assessment?

PubMed

Eliav, Eli; Teich, Sorin; Nitzan, Dorit; El Raziq, Daood Abid; Nahlieli, Oded; Tal, Michael; Gracely, Richard H; Benoliel, Rafael

2003-08-01

Heat and electrical detection thresholds were assessed in 72 patients suffering from painful temporomandibular disorder. Employing widely accepted criteria, 44 patients were classified as suffering from temporomandibular joint (TMJ) arthralgia (i.e. pain originating from the TMJ) and 28 from myalgia (i.e. pain originating from the muscles of mastication). Electrical stimulation was employed to assess thresholds in large myelinated nerve fibers (Abeta) and heat application to assess thresholds in unmyelinated nerve fibers (C). The sensory tests were performed bilaterally in three trigeminal nerve sites: the auriculotemporal nerve territory (AUT), buccal nerve territory (BUC) and the mental nerve territory (MNT). In addition, 22 healthy asymptomatic controls were examined. A subset of ten arthralgia patients underwent arthrocentesis and electrical detection thresholds were additionally assessed following the procedure. Electrical detection threshold ratios were calculated by dividing the affected side by the control side, thus reduced ratios indicate hypersensitivity of the affected side. In control patients, ratios obtained at all sites did not vary significantly from the expected value of 'one' (mean with 95% confidence intervals; AUT, 1:0.95-1.06; BUC, 1.01:0.93-1.11; MNT, 0.97:0.88-1.05, all areas one sample analysis P>0.05). In arthralgia patients mean ratios (+/-SEM) obtained for the AUT territory (0.63+/-0.03) were significantly lower compared to ratios for the MNT (1.02+/-0.03) and BUC (0.96+/-0.04) territories (repeated measures analysis of variance (RANOVA), P<0.0001) and compared to the AUT ratios in myalgia (1.27+/-0.09) and control subjects (1+/-0.06, ANOVA, P<0.0001). In the myalgia group the electrical detection threshold ratios in the AUT territory were significantly elevated compared to the AUT ratios in control subjects (Dunnett test, P<0.05), but only approached statistical significance compared to the MNT (1.07+/-0.04) and BUC (1.11+/-0.06) territories (RANOVA, F(2,27)=3.12, P=0.052). There were no significant differences between and within the groups for electrical detection threshold ratios in the BUC and MNT nerve territories, and for the heat detection thresholds in all tested sites. Following arthrocentesis, mean electrical detection threshold ratios in the AUT territory were significantly elevated from 0.64+/-0.06 to 0.99+/-0.04 indicating resolution of the hypersensitivity (paired t-test, P=0.001). In conclusion, large myelinated fiber hypersensitivity is found in the skin overlying TMJs with clinical pain and pathology but is not found in controls. In patients with muscle-related facial pain there was significant elevation of the electrical detection threshold in the AUT region.

Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies

PubMed Central

Bernal-Casas, David; Fang, Zhongnan; Lee, Jin Hyung

2017-01-01

A large number of fMRI studies have shown that the temporal dynamics of evoked BOLD responses can be highly heterogeneous. Failing to model heterogeneous responses in statistical analysis can lead to significant errors in signal detection and characterization and alter the neurobiological interpretation. However, to date it is not clear that, out of a large number of options, which methods are robust against variability in the temporal dynamics of BOLD responses in block-design studies. Here, we used rodent optogenetic fMRI data with heterogeneous BOLD responses and simulations guided by experimental data as a means to investigate different analysis methods’ performance against heterogeneous BOLD responses. Evaluations are carried out within the general linear model (GLM) framework and consist of standard basis sets as well as independent component analysis (ICA). Analyses show that, in the presence of heterogeneous BOLD responses, conventionally used GLM with a canonical basis set leads to considerable errors in the detection and characterization of BOLD responses. Our results suggest that the 3rd and 4th order gamma basis sets, the 7th to 9th order finite impulse response (FIR) basis sets, the 5th to 9th order B-spline basis sets, and the 2nd to 5th order Fourier basis sets are optimal for good balance between detection and characterization, while the 1st order Fourier basis set (coherence analysis) used in our earlier studies show good detection capability. ICA has mostly good detection and characterization capabilities, but detects a large volume of spurious activation with the control fMRI data. PMID:27993672

Detection of cryptic pathogenic copy number variations and constitutional loss of heterozygosity using high resolution SNP microarray analysis in 117 patients referred for cytogenetic analysis and impact on clinical practice.

PubMed

Bruno, D L; Ganesamoorthy, D; Schoumans, J; Bankier, A; Coman, D; Delatycki, M; Gardner, R J M; Hunter, M; James, P A; Kannu, P; McGillivray, G; Pachter, N; Peters, H; Rieubland, C; Savarirayan, R; Scheffer, I E; Sheffield, L; Tan, T; White, S M; Yeung, A; Bowman, Z; Ngo, C; Choy, K W; Cacheux, V; Wong, L; Amor, D J; Slater, H R

2009-02-01

Microarray genome analysis is realising its promise for improving detection of genetic abnormalities in individuals with mental retardation and congenital abnormality. Copy number variations (CNVs) are now readily detectable using a variety of platforms and a major challenge is the distinction of pathogenic from ubiquitous, benign polymorphic CNVs. The aim of this study was to investigate replacement of time consuming, locus specific testing for specific microdeletion and microduplication syndromes with microarray analysis, which theoretically should detect all known syndromes with CNV aetiologies as well as new ones. Genome wide copy number analysis was performed on 117 patients using Affymetrix 250K microarrays. 434 CNVs (195 losses and 239 gains) were found, including 18 pathogenic CNVs and 9 identified as "potentially pathogenic". Almost all pathogenic CNVs were larger than 500 kb, significantly larger than the median size of all CNVs detected. Segmental regions of loss of heterozygosity larger than 5 Mb were found in 5 patients. Genome microarray analysis has improved diagnostic success in this group of patients. Several examples of recently discovered "new syndromes" were found suggesting they are more common than previously suspected and collectively are likely to be a major cause of mental retardation. The findings have several implications for clinical practice. The study revealed the potential to make genetic diagnoses that were not evident in the clinical presentation, with implications for pretest counselling and the consent process. The importance of contributing novel CNVs to high quality databases for genotype-phenotype analysis and review of guidelines for selection of individuals for microarray analysis is emphasised.

The presence-absence coliform test for monitoring drinking water quality.

PubMed Central

Rice, E W; Geldreich, E E; Read, E J

1989-01-01

The concern for improved monitoring of the sanitary quality of drinking water has prompted interest in alternative methods for the detection of total coliform bacteria. A simplified qualitative presence-absence test has been proposed as an alternate procedure for detecting coliform bacteria in potable water. In this paper data from four comparative studies were analyzed to compare the recovery of total coliform bacteria from drinking water using the presence-absence test, the multiple fermentation tube procedure, and the membrane filter technique. The four studies were of water samples taken from four different geographic areas of the United States: Hawaii, New England (Vermont and New Hampshire), Oregon, and Pennsylvania. Analysis of the results of these studies were compared, based upon the number of positive samples detected by each method. Combined recoveries showed the presence-absence test detected significantly higher numbers of samples with coliforms than either the fermentation tube or membrane filter methods, P less than 0.01. The fermentation tube procedure detected significantly more positive samples than the membrane filter technique, P less than 0.01. Based upon the analysis of the combined data base, it is clear that the presence-absence test is as sensitive as the current coliform methods for the examination of potable water. The presence-absence test offers a viable alternative to water utility companies that elect to use the frequency-of-occurrence approach for compliance monitoring. PMID:2493663

Reduced-Order Modeling and Wavelet Analysis of Turbofan Engine Structural Response Due to Foreign Object Damage (FOD) Events

NASA Technical Reports Server (NTRS)

Turso, James; Lawrence, Charles; Litt, Jonathan

2004-01-01

The development of a wavelet-based feature extraction technique specifically targeting FOD-event induced vibration signal changes in gas turbine engines is described. The technique performs wavelet analysis of accelerometer signals from specified locations on the engine and is shown to be robust in the presence of significant process and sensor noise. It is envisioned that the technique will be combined with Kalman filter thermal/health parameter estimation for FOD-event detection via information fusion from these (and perhaps other) sources. Due to the lack of high-frequency FOD-event test data in the open literature, a reduced-order turbofan structural model (ROM) was synthesized from a finite element model modal analysis to support the investigation. In addition to providing test data for algorithm development, the ROM is used to determine the optimal sensor location for FOD-event detection. In the presence of significant noise, precise location of the FOD event in time was obtained using the developed wavelet-based feature.

Reduced-Order Modeling and Wavelet Analysis of Turbofan Engine Structural Response Due to Foreign Object Damage "FOD" Events

NASA Technical Reports Server (NTRS)

Turso, James A.; Lawrence, Charles; Litt, Jonathan S.

2007-01-01

The development of a wavelet-based feature extraction technique specifically targeting FOD-event induced vibration signal changes in gas turbine engines is described. The technique performs wavelet analysis of accelerometer signals from specified locations on the engine and is shown to be robust in the presence of significant process and sensor noise. It is envisioned that the technique will be combined with Kalman filter thermal/ health parameter estimation for FOD-event detection via information fusion from these (and perhaps other) sources. Due to the lack of high-frequency FOD-event test data in the open literature, a reduced-order turbofan structural model (ROM) was synthesized from a finite-element model modal analysis to support the investigation. In addition to providing test data for algorithm development, the ROM is used to determine the optimal sensor location for FOD-event detection. In the presence of significant noise, precise location of the FOD event in time was obtained using the developed wavelet-based feature.

Forest Disturbance Analysis with LANDSAT-8 Oli Data Related to a Parametric Wind Field: a Case Study for Typhoon Rammasun (201409)

NASA Astrophysics Data System (ADS)

Tan, C.; Fang, W.

2018-04-01

Forest disturbance induced by tropical cyclone often has significant and profound effects on the structure and function of forest ecosystem. Detection and analysis of post-disaster forest disturbance based on remote sensing technology has been widely applied. At present, it is necessary to conduct further quantitative analysis of the magnitude of forest disturbance with the intensity of typhoon. In this study, taking the case of super typhoon Rammasun (201409), we analysed the sensitivity of four common used remote sensing indices and explored the relationship between remote sensing index and corresponding wind speeds based on pre-and post- Landsat-8 OLI (Operational Land Imager) images and a parameterized wind field model. The results proved that NBR is the most sensitive index for the detection of forest disturbance induced by Typhoon Rammasun and the variation of NBR has a significant linear dependence relation with the simulated 3-second gust wind speed.

Automatic detection and recognition of signs from natural scenes.

PubMed

Chen, Xilin; Yang, Jie; Zhang, Jing; Waibel, Alex

2004-01-01

In this paper, we present an approach to automatic detection and recognition of signs from natural scenes, and its application to a sign translation task. The proposed approach embeds multiresolution and multiscale edge detection, adaptive searching, color analysis, and affine rectification in a hierarchical framework for sign detection, with different emphases at each phase to handle the text in different sizes, orientations, color distributions and backgrounds. We use affine rectification to recover deformation of the text regions caused by an inappropriate camera view angle. The procedure can significantly improve text detection rate and optical character recognition (OCR) accuracy. Instead of using binary information for OCR, we extract features from an intensity image directly. We propose a local intensity normalization method to effectively handle lighting variations, followed by a Gabor transform to obtain local features, and finally a linear discriminant analysis (LDA) method for feature selection. We have applied the approach in developing a Chinese sign translation system, which can automatically detect and recognize Chinese signs as input from a camera, and translate the recognized text into English.

Two particle tracking and detection in a single Gaussian beam optical trap.

PubMed

Praveen, P; Yogesha; Iyengar, Shruthi S; Bhattacharya, Sarbari; Ananthamurthy, Sharath

2016-01-20

We have studied in detail the situation wherein two microbeads are trapped axially in a single-beam Gaussian intensity profile optical trap. We find that the corner frequency extracted from a power spectral density analysis of intensity fluctuations recorded on a quadrant photodetector (QPD) is dependent on the detection scheme. Using forward- and backscattering detection schemes with single and two laser wavelengths along with computer simulations, we conclude that fluctuations detected in backscattering bear true position information of the bead encountered first in the beam propagation direction. Forward scattering, on the other hand, carries position information of both beads with substantial contribution from the bead encountered first along the beam propagation direction. Mie scattering analysis further reveals that the interference term from the scattering of the two beads contributes significantly to the signal, precluding the ability to resolve the positions of the individual beads in forward scattering. In QPD-based detection schemes, detection through backscattering, thereby, is imperative to track the true displacements of axially trapped microbeads for possible studies on light-mediated interbead interactions.

Significant Linkage for Tourette Syndrome in a Large French Canadian Family

PubMed Central

Mérette, Chantal; Brassard, Andrée; Potvin, Anne; Bouvier, Hélène; Rousseau, François; Émond, Claudia; Bissonnette, Luc; Roy, Marc-André; Maziade, Michel; Ott, Jurg; Caron, Chantal

2000-01-01

Family and twin studies provide strong evidence that genetic factors are involved in the transmission of Gilles de la Tourette syndrome (TS) and related psychiatric disorders. To detect the underlying susceptibility gene(s) for TS, we performed linkage analysis in one large French Canadian family (127 members) from the Charlevoix region, in which 20 family members were definitely affected by TS and 20 others showed related tic disorders. Using model-based linkage analysis, we observed a LOD score of 3.24 on chromosome 11 (11q23). This result was obtained in a multipoint approach involving marker D11S1377, the marker for which significant linkage disequilibrium with TS recently has been detected in an Afrikaner population. Altogether, 25 markers were studied, and, for level of significance, we derived a criterion that took into account the multiple testing arising from the use of three phenotype definitions and three modes of inheritance, a procedure that yielded a LOD score of 3.18. Hence, even after adjustment for multiple testing, the present study shows statistically significant evidence for genetic linkage with TS. PMID:10986045

Quality Matters: Systematic Analysis of Endpoints Related to “Cellular Life” in Vitro Data of Radiofrequency Electromagnetic Field Exposure

PubMed Central

Simkó, Myrtill; Remondini, Daniel; Zeni, Olga; Scarfi, Maria Rosaria

2016-01-01

Possible hazardous effects of radiofrequency electromagnetic fields (RF-EMF) at low exposure levels are controversially discussed due to inconsistent study findings. Therefore, the main focus of the present study is to detect if any statistical association exists between RF-EMF and cellular responses, considering cell proliferation and apoptosis endpoints separately and with both combined as a group of “cellular life” to increase the statistical power of the analysis. We searched for publications regarding RF-EMF in vitro studies in the PubMed database for the period 1995–2014 and extracted the data to the relevant parameters, such as cell culture type, frequency, exposure duration, SAR, and five exposure-related quality criteria. These parameters were used for an association study with the experimental outcome in terms of the defined endpoints. We identified 104 published articles, from which 483 different experiments were extracted and analyzed. Cellular responses after exposure to RF-EMF were significantly associated to cell lines rather than to primary cells. No other experimental parameter was significantly associated with cellular responses. A highly significant negative association with exposure condition-quality and cellular responses was detected, showing that the more the quality criteria requirements were satisfied, the smaller the number of detected cellular responses. According to our knowledge, this is the first systematic analysis of specific RF-EMF bio-effects in association to exposure quality, highlighting the need for more stringent quality procedures for the exposure conditions. PMID:27420084

Accuracy of noncycloplegic retinoscopy, retinomax autorefractor, and SureSight vision screener for detecting significant refractive errors.

PubMed

Kulp, Marjean Taylor; Ying, Gui-Shuang; Huang, Jiayan; Maguire, Maureen; Quinn, Graham; Ciner, Elise B; Cyert, Lynn A; Orel-Bixler, Deborah A; Moore, Bruce D

2014-03-06

To evaluate, by receiver operating characteristic (ROC) analysis, the ability of noncycloplegic retinoscopy (NCR), Retinomax Autorefractor (Retinomax), and SureSight Vision Screener (SureSight) to detect significant refractive errors (RE) among preschoolers. Refraction results of eye care professionals using NCR, Retinomax, and SureSight (n = 2588) and of nurse and lay screeners using Retinomax and SureSight (n = 1452) were compared with masked cycloplegic retinoscopy results. Significant RE was defined as hyperopia greater than +3.25 diopters (D), myopia greater than 2.00 D, astigmatism greater than 1.50 D, and anisometropia greater than 1.00 D interocular difference in hyperopia, greater than 3.00 D interocular difference in myopia, or greater than 1.50 D interocular difference in astigmatism. The ability of each screening test to identify presence, type, and/or severity of significant RE was summarized by the area under the ROC curve (AUC) and calculated from weighted logistic regression models. For detection of each type of significant RE, AUC of each test was high; AUC was better for detecting the most severe levels of RE than for all REs considered important to detect (AUC 0.97-1.00 vs. 0.92-0.93). The area under the curve of each screening test was high for myopia (AUC 0.97-0.99). Noncycloplegic retinoscopy and Retinomax performed better than SureSight for hyperopia (AUC 0.92-0.99 and 0.90-0.98 vs. 0.85-0.94, P ≤ 0.02), Retinomax performed better than NCR for astigmatism greater than 1.50 D (AUC 0.95 vs. 0.90, P = 0.01), and SureSight performed better than Retinomax for anisometropia (AUC 0.85-1.00 vs. 0.76-0.96, P ≤ 0.07). Performance was similar for nurse and lay screeners in detecting any significant RE (AUC 0.92-1.00 vs. 0.92-0.99). Each test had a very high discriminatory power for detecting children with any significant RE.

Detection of caffeine in tea, instant coffee, green tea beverage, and soft drink by direct analysis in real time (DART) source coupled to single-quadrupole mass spectrometry.

PubMed

Wang, Lei; Zhao, Pengyue; Zhang, Fengzu; Bai, Aijuan; Pan, Canping

2013-01-01

Ambient ionization direct analysis in real time (DART) coupled to single-quadrupole MS (DART-MS) was evaluated for rapid detection of caffeine in commercial samples without chromatographic separation or sample preparation. Four commercial samples were examined: tea, instant coffee, green tea beverage, and soft drink. The response-related parameters were optimized for the DART temperature and MS fragmentor. Under optimal conditions, the molecular ion (M+H)+ was the major ion for identification of caffeine. The results showed that DART-MS is a promising tool for the quick analysis of important marker molecules in commercial samples. Furthermore, this system has demonstrated significant potential for high sample throughput and real-time analysis.

Long-term behaviour and cross-correlation water quality analysis of the River Elbe, Germany.

PubMed

Lehmann, A; Rode, M

2001-06-01

This study analyses weekly data samples from the river Elbe at Magdeburg between 1984 and 1996 to investigate the changes in metabolism and water quality in the river Elbe since the German reunification in 1990. Modelling water quality variables by autoregressive component models and ARIMA models reveals the improvement of water quality due to the reduction of waste water emissions since 1990. The models are used to determine the long-term and seasonal behaviour of important water quality variables. Organic and heavy metal pollution parameters showed a significant decrease since 1990, however, no significant change of chlorophyll-a as a measure for primary production could be found. A new procedure for testing the significance of a sample correlation coefficient is discussed, which is able to detect spurious sample correlation coefficients without making use of time-consuming prewhitening. The cross-correlation analysis is applied to hydrophysical, biological, and chemical water quality variables of the river Elbe since 1984. Special emphasis is laid on the detection of spurious sample correlation coefficients.

CHARACTERIZATION OF THE COMPLETE FIBER NETWORK TOPOLOGY OF PLANAR FIBROUS TISSUES AND SCAFFOLDS

PubMed Central

D'Amore, Antonio; Stella, John A.; Wagner, William R.; Sacks, Michael S.

2010-01-01

Understanding how engineered tissue scaffold architecture affects cell morphology, metabolism, phenotypic expression, as well as predicting material mechanical behavior have recently received increased attention. In the present study, an image-based analysis approach that provides an automated tool to characterize engineered tissue fiber network topology is presented. Micro-architectural features that fully defined fiber network topology were detected and quantified, which include fiber orientation, connectivity, intersection spatial density, and diameter. Algorithm performance was tested using scanning electron microscopy (SEM) images of electrospun poly(ester urethane)urea (ES-PEUU) scaffolds. SEM images of rabbit mesenchymal stem cell (MSC) seeded collagen gel scaffolds and decellularized rat carotid arteries were also analyzed to further evaluate the ability of the algorithm to capture fiber network morphology regardless of scaffold type and the evaluated size scale. The image analysis procedure was validated qualitatively and quantitatively, comparing fiber network topology manually detected by human operators (n=5) with that automatically detected by the algorithm. Correlation values between manual detected and algorithm detected results for the fiber angle distribution and for the fiber connectivity distribution were 0.86 and 0.93 respectively. Algorithm detected fiber intersections and fiber diameter values were comparable (within the mean ± standard deviation) with those detected by human operators. This automated approach identifies and quantifies fiber network morphology as demonstrated for three relevant scaffold types and provides a means to: (1) guarantee objectivity, (2) significantly reduce analysis time, and (3) potentiate broader analysis of scaffold architecture effects on cell behavior and tissue development both in vitro and in vivo. PMID:20398930

The impact of digital mammography on screening a young cohort of women for breast cancer in an urban specialist breast unit.

PubMed

Perry, Nicholas M; Patani, N; Milner, S E; Pinker, K; Mokbel, K; Allgood, P C; Duffy, S W

2011-04-01

To compare the diagnostic performance of full-field digital mammography (FFDM) with screen-film mammography (SFM) in a corporate screening programme including younger women. Data were available on 14,946 screening episodes, 5010 FFDM and 9936 SFM. Formal analysis was by logistic regression, adjusting for age and calendar year. FFDM is compared with SFM with reference to cancer detection rates, cancers presenting as clustering microcalcifications, recall rates and PPV of recall. Overall detection rates were 6.4 cancers per thousand screens for FFDM and 2.8 per thousand for SFM (p < 0.001). In women aged 50+ cancer detection was significantly higher for FFDM at 8.6 per thousand vs. 4.0 per thousand, (p = 0.002). In women <50, cancer detection was also significantly higher for FFDM at 4.3 per thousand vs. 1.4 per thousand, (p = 0.02). Cancers detected as clustering microcalcifications increased from 0.4 per thousand with SFM to 2.0 per thousand with FFDM. Rates of assessment recall were higher for FFDM (7.3% vs. 5.0%, p < 0.001). FFDM provided a higher PPV for assessment recall, (32 cancers/364 recalls, 8.8%) than SFM, (28 cancers/493 recalls, 5.7%). Cancer detection rates were significantly higher for FFDM than for SFM, especially for women <50, and cancers detected as clustering microcalcifications.

Social significance of community structure: Statistical view

NASA Astrophysics Data System (ADS)

Li, Hui-Jia; Daniels, Jasmine J.

2015-01-01

Community structure analysis is a powerful tool for social networks that can simplify their topological and functional analysis considerably. However, since community detection methods have random factors and real social networks obtained from complex systems always contain error edges, evaluating the significance of a partitioned community structure is an urgent and important question. In this paper, integrating the specific characteristics of real society, we present a framework to analyze the significance of a social community. The dynamics of social interactions are modeled by identifying social leaders and corresponding hierarchical structures. Instead of a direct comparison with the average outcome of a random model, we compute the similarity of a given node with the leader by the number of common neighbors. To determine the membership vector, an efficient community detection algorithm is proposed based on the position of the nodes and their corresponding leaders. Then, using a log-likelihood score, the tightness of the community can be derived. Based on the distribution of community tightness, we establish a connection between p -value theory and network analysis, and then we obtain a significance measure of statistical form . Finally, the framework is applied to both benchmark networks and real social networks. Experimental results show that our work can be used in many fields, such as determining the optimal number of communities, analyzing the social significance of a given community, comparing the performance among various algorithms, etc.

Altered retinal microRNA expression profiles in early diabetic retinopathy: an in silico analysis.

PubMed

Xiong, Fen; Du, Xinhua; Hu, Jianyan; Li, Tingting; Du, Shanshan; Wu, Qiang

2014-07-01

MicroRNAs (miRNAs) - as negative regulators of target genes - are associated with various human diseases, but their precise role(s) in diabetic retinopathy (DR) remains to be elucidated. The aim of this study was to elucidate the involvement of miRNAs in early DR using in silico analysis to explore their gene expression patterns. We used the streptozotocin (STZ)-induced diabetic rat to investigate the roles of miRNAs in early DR. Retinal miRNA expression profiles from diabetic versus healthy control rats were examined by miRNA array analysis. Based on several bioinformatic systems, specifically, gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, we identified signatures of the potential pathological processes, gene functions, and signaling pathways that are influenced by dysregulated miRNAs. We used quantitative real-time polymerase chain reaction (qRT-PCR) to validate six (i.e. those with significant changes in expression levels) of the 17 miRNAs that were detected in the miRNA array. We also describe the significant role of the miRNA-gene network, which is based on the interactions between miRNAs and target genes. GO analysis of the 17 miRNAs detected in the miRNA array analysis revealed the most prevalent miRNAs to be those related to biological processes, olfactory bulb development and axonogenesis. These miRNAs also exert significant influence on additional pathways, including the mitogen-activated protein and calcium signaling pathways. Six of the seventeen miRNAs were chosen for qRT-PCR validation. With the exception of a slight difference in miRNA-350, our results are in close agreement with the differential expressions detected by array analysis. This study, which describes miRNA expression during the early developmental phases of DR, revealed extensive miRNA interactions. Based on both their target genes and signaling pathways, we suggest that miRNAs perform critical regulatory functions during the early stages of DR evolution.

Metastatic site location influences the diagnostic accuracy of ctDNA EGFR- mutation testing in NSCLC patients: a pooled analysis.

PubMed

Passiglia, Francesco; Rizzo, Sergio; Rolfo, Christian; Galvano, Antonio; Bronte, Enrico; Incorvaia, Lorena; Listi, Angela; Barraco, Nadia; Castiglia, Marta; Calo, Valentina; Bazan, Viviana; Russo, Antonio

2018-03-08

Recent studies evaluated the diagnostic accuracy of circulating tumor DNA (ctDNA) in the detection of epidermal growth factor receptor (EGFR) mutations from plasma of NSCLC patients, overall showing a high concordance as compared to standard tissue genotyping. However it is less clear if the location of metastatic site may influence the ability to identify EGFR mutations in plasma. This pooled analysis aims to evaluate the association between the metastatic site location and the sensitivity of ctDNA analysis in detecting EGFR mutations in NSCLC patients. Data from all published studies, evaluating the sensitivity of plasma-based EGFR-mutation testing, stratified by metastatic site location (extrathoracic (M1b) vs intrathoracic (M1a)) were collected by searching in PubMed, Cochrane Library, American Society of Clinical Oncology, and World Conference of Lung Cancer, meeting proceedings. Pooled Odds ratio (OR) and 95% confidence intervals (95% CIs) were calculated for the ctDNA analysis sensitivity, according to metastatic site location. A total of ten studies, with 1425 patients, were eligible. Pooled analysis showed that the sensitivity of ctDNA-based EGFR-mutation testing is significantly higher in patients with M1b vs M1a disease (OR: 5.09; 95% CIs: 2.93 - 8.84). A significant association was observed for both EGFR-activating (OR: 4.30, 95% CI: 2.35-7.88) and resistant T790M mutations (OR: 11.89, 95% CI: 1.45-97.22), regardless of the use of digital-PCR (OR: 5.85, 95% CI: 3.56-9.60) or non-digital PCR technologies (OR: 2.96, 95% CI: 2.24-3.91). These data suggest that the location of metastatic sites significantly influences the diagnostic accuracy of ctDNA analysis in detecting EGFR mutations in NSCLC patients. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Capillary electrophoresis with electrochemiluminescence detection for the simultaneous determination of cisatracurium besylate and its degradation products in pharmaceutical preparations.

PubMed

Zuo, Ming; Gao, Jieying; Zhang, Xiaoqing; Cui, Yue; Fan, Zimian; Ding, Min

2015-07-01

Capillary electrophoresis with electrochemiluminescence detection for the simultaneous analysis of cisatracurium besylate and its degradation products (laudanosine, quaternary monoacrylate) in pharmaceutical preparation was developed and fully validated. The significant parameters that influence capillary electrophoresis separation and electrochemiluminescence detection were optimized. The total analysis time of the analytes was 15 min. The linearities of the method were 0.1∼40.0 μg/mL for cisatracurium besylate and 0.04∼8.00 μg/mL for laudanosine, with correlation coefficients (r) of 0.999 and 0.998, respectively. The detection limits (S/N = 3) were 83.0 ng/mL for cisatracurium besylate and 32.0 ng/mL for laudanosine. The intraday relative standard deviations of the analytes were <3.0%, and the interday relative standard deviations were <8.0%. The developed method was cost-effective, sensitive, fast, and resource-saving, which was suitable for the ingredient analysis in pharmaceutical preparation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Detection and discrimination of microorganisms on various substrates with quantum cascade laser spectroscopy

NASA Astrophysics Data System (ADS)

Padilla-Jiménez, Amira C.; Ortiz-Rivera, William; Rios-Velazquez, Carlos; Vazquez-Ayala, Iris; Hernández-Rivera, Samuel P.

2014-06-01

Investigations focusing on devising rapid and accurate methods for developing signatures for microorganisms that could be used as biological warfare agents' detection, identification, and discrimination have recently increased significantly. Quantum cascade laser (QCL)-based spectroscopic systems have revolutionized many areas of defense and security including this area of research. In this contribution, infrared spectroscopy detection based on QCL was used to obtain the mid-infrared (MIR) spectral signatures of Bacillus thuringiensis, Escherichia coli, and Staphylococcus epidermidis. These bacteria were used as microorganisms that simulate biothreats (biosimulants) very truthfully. The experiments were conducted in reflection mode with biosimulants deposited on various substrates including cardboard, glass, travel bags, wood, and stainless steel. Chemometrics multivariate statistical routines, such as principal component analysis regression and partial least squares coupled to discriminant analysis, were used to analyze the MIR spectra. Overall, the investigated infrared vibrational techniques were useful for detecting target microorganisms on the studied substrates, and the multivariate data analysis techniques proved to be very efficient for classifying the bacteria and discriminating them in the presence of highly IR-interfering media.

Diagnostic Performance of (18)F-Fluorodeoxyglucose in 162 Small Pulmonary Nodules Incidentally Detected in Subjects Without a History of Malignancy.

PubMed

Calcagni, Maria Lucia; Taralli, Silvia; Cardillo, Giuseppe; Graziano, Paolo; Ialongo, Pasquale; Mattoli, Maria Vittoria; Di Franco, Davide; Caldarella, Carmelo; Carleo, Francesco; Indovina, Luca; Giordano, Alessandro

2016-04-01

Solitary pulmonary nodule (SPN) still represents a diagnostic challenge. The aim of our study was to evaluate the diagnostic performance of (18)F-fluorodeoxyglucose positron emission tomography-computed tomography in one of the largest samples of small SPNs, incidentally detected in subjects without a history of malignancy (nonscreening population) and undetermined at computed tomography. One-hundred and sixty-two small (>0.8 to 1.5 cm) and, for comparison, 206 large nodules (>1.5 to 3 cm) were retrospectively evaluated. Diagnostic performance of (18)F-fluorodeoxyglucose visual analysis, receiver-operating characteristic (ROC) analysis for maximum standardized uptake value (SUVmax), and Bayesian analysis were assessed using histology or radiological follow-up as a golden standard. In 162 small nodules, (18)F-fluorodeoxyglucose visual and ROC analyses (SUVmax = 1.3) provided 72.6% and 77.4% sensitivity and 88.0% and 82.0% specificity, respectively. The prevalence of malignancy was 38%; Bayesian analysis provided 78.8% positive and 16.0% negative posttest probabilities of malignancy. In 206 large nodules (18)F-fluorodeoxyglucose visual and ROC analyses (SUVmax = 1.9) provided 89.5% and 85.1% sensitivity and 70.8% and 79.2% specificity, respectively. The prevalence of malignancy was 65%; Bayesian analysis provided 85.0% positive and 21.6% negative posttest probabilities of malignancy. In both groups, malignant nodules had a significant higher SUVmax (p < 0.0001) than benign nodules. Only in the small group, malignant nodules were significantly larger (p = 0.0054) than benign ones. (18)F-fluorodeoxyglucose can be clinically relevant to rule in and rule out malignancy in undetermined small SPNs, incidentally detected in nonscreening population with intermediate pretest probability of malignancy, as well as in larger ones. Visual analysis can be considered an optimal diagnostic criterion, adequately detecting a wide range of malignant nodules with different metabolic activity. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Diagnostic performance and safety of a three-dimensional 14-core systematic biopsy method.

PubMed

Takeshita, Hideki; Kawakami, Satoru; Numao, Noboru; Sakura, Mizuaki; Tatokoro, Manabu; Yamamoto, Shinya; Kijima, Toshiki; Komai, Yoshinobu; Saito, Kazutaka; Koga, Fumitaka; Fujii, Yasuhisa; Fukui, Iwao; Kihara, Kazunori

2015-03-01

To investigate the diagnostic performance and safety of a three-dimensional 14-core biopsy (3D14PBx) method, which is a combination of the transrectal six-core and transperineal eight-core biopsy methods. Between December 2005 and August 2010, 1103 men underwent 3D14PBx at our institutions and were analysed prospectively. Biopsy criteria included a PSA level of 2.5-20 ng/mL or abnormal digital rectal examination (DRE) findings, or both. The primary endpoint of the study was diagnostic performance and the secondary endpoint was safety. We applied recursive partitioning to the entire study cohort to delineate the unique contribution of each sampling site to overall and clinically significant cancer detection. Prostate cancer was detected in 503 of the 1103 patients (45.6%). Age, family history of prostate cancer, DRE, PSA, percentage of free PSA and prostate volume were associated with the positive biopsy results significantly and independently. Of the 503 cancers detected, 39 (7.8%) were clinically locally advanced (≥cT3a), 348 (69%) had a biopsy Gleason score (GS) of ≥7, and 463 (92%) met the definition of biopsy-based significant cancer. Recursive partitioning analysis showed that each sampling site contributed uniquely to both the overall and the biopsy-based significant cancer detection rate of the 3D14PBx method. The overall cancer-positive rate of each sampling site ranged from 14.5% in the transrectal far lateral base to 22.8% in the transrectal far lateral apex. As of August 2010, 210 patients (42%) had undergone radical prostatectomy, of whom 55 (26%) were found to have pathologically non-organ-confined disease, 174 (83%) had prostatectomy GS ≥7 and 185 (88%) met the definition of prostatectomy-based significant cancer. This is the first prospective analysis of the diagnostic performance of an extended biopsy method, which is a simplified version of the somewhat redundant super-extended three-dimensional 26-core biopsy. As expected, each sampling site uniquely contributed not only to overall cancer detection, but also to significant cancer detection. 3D14PBx is a feasible systematic biopsy method in men with PSA <20 ng/mL. © 2014 The Authors. BJU International © 2014 BJU International.

Network hydraulics inclusion in water quality event detection using multiple sensor stations data.

PubMed

Oliker, Nurit; Ostfeld, Avi

2015-09-01

Event detection is one of the current most challenging topics in water distribution systems analysis: how regular on-line hydraulic (e.g., pressure, flow) and water quality (e.g., pH, residual chlorine, turbidity) measurements at different network locations can be efficiently utilized to detect water quality contamination events. This study describes an integrated event detection model which combines multiple sensor stations data with network hydraulics. To date event detection modelling is likely limited to single sensor station location and dataset. Single sensor station models are detached from network hydraulics insights and as a result might be significantly exposed to false positive alarms. This work is aimed at decreasing this limitation through integrating local and spatial hydraulic data understanding into an event detection model. The spatial analysis complements the local event detection effort through discovering events with lower signatures by exploring the sensors mutual hydraulic influences. The unique contribution of this study is in incorporating hydraulic simulation information into the overall event detection process of spatially distributed sensors. The methodology is demonstrated on two example applications using base runs and sensitivity analyses. Results show a clear advantage of the suggested model over single-sensor event detection schemes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dual-focus Magnification, High-Definition Endoscopy Improves Pathology Detection in Direct-to-Test Diagnostic Upper Gastrointestinal Endoscopy.

PubMed

Bond, Ashley; Burkitt, Michael D; Cox, Trevor; Smart, Howard L; Probert, Chris; Haslam, Neil; Sarkar, Sanchoy

2017-03-01

In the UK, the majority of diagnostic upper gastrointestinal (UGI) endoscopies are a result of direct-to-test referral from the primary care physician. The diagnostic yield of these tests is relatively low, and the burden high on endoscopy services. Dual-focus magnification, high-definition endoscopy is expected to improve detection and classification of UGI mucosal lesions and also help minimize biopsies by allowing better targeting. This is a retrospective study of patients attending for direct-to-test UGI endoscopy from January 2015 to June 2015. The primary outcome of interest was the identification of significant pathology. Detection of significant pathology was modelled using logistic regression. 500 procedures were included. The mean age of patients was 61.5 (±15.6) years; 60.8% of patients were female. Ninety-four gastroscopies were performed using dual-focus magnification high-definition endoscopy. Increasing age, male gender, type of endoscope, and type of operator were all identified as significant factors influencing the odds of detecting significant mucosal pathology. Use of dual-focus magnification, high-definition endoscopy was associated with an odds ratio of 1.87 (95%CI 1.11-3.12) favouring the detection of significant pathology. Subsequent analysis suggested that the increased detection of pathology during dual-focus magnification, high-definition endoscopy also influenced patient follow-up and led to a 3.0 fold (p=0.04) increase in the proportion of patients entered into an UGI endoscopic surveillance program. Dual-focus magnification, high-definition endoscopy improved the diagnostic yield for significant mucosal pathology in patients referred for direct-to-test endoscopy. If this finding is recapitulated elsewhere it will have substantial impact on the provision of UGI endoscopic services.

Epstein-Barr virus is associated with periodontal diseases: A meta-analysis based on 21 case-control studies.

PubMed

Gao, Zilong; Lv, Juan; Wang, Min

2017-02-01

Some controversies still exist between the detection of Epstein-Barr virus (EBV)'s DNA and risks of periodontal diseases. Hence, a comprehensive meta-analysis on all available literatures was performed to clarify the relationship between EBV and preidontitis.A comprehensive search was conducted within the PUBMED, EMBASE, and WANFANG databases up to October 10th, 2016 according to inclusion and exclusion criteria and finally 21 case-control literatures were obtained. The outcomes including odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of associations. Publication bias was determined by Begg or Egger test. Sensitivity analysis was used to investigate reliability and stability of the results.According to the data from included trials, the association between overall increased risks of periodontitis and the detection of EBV was significant (OR = 6.199, 95% CI = 3.119-12.319, P < 0.001). In the disease-type analysis, the pooled ORs for chronic periodontitis and aggressive periodontitis were 6.586 (95% CI = 3.042-14.262, P < 0.001) and 8.361 (95% CI = 2.109-33.143, P = 0.003), respectively. In the subgroup analysis of ethnicity, our results suggested that high EBV-detecting frequencies were correlated with increased risks of periodontitis in Asians, Europeans, and Americans (P < 0.001). Subgroup analysis by the sample type showed that subgingival plaque (SgP) samples and tissue samples were available for EBV detecting (P < 0.001). Detecting EBV of samples in ≥5 (6) mm sites of periodontal pockets were easier than in ≤3-mm sites (P = 0.023).This meta-analysis indicates that high frequent detection of EBV correlates with increased risk of periodontal diseases. SgP and tissue are available for detecting EBV in patients of periodontitis. At last, our results suggest that detecting EBV of samples in =5 (6) mm sites of periodontal pockets are more sensitive than in ≤3-mm sites.

Do obesity and weight loss affect vocal function?

PubMed

Solomon, Nancy Pearl; Helou, Leah B; Dietrich-Burns, Katie; Stojadinovic, Alexander

2011-02-01

Obesity may be associated with increased tissue bulk in the laryngeal airway, neck, and chest wall, and as such may affect vocal function. Eight obese and eight nonobese adults participated in this study; the obese participants underwent bariatric surgical procedures. This mixed-design study included cross-sectional analysis for group differences and longitudinal analysis for multidimensional changes in vocal function from four assessments collected over 6 months. No significant differences were detected between groups from the preoperative assessment. Further, no changes were detected over time for acoustic parameters, maximum phonation time, laryngeal airway resistance, and airflow during a sustained vowel for either group. Only minor differences were detected for strain, pitch, and loudness perceptions of voice over time, but not between groups. Phonation threshold pressure (PTP), at comfortable and high pitches (30% and 80% of the F0 range) changed significantly over time, but not between groups. Examination of individual data revealed a trend for PTP at 30% F0 to decrease as body mass index decreased. PTP may be informative for assessing vocal function in clients who present with obesity and voice symptoms. © Thieme Medical Publishers.

Electronic waste leachate-mediated DNA fragmentation and cell death by apoptosis in mouse fibroblast (NIH/3T3) cell line.

PubMed

Alabi, Okunola A; Bakare, Adekunle A; Filippin-Monteiro, Fabíola B; Sierra, Jelver A; Creczynski-Pasa, Tânia B

2013-08-01

This study investigated the apoptotic effect of electronic waste on fibroblast cell line. Cells were treated with different concentrations of the leachate for 24h. Cell viability was detected by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) test, nuclear morphology of cells was explored by acridine orange (AO)/ethidium bromide (EB) double staining, mitochondrial membrane potential was evaluated using JC-1 probe while cell cycle analysis was conducted using flow cytometry. The oxidative status was detected using DCFH-DA (dichlorofluorescin diacetate) probe and the relationship between cell death and ROS (reactive oxygen species) was investigated using N-acetylcysteine. Results showed an increased cell death as detected by MTT assay and AO/EB staining. Cell cycle analysis indicated an induction of sub/G1 events while JC-1 probe showed significant disruption of mitochondrial membrane potential. There was significant induction of ROS, while N-acetylcysteine protected the cells from DNA damage. These suggest apoptotic pathway as a possible mechanism of e-waste induced cyto-genotoxicity. Copyright © 2013 Elsevier Inc. All rights reserved.

Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics

PubMed Central

Van, Phu T.; Schmid, Amy K.; King, Nichole L.; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T.; Goo, Young-Ah; Deutsch, Eric W.; Reiss, David J.; Mallick, Parag; Baliga, Nitin S.

2009-01-01

The relatively small numbers of proteins and fewer possible posttranslational modifications in microbes provides a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has helped highlight plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics. PMID:18652504

Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases.

PubMed

Ahmed, Towfiq; Haraldsen, Jason T; Rehr, John J; Di Ventra, Massimiliano; Schuller, Ivan; Balatsky, Alexander V

2014-03-28

Nanopore-based sequencing has demonstrated a significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multilayered graphene-based nanopore device architecture for the recognition of single biomolecules. Molecular detection and analysis can be accomplished through the detection of transverse currents as the molecule or DNA base translocates through the nanopore. To increase the overall signal-to-noise ratio and the accuracy, we implement a new 'multi-point cross-correlation' technique for identification of DNA bases or other molecules on the single molecular level. We demonstrate that the cross-correlations between each nanopore will greatly enhance the transverse current signal for each molecule. We implement first-principles transport calculations for DNA bases surveyed across a multilayered graphene nanopore system to illustrate the advantages of the proposed geometry. A time-series analysis of the cross-correlation functions illustrates the potential of this method for enhancing the signal-to-noise ratio. This work constitutes a significant step forward in facilitating fingerprinting of single biomolecules using solid state technology.

PubMed

Miranda, Geraldo Elias; Melani, Rodolfo Francisco Haltenhoff; Francisquini, Luiz; Daruge, Eduardo

2017-01-01

The aim of this study was to identify the combination of wavelength and filter that best detects tooth and bone, and to determine which biological materials (enamel, dental root or bone) have highest fluorescence intensity when exposed to an alternate light source (ALS). Tooth and bone samples were lighted with ALS and photographed. Adobe Photoshop™ and ImageJ™ softwares were used for image analysis. Data obtained by measuring the photograph pixels were subjected to analysis of variance. The mean values of significant effects were compared by the Tukey test. In all tests, the significance level was set at p≤0.05 and the values calculated by the SAS system. The results showed that the best combination for detecting tooth and bone is an illumination wavelength of 455 nm with an orange filter. The fluorescence of dental root is greater than that of enamel, which in turn is greater than that of bone. The biological material had markedly higher fluorescence than the inert material. This knowledge can help the forensic expert to screen and detect biological materials, for example in situations where there are fragmented teeth and small bones, both at the scene and in the laboratory.

Investigating MALDI MSI parameters (Part 2) - On the use of a mechanically shuttered trigger system for improved laser energy stability.

PubMed

Steven, Rory T; Dexter, Alex; Bunch, Josephine

2016-07-15

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is now widely used to desorb, ionize and detect molecules from complex samples and tissue sections. The detected ion intensity within MALDI MS and MSI is intimately linked to the laser energy per pulse incident upon the sample during analysis. Laser energy/power stability can be significantly affected by the manner in which the laser is operated. High-repetition rate diode-pumped solid-state (DPSS) lasers are being increasingly adopted to enable high-throughput MALDI MSI analysis. Within this work two different laser-triggering setups are used to demonstrate the effect of laser energy instabilities due to spiking and thermal control phenomena and a setup with a shutter to remove these effects. The effect of non-equilibrium laser operation on MALDI MSI data versus the more stable laser pulse energy of the shutter-triggered system is demonstrated in thin films of α-cyano-4-hydroxycinnamic acid (CHCA) and for imaging of murine brain tissue sections. Significant unwanted variations in absolute and relative detected ion intensity are shown where energy variation is introduced by these phenomena, which return to equilibrium within the setup employed here over timescales relevant to MALDI MS analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Role of male genetic factors in recurrent pregnancy loss in Northeast China.

PubMed

Dai, Rulin; Pan, Yuan; Fu, Yan; Liu, Qian; Han, Weifeng; Liu, Ruizhi

2018-05-01

This study aimed to investigate the roles of male genetic factors, including Y chromosome microdeletions and chromosomal heteromorphism, in recurrent pregnancy loss (RPL) in Northeast China. We evaluated 1072 male patients from Northeast China whose wives had a history of two or more consecutive miscarriages. We also selected 971 infertile and 200 fertile men as control groups. Semen analysis was carried out by computer-assisted sperm analysis. Y chromosome microdeletions were detected by polymerase chain reaction and chromosomes were evaluated by karyotype analysis. There were no microdeletions in the RPL and fertile control groups, but 112 of the infertile men had Y chromosome microdeletions. Chromosomal heteromorphism was detected in all the groups. Patients in the infertile control group had a significantly higher percentage (2.16%) of Y variation (Yqh±) heteromorphism compared with the RPL group, but there were no significant differences in the incidences of chromosomal heteromorphism among the other groups. Y chromosome microdeletions and chromosomal heteromorphism are not associated with RPL in Northeast China. Some RPL males had structural chromosome anomalies, all of which were reciprocal translocations. We suggest that it may not be necessary to detect Y chromosome microdeletions in RPL males with Yqh±. Copyright © 2018 Elsevier B.V. All rights reserved.

Automated model-based quantitative analysis of phantoms with spherical inserts in FDG PET scans.

PubMed

Ulrich, Ethan J; Sunderland, John J; Smith, Brian J; Mohiuddin, Imran; Parkhurst, Jessica; Plichta, Kristin A; Buatti, John M; Beichel, Reinhard R

2018-01-01

Quality control plays an increasingly important role in quantitative PET imaging and is typically performed using phantoms. The purpose of this work was to develop and validate a fully automated analysis method for two common PET/CT quality assurance phantoms: the NEMA NU-2 IQ and SNMMI/CTN oncology phantom. The algorithm was designed to only utilize the PET scan to enable the analysis of phantoms with thin-walled inserts. We introduce a model-based method for automated analysis of phantoms with spherical inserts. Models are first constructed for each type of phantom to be analyzed. A robust insert detection algorithm uses the model to locate all inserts inside the phantom. First, candidates for inserts are detected using a scale-space detection approach. Second, candidates are given an initial label using a score-based optimization algorithm. Third, a robust model fitting step aligns the phantom model to the initial labeling and fixes incorrect labels. Finally, the detected insert locations are refined and measurements are taken for each insert and several background regions. In addition, an approach for automated selection of NEMA and CTN phantom models is presented. The method was evaluated on a diverse set of 15 NEMA and 20 CTN phantom PET/CT scans. NEMA phantoms were filled with radioactive tracer solution at 9.7:1 activity ratio over background, and CTN phantoms were filled with 4:1 and 2:1 activity ratio over background. For quantitative evaluation, an independent reference standard was generated by two experts using PET/CT scans of the phantoms. In addition, the automated approach was compared against manual analysis, which represents the current clinical standard approach, of the PET phantom scans by four experts. The automated analysis method successfully detected and measured all inserts in all test phantom scans. It is a deterministic algorithm (zero variability), and the insert detection RMS error (i.e., bias) was 0.97, 1.12, and 1.48 mm for phantom activity ratios 9.7:1, 4:1, and 2:1, respectively. For all phantoms and at all contrast ratios, the average RMS error was found to be significantly lower for the proposed automated method compared to the manual analysis of the phantom scans. The uptake measurements produced by the automated method showed high correlation with the independent reference standard (R 2 ≥ 0.9987). In addition, the average computing time for the automated method was 30.6 s and was found to be significantly lower (P ≪ 0.001) compared to manual analysis (mean: 247.8 s). The proposed automated approach was found to have less error when measured against the independent reference than the manual approach. It can be easily adapted to other phantoms with spherical inserts. In addition, it eliminates inter- and intraoperator variability in PET phantom analysis and is significantly more time efficient, and therefore, represents a promising approach to facilitate and simplify PET standardization and harmonization efforts. © 2017 American Association of Physicists in Medicine.

Significant Scales in Community Structure

NASA Astrophysics Data System (ADS)

Traag, V. A.; Krings, G.; van Dooren, P.

2013-10-01

Many complex networks show signs of modular structure, uncovered by community detection. Although many methods succeed in revealing various partitions, it remains difficult to detect at what scale some partition is significant. This problem shows foremost in multi-resolution methods. We here introduce an efficient method for scanning for resolutions in one such method. Additionally, we introduce the notion of ``significance'' of a partition, based on subgraph probabilities. Significance is independent of the exact method used, so could also be applied in other methods, and can be interpreted as the gain in encoding a graph by making use of a partition. Using significance, we can determine ``good'' resolution parameters, which we demonstrate on benchmark networks. Moreover, optimizing significance itself also shows excellent performance. We demonstrate our method on voting data from the European Parliament. Our analysis suggests the European Parliament has become increasingly ideologically divided and that nationality plays no role.

Auditory false perception in schizophrenia: Development and validation of auditory signal detection task.

PubMed

Chhabra, Harleen; Sowmya, Selvaraj; Sreeraj, Vanteemar S; Kalmady, Sunil V; Shivakumar, Venkataram; Amaresha, Anekal C; Narayanaswamy, Janardhanan C; Venkatasubramanian, Ganesan

2016-12-01

Auditory hallucinations constitute an important symptom component in 70-80% of schizophrenia patients. These hallucinations are proposed to occur due to an imbalance between perceptual expectation and external input, resulting in attachment of meaning to abstract noises; signal detection theory has been proposed to explain these phenomena. In this study, we describe the development of an auditory signal detection task using a carefully chosen set of English words that could be tested successfully in schizophrenia patients coming from varying linguistic, cultural and social backgrounds. Schizophrenia patients with significant auditory hallucinations (N=15) and healthy controls (N=15) performed the auditory signal detection task wherein they were instructed to differentiate between a 5-s burst of plain white noise and voiced-noise. The analysis showed that false alarms (p=0.02), discriminability index (p=0.001) and decision bias (p=0.004) were significantly different between the two groups. There was a significant negative correlation between false alarm rate and decision bias. These findings extend further support for impaired perceptual expectation system in schizophrenia patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

PubMed Central

Hori, Kiyosumi; Kataoka, Tomomori; Miura, Kiyoyuki; Yamaguchi, Masayuki; Saka, Norikuni; Nakahara, Takahiro; Sunohara, Yoshihiro; Ebana, Kaworu; Yano, Masahiro

2012-01-01

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars. PMID:23226082

Use of next-generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia.

PubMed

Iacocca, Michael A; Wang, Jian; Dron, Jacqueline S; Robinson, John F; McIntyre, Adam D; Cao, Henian; Hegele, Robert A

2017-11-01

Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene ( LDLR ). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential because ∼10% of FH cases are attributed to CNVs in LDLR ; accounting for them decreases false negative findings. Here, we determined the potential of replacing MLPA with bioinformatic analysis applied to NGS data, which uses depth-of-coverage analysis as its principal method to identify whole-exon CNV events. In analysis of 388 FH patient samples, there was 100% concordance in LDLR CNV detection between these two methods: 38 reported CNVs identified by MLPA were also successfully detected by our NGS method, while 350 samples negative for CNVs by MLPA were also negative by NGS. This result suggests that MLPA can be removed from the routine diagnostic screening for FH, significantly reducing associated costs, resources, and analysis time, while promoting more widespread assessment of this important class of mutations across diagnostic laboratories. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

Microarray-based comparative genomic hybridization analysis in neonates with congenital anomalies: detection of chromosomal imbalances.

PubMed

Emy Dorfman, Luiza; Leite, Júlio César L; Giugliani, Roberto; Riegel, Mariluce

2015-01-01

To identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array-CGH) in DNA samples of neonates with congenital anomalies of unknown cause from a birth defects monitoring program at a public maternity hospital. A blind genomic analysis was performed retrospectively in 35 stored DNA samples of neonates born between July of 2011 and December of 2012. All potential DNA copy number variations detected (CNVs) were matched with those reported in public genomic databases, and their clinical significance was evaluated. Out of a total of 35 samples tested, 13 genomic imbalances were detected in 12/35 cases (34.3%). In 4/35 cases (11.4%), chromosomal imbalances could be defined as pathogenic; in 5/35 (14.3%) cases, DNA CNVs of uncertain clinical significance were identified; and in 4/35 cases (11.4%), normal variants were detected. Among the four cases with results considered causally related to the clinical findings, two of the four (50%) showed causative alterations already associated with well-defined microdeletion syndromes. In two of the four samples (50%), the chromosomal imbalances found, although predicted as pathogenic, had not been previously associated with recognized clinical entities. Array-CGH analysis allowed for a higher rate of detection of chromosomal anomalies, and this determination is especially valuable in neonates with congenital anomalies of unknown etiology, or in cases in which karyotype results cannot be obtained. Moreover, although the interpretation of the results must be refined, this method is a robust and precise tool that can be used in the first-line investigation of congenital anomalies, and should be considered for prospective/retrospective analyses of DNA samples by birth defect monitoring programs. Copyright © 2014 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Dual color fluorescence quantitative detection of specific single-stranded DNA with molecular beacons and nucleic acid dye SYBR Green I.

PubMed

Xiang, Dong-Shan; Zhou, Guo-Hua; Luo, Ming; Ji, Xing-Hu; He, Zhi-Ke

2012-08-21

We have developed a dual color fluorescence quantitative detection method for specific single-stranded DNA with molecular beacons (MBs) and nucleic acid dye SYBR Green I by synchronous scanning fluorescence spectrometry. It is demonstrated by a reverse-transcription oligonucleotide sequence (target DNA, 33 bases) of RNA fragment of human immunodeficiency virus (HIV) as a model system. In the absence of target DNA, the MBs are in the stem-closed state, the fluorescence of 5-carboxy-X-rhodamine (ROX) is quenched by black hole quencher-2 (BHQ-2), and the interaction between SYBR Green I and the MBs is very weak. At this time the fluorescence signals of ROX and SYBR Green I are all very weak. In the presence of target DNA, MBs hybridize with target DNA and form a double-strand structure, the fluorophore ROX is separated from the quencher BHQ-2, and the fluorescence of ROX recovers. At the same time, SYBR Green I binds to hybridized dsDNA, whose fluorescence intensity is significantly enhanced. Thus, dual color fluorescence quantitative detection for the target DNA can be realized by synchronous scanning fluorescence spectrometry. In this strategy, the fluorescence signal of SYBR Green I is far larger than that of ROX, so the quantitative analysis of target DNA with the fluorescence intensity of SYBR Green I can significantly improve the detection sensitivity. In addition, the false-positive signals of MBs do not affect the fluorescence signals of nucleic acid dye SYBR Green I. Thereby, in the analysis of complex samples, quantitative analysis of target DNA with SYBR Green I can avoid the false-positive signals of MBs and improve the detection accuracy.

Comparison of Core-Needle Biopsy and Fine-Needle Aspiration for Evaluating Thyroid Incidentalomas Detected by 18F-Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography: A Propensity Score Analysis.

PubMed

Suh, Chong Hyun; Choi, Young Jun; Lee, Jong Jin; Shim, Woo Hyun; Baek, Jung Hwan; Chung, Han Cheol; Shong, Young Kee; Song, Dong Eun; Sung, Tae Yon; Lee, Jeong Hyun

2017-10-01

This study used a propensity score analysis to assess the roles of core-needle biopsy (CNB) and fine-needle aspiration (FNA) in the evaluation of thyroid incidentalomas detected on 18 F-fluorodeoxyglucose positron emission tomography/computed tomography ( 18 F-FDG PET/CT). The study population was obtained from a historical cohort who underwent 18 F-FDG PET/CT between October 2008 and September 2015. Patients were included who underwent ultrasound-guided CNB or FNA for incidental focal uptake of 18 F-FDG in the thyroid gland on PET/CT. The primary study outcomes included the inconclusive result rates in the CNB and FNA groups. The secondary outcome measures included the non-diagnostic result rate and the diagnostic performance for neoplasms. Multivariate analysis, propensity score matching, and inverse probability weighting were conducted. A total of 1360 nodules from 1338 patients were included in this study: 859 nodules from 850 patients underwent FNA, and 501 nodules from 488 patients underwent CNB. Compared to FNA, CNB demonstrated a significantly lower inconclusive result rate in the pooled cohort (23.8% vs. 35.4%; p < 0.001), propensity score-matched cohorts (22.9% vs. 36.6%; p < 0.001), and with inverse probability weighting (22.4% vs. 35.2%; p < 0.001). Non-diagnostic result rates were also significantly lower in CNB than in FNA. The diagnostic performance of the two groups in the pooled and matched cohorts was similar, with no significant differences found. The significantly lower inconclusive result rates in CNB than in FNA were consistent within the propensity score-matched cohorts. Therefore, CNB appears to be a promising diagnostic tool for patients with thyroid incidentalomas detected on 18 F-FDG PET/CT.

Decision-making by experienced rugby referees: use of perceptual information and episodic memory.

PubMed

MacMahon, Clare; Ste-Marie, Diane M

2002-10-01

The expertise paradigm was used in two studies to examine decision-making by rugby referees. Videoclips were used to assess infraction detection and knowledge base, or sources of information used. In Study 1, referees of high and low experience were compared, and in Study 2 referees and players were compared. Analysis by signal detection used a framework to classify types of information. Study 1 yielded no differences in detection of infractions as a function of experience, however, referees of high experience used significantly more sources of information than the group with low experience across all categories of information. In Study 2, there were no significant differences between referees and players, with the exception that referees displayed greater use of episodic memory information in decision-making.

Enhanced Detection of Chromosomal Abnormalities in Chronic Lymphocytic Leukemia by Conventional Cytogenetics Using CpG Oligonucleotide in Combination with Pokeweed Mitogen and Phorbol Myristate Acetate

PubMed Central

Muthusamy, Natarajan; Breidenbach, Heather; Andritsos, Leslie; Flynn, Joseph; Jones, Jeffrey; Ramanunni, Asha; Mo, Xiaokui; Jarjoura, David; Byrd, John C.; Heerema, Nyla A.

2011-01-01

Reproducible cytogenetic analysis in CLL has been limited by the inability to obtain reliable metaphase cells for analysis. CpG oligonucleotide and cytokine stimulation have been shown to improve metaphase analysis of CLL cytogenetic abnormalities, but is limited by variability in the cytokine receptor levels, stability and biological activity of the cytokine in culture conditions and high costs associated with these reagents. We report here use of a novel, stable CpG, GNKG168 along with pokeweed mitogen (PWM) and phorbol 12-myristate 13-acetate (PMA) for conventional cytogenetic assessment in CLL. We demonstrate that the combined use of GNKG168+PWM/PMA increased the sensitivity of detection of chromosomal abnormalities compared to PWM/PMA (n=207, odds ratio=2.2, p=0.0002) and GNKG168 (n=219, odds ratio=1.5, p=0.0452). Further, a significant increase in sensitivity to detect complexity ≥3 with GNKG168+PWM/PMA compared to GNKG168 alone (odds ratio 8.0, p=0.0022) or PWM/PMA alone (odds ratio 9.6, p=0.0007) was observed. The trend toward detection of higher complexity was significantly greater with GNKG168+PWM/PMA compared to GNKG168 alone (p=0.0412). The increased sensitivity was mainly attributed to the addition of PWM/PMA with GNKG168 because GNKG168 alone showed no difference in sensitivity for detection of complex abnormalities (p=0.17). Comparison of fluorescence in situ hybridization (FISH) results with karyotypic results showed a high degree of consistency, although some complex karyotypes were present in cases with no adverse FISH abnormality. These studies provide evidence for potential use of GNKG168 in combination with PWM and PMA in karyotypic analysis of CLL patient samples to better identify chromosomal abnormalities for risk stratification. PMID:21494579

Assessment of cell culture and polymerase chain reaction procedures for the detection of polioviruses in wastewater.

PubMed Central

Grabow, W. O.; Botma, K. L.; de Villiers, J. C.; Clay, C. G.; Erasmus, B.

1999-01-01

WHO considers that environmental surveillance for wild-type polioviruses is potentially important for surveillance for acute flaccid paralysis as a means of confirming eradication of poliomyelitis. The present study investigated methods for detecting polioviruses in a variety of water environments in South Africa. Most polioviruses were isolated on L20B mouse cells, which, however, were not selective: 16 reoviruses and 8 enteroviruses, apparently animal strains, were also isolated on these cells. Vaccine strains of polioviruses were isolated from surface waters during and shortly after two rounds of mass vaccination of children in an informal settlement where there was no sewerage. The results demonstrated the feasibility of poliovirus surveillance in such settlements. It was also evident that neither poliovirus vaccine strains nor other viruses were likely to interfere significantly with the detection of wild-type polioviruses. Optimal isolation of polioviruses was accomplished by parallel inoculation of L20B mouse cells and at least the PLC/PRF/5 human liver and buffalo green monkey (BGM) kidney cell lines. Analysis of cell cultures using the polymerase chain reaction revealed that 319 test samples contained at least 263 human enteroviruses that failed to produce a cytopathogenic effect. This type of analysis thus significantly increased the sensitivity of enterovirus detection. PMID:10680244

MYC protein expression is detected in plasma cell myeloma but not in monoclonal gammopathy of undetermined significance (MGUS).

PubMed

Xiao, Ruobing; Cerny, Jan; Devitt, Katherine; Dresser, Karen; Nath, Rajneesh; Ramanathan, Muthalagu; Rodig, Scott J; Chen, Benjamin J; Woda, Bruce A; Yu, Hongbo

2014-06-01

It has been recognized that monoclonal gammopathy of undetermined significance (MGUS) precedes a diagnosis of plasma cell myeloma in most patients. Recent gene expression array analysis has revealed that an MYC activation signature is detected in plasma cell myeloma but not in MGUS. In this study, we performed immunohistochemical studies using membrane CD138 and nuclear MYC double staining on bone marrow biopsies from patients who met the diagnostic criteria of plasma cell myeloma or MGUS. Our study demonstrated nuclear MYC expression in CD138-positive plasma cells in 22 of 26 (84%) plasma cell myeloma samples and in none of the 29 bone marrow samples from patients with MGUS. In addition, our data on the follow-up biopsies from plasma cell myeloma patients with high MYC expression demonstrated that evaluation of MYC expression in plasma cells can be useful in detecting residual disease. We also demonstrated that plasma cells gained MYC expression in 5 of 8 patients (62.5%) when progressing from MGUS to plasma cell myeloma. Analysis of additional lymphomas with plasmacytic differentiation, including lymphoplasmacytic lymphoma, marginal zone lymphoma, and plasmablastic lymphoma, reveals that MYC detection can be a useful tool in the diagnosis of plasma cell myeloma.

[Role of video electroencephalogram in diagnosis and localization of epilepsy in children].

PubMed

Yang, Xiao-Yan; Long, Li-Li; Xiao, Bo

2016-10-01

To study the role of video electroencephalogram (VEEG) versus regular electroencephalogram (REEG) in the diagnosis of epilepsy and localization of origin of epileptic discharge in children through a comparative analysis. A retrospective analysis was performed for the clinical data of 223 children with clinical paroxysmal symptoms in the past and suspected epilepsy. VEEG and REEG were compared from the aspects of monitoring of clinical seizures, interictal epileptiform discharge (IED), localization of the origin of IED, and identification of non-epileptic seizures, and the detection rate of IED during awakening and sleep stages was also compared. Compared with REEG, VEEG had significantly higher detection rates of IED and synchronous clinical seizures in children with epileptiform discharge (P<0.01). Of all children, 86 were diagnosed with epilepsy, 78 were diagnosed with epilepsy syndrome, 31 were diagnosed with non-epileptic seizures, and 81 had a definite location of the origin of epileptic discharge according to the VEEG. The detection rate of IED in the sleep stage was higher than that in the awakening stage (46% vs 13.2%; P<0.01), and IED was mainly detected in the NREM I-II stages according to the VEEG. VEEG has a significantly better performance than REEG in the diagnosis and localization of epilepsy in children and has a high value in clinical practice.

Advancing the detection of steady-state visual evoked potentials in brain-computer interfaces

NASA Astrophysics Data System (ADS)

Abu-Alqumsan, Mohammad; Peer, Angelika

2016-06-01

Objective. Spatial filtering has proved to be a powerful pre-processing step in detection of steady-state visual evoked potentials and boosted typical detection rates both in offline analysis and online SSVEP-based brain-computer interface applications. State-of-the-art detection methods and the spatial filters used thereby share many common foundations as they all build upon the second order statistics of the acquired Electroencephalographic (EEG) data, that is, its spatial autocovariance and cross-covariance with what is assumed to be a pure SSVEP response. The present study aims at highlighting the similarities and differences between these methods. Approach. We consider the canonical correlation analysis (CCA) method as a basis for the theoretical and empirical (with real EEG data) analysis of the state-of-the-art detection methods and the spatial filters used thereby. We build upon the findings of this analysis and prior research and propose a new detection method (CVARS) that combines the power of the canonical variates and that of the autoregressive spectral analysis in estimating the signal and noise power levels. Main results. We found that the multivariate synchronization index method and the maximum contrast combination method are variations of the CCA method. All three methods were found to provide relatively unreliable detections in low signal-to-noise ratio (SNR) regimes. CVARS and the minimum energy combination methods were found to provide better estimates for different SNR levels. Significance. Our theoretical and empirical results demonstrate that the proposed CVARS method outperforms other state-of-the-art detection methods when used in an unsupervised fashion. Furthermore, when used in a supervised fashion, a linear classifier learned from a short training session is able to estimate the hidden user intention, including the idle state (when the user is not attending to any stimulus), rapidly, accurately and reliably.

Early discrimination of nasopharyngeal carcinoma based on tissue deoxyribose nucleic acid surface-enhanced Raman spectroscopy analysis

NASA Astrophysics Data System (ADS)

Qiu, Sufang; Li, Chao; Lin, Jinyong; Xu, Yuanji; Lu, Jun; Huang, Qingting; Zou, Changyan; Chen, Chao; Xiao, Nanyang; Lin, Duo; Chen, Rong; Pan, Jianji; Feng, Shangyuan

2016-12-01

Surface-enhanced Raman spectroscopy (SERS) was employed to detect deoxyribose nucleic acid (DNA) variations associated with the development of nasopharyngeal carcinoma (NPC). Significant SERS spectral differences between the DNA extracted from early NPC, advanced NPC, and normal nasopharyngeal tissue specimens were observed at 678, 729, 788, 1337, 1421, 1506, and 1573 cm-1, which reflects the genetic variations in NPC. Principal component analysis combined with discriminant function analysis for early NPC discrimination yielded a diagnostic accuracy of 86.8%, 92.3%, and 87.9% for early NPC, advanced NPC, and normal nasopharyngeal tissue DNA, respectively. In this exploratory study, we demonstrated the potential of SERS for early detection of NPC based on the DNA molecular study of biopsy tissues.

Detection of Reduced Nitrogen Compounds at Rocknest Using the Sample Analysis At Mars (SAM) Instrument on the Mars Science Laboratory (MSL)

NASA Technical Reports Server (NTRS)

Stern, J. C.; Steele, A.; Brunner, A.; Coll, P.; Eigenbrode, J.; Franz, H. B.; Freissinet, C.; Glavin, D.; Jones, J. H.; Navarro-Gonzalez, R.;

Effect of reconstruction methods and x-ray tube current–time product on nodule detection in an anthropomorphic thorax phantom: A crossed-modality JAFROC observer study

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

Thompson, J. D., E-mail: j.d.thompson@salford.ac.uk; Chakraborty, D. P.; Szczepura, K.

Purpose: To evaluate nodule detection in an anthropomorphic chest phantom in computed tomography (CT) images reconstructed with adaptive iterative dose reduction 3D (AIDR{sup 3D}) and filtered back projection (FBP) over a range of tube current–time product (mAs). Methods: Two phantoms were used in this study: (i) an anthropomorphic chest phantom was loaded with spherical simulated nodules of 5, 8, 10, and 12 mm in diameter and +100, −630, and −800 Hounsfield units electron density; this would generate CT images for the observer study; (ii) a whole-body dosimetry verification phantom was used to ultimately estimate effective dose and risk according tomore » the model of the BEIR VII committee. Both phantoms were scanned over a mAs range (10, 20, 30, and 40), while all other acquisition parameters remained constant. Images were reconstructed with both AIDR{sup 3D} and FBP. For the observer study, 34 normal cases (no nodules) and 34 abnormal cases (containing 1–3 nodules, mean 1.35 ± 0.54) were chosen. Eleven observers evaluated images from all mAs and reconstruction methods under the free-response paradigm. A crossed-modality jackknife alternative free-response operating characteristic (JAFROC) analysis method was developed for data analysis, averaging data over the two factors influencing nodule detection in this study: mAs and image reconstruction (AIDR{sup 3D} or FBP). A Bonferroni correction was applied and the threshold for declaring significance was set at 0.025 to maintain the overall probability of Type I error at α = 0.05. Contrast-to-noise (CNR) was also measured for all nodules and evaluated by a linear least squares analysis. Results: For random-reader fixed-case crossed-modality JAFROC analysis, there was no significant difference in nodule detection between AIDR{sup 3D} and FBP when data were averaged over mAs [F(1, 10) = 0.08, p = 0.789]. However, when data were averaged over reconstruction methods, a significant difference was seen between multiple pairs of mAs settings [F(3, 30) = 15.96, p < 0.001]. Measurements of effective dose and effective risk showed the expected linear dependence on mAs. Nodule CNR was statistically higher for simulated nodules on images reconstructed with AIDR{sup 3D} (p < 0.001). Conclusions: No significant difference in nodule detection performance was demonstrated between images reconstructed with FBP and AIDR{sup 3D}. mAs was found to influence nodule detection, though further work is required for dose optimization.« less

GC-MS analysis of headspace and liquid extracts for metabolomic differentiation of citrus Huanglongbing and zinc deficiency in leaves of 'Valencia' sweet orange from commercial groves.

PubMed

Cevallos-Cevallos, Juan Manuel; García-Torres, Rosalía; Etxeberria, Edgardo; Reyes-De-Corcuera, José Ignacio

2011-01-01

Citrus Huanglongbing (HLB) is considered the most destructive citrus disease worldwide. Symptoms-based detection of HLB is difficult due to similarities with zinc deficiency. To find metabolic differences between leaves from HLB-infected, zinc-deficient, and healthy 'Valencia' orange trees by using GC-MS based metabolomics. Analysis based on GC-MS methods for untargeted metabolite analysis of citrus leaves was developed and optimized. Sample extracts from healthy, zinc deficient, or HLB-infected sweet orange leaves were submitted to headspace solid phase micro-extraction (SPME) and derivatization treatments prior to GC-MS analysis. Principal components analysis achieved correct classification of all the derivatized liquid extracts. Analysis of variance revealed 6 possible biomarkers for HLB, of which 5 were identified as proline, β-elemene, (-)trans- caryophyllene, and α-humulene. Significant (P < 0.05) differences in oxo-butanedioic acid, arabitol, and neo-inositol were exclusively detected in samples from plants with zinc deficiency. Levels of isocaryophyllen, α-selinene, β-selinene, and fructose were significantly (P < 0.05) different in healthy leaves only. Results suggest the potential of using identified HLB biomarkers for rapid differentiation of HLB from zinc deficiency. Copyright © 2010 John Wiley & Sons, Ltd.

Tomosynthesis for the early detection of pulmonary emphysema: diagnostic performance compared with chest radiography, using multidetector computed tomography as reference.

PubMed

Yamada, Yoshitake; Jinzaki, Masahiro; Hashimoto, Masahiro; Shiomi, Eisuke; Abe, Takayuki; Kuribayashi, Sachio; Ogawa, Kenji

2013-08-01

To compare the diagnostic performance of tomosynthesis with that of chest radiography for the detection of pulmonary emphysema, using multidetector computed tomography (MDCT) as reference. Forty-eight patients with and 63 without pulmonary emphysema underwent chest MDCT, tomosynthesis and radiography on the same day. Two blinded radiologists independently evaluated the tomosynthesis images and radiographs for the presence of pulmonary emphysema. Axial and coronal MDCT images served as the reference standard and the percentage lung volume with attenuation values of -950 HU or lower (LAA-950) was evaluated to determine the extent of emphysema. Receiver-operating characteristic (ROC) analysis and generalised estimating equations model were used. ROC analysis revealed significantly better performance (P < 0.0001) of tomosynthesis than radiography for the detection of pulmonary emphysema. The average sensitivity, specificity, positive predictive value and negative predictive value of tomosynthesis were 0.875, 0.968, 0.955 and 0.910, respectively, whereas the values for radiography were 0.479, 0.913, 0.815 and 0.697, respectively. For both tomosynthesis and radiography, the sensitivity increased with increasing LAA-950. The diagnostic performance of tomosynthesis was significantly superior to that of radiography for the detection of pulmonary emphysema. In both tomosynthesis and radiography, the sensitivity was affected by the LAA-950. • Tomosynthesis showed significantly better diagnostic performance for pulmonary emphysema than radiography. • Interobserver agreement for tomosynthesis was significantly higher than that for radiography. • Sensitivity increased with increasing LAA -950 in both tomosynthesis and radiography. • Tomosynthesis imparts a similar radiation dose to two projection chest radiography. • Radiation dose and cost of tomosynthesis are lower than those of MDCT.

Renal cell carcinoma: incidental detection and pathological staging.

PubMed

Siow, W Y; Yip, S K; Ng, L G; Tan, P H; Cheng, W S; Foo, K T

2000-10-01

In developed countries, there has been increased incidental detection of renal cell carcinoma (RCC). The incidence, pathological stage and survival of incidentally detected carcinoma in a developing country in Asia where, from 1990 to 1998, 165 renal cell carcinomas were identified. The clinical presentation, diagnostic-imaging modality employed, pathological staging and patient survival was reviewed. Incidental renal cancers included those that were diagnosed through health screening or detected incidentally through imaging studies for other conditions. The survival between these incidentally detected lesions and their symptomatic counterparts (suspected group) was compared. Sixty-four patients (39%) had their tumours detected incidentally, including 39 who were entirely asymptomatic and 25 who presented with non-specific symptoms, not initially suggestive of RCC. For the entire group, computed tomography provided the definitive diagnosis in 81% of cases. The incidental detection group had significantly smaller size of tumour (5.9 cm c.f. 7.6 cm), lower stage and lower histological grading. In particular, 78% of patients with incidental RCC had stage I or II diseases (TNM stage classification), compared with 57% of patients with suspected tumour (p < 0.05; Chi-square test). The disease free survival was significantly better for those with incidental detection (86% c.f. 66% at last follow up; p < 0.05; log-rank test) over a mean follow up period of 33 months (range 1-91). Regression analysis showed that stage of disease was the only independent variable predictive of clinical outcome. In conclusion, that significant numbers of RCC were detected incidentally. These tumours were of a lower clinical pathological stage and had a better prognosis.

[Sub-health status of middle school teachers and its correlation analysis with occupational stress].

PubMed

Chang, W J; Shao, H M; Zhi, X Y; Xu, J; Xie, J

2017-08-20

Objective: To study the distribution of sub-health and occupational stress as well as their correlation among middle school teachers in Tianjin, then provide evidences for prevention and control of the status of sub-health. Methods: A total of 3 522 middle school teachers from six districts of Tianjin were recruited with stratified cluster sampling strategy for the investigation of Sub-Health Measurement Scale version 1.0 (SHMS V1.0) and Occupational Stress Inventory-Revised Edition (OSI-R) . Results: Detection rate of sub-health status among Tianjin middle school teachers was 58.55%. Men had significantly lower sub-health detection rate (55.19%) than women (59.71%) . Sub-health detection rate increased with age ( P <0.05) , the sub-health detection rate among middle school teachers more than 50 years old was the highest (66.84%) . The mean score of OSI-R was 403.18±41.80 with the scores of 176.00±21.05, 103.17±17.53, and 124.02±20.28 for ORQ, PSQ, PRQ, respectively, which showed significantly difference compared with the occupational stress norm of China ( P <0.001) . The mean scores of OSI-R, ORQ, PSQ, PRQ in different health status were significantly different ( P <0.001) . The partial correlation analysis between the scores of sub-health and occupational stress of middle school teachers showed that the scores of occupational role and personal strain were negatively correlated with the scores of sub-health state ( P < 0.001) , while, there was significantly positive correlation between the scores of personal resource and the scores of sub-health state ( P <0.001) . Conclusion: Sub-health detection rate of middle school teachers in Tianjin is higher. Effective measures should be taken to appropriately mitigate the occupational stress level of middle school teachers, increase personal resources, and scientific and effective health guidance and education should be strengthened.

Sulfur analysis by inductively coupled plasma-mass spectrometry: A review

NASA Astrophysics Data System (ADS)

Giner Martínez-Sierra, J.; Galilea San Blas, O.; Marchante Gayón, J. M.; García Alonso, J. I.

2015-06-01

In recent years the number of applications of sulfur (S) analysis using inductively coupled plasma mass spectrometry (ICP-MS) as detector has increased significantly. In this article we describe in some depth the application of ICP-MS for S analysis with emphasis placed on the sulfur-specific detection by hyphenated techniques such as LC, GC, CE and LA coupled on-line to ICP-MS. The different approaches available for sulfur isotope ratio measurements by ICP-MS are also detailed. Particular attention has been paid to the quantification of peptides/proteins and the analysis of metallopeptides/metalloproteins via sulfur by LC-ICP-MS. Likewise, the speciation analysis of metal-based pharmaceuticals and metallodrugs and non-metal selective detection of pharmaceuticals via S are highlighted. Labeling procedures for metabolic applications are also included. Finally, the measurement of natural variations in S isotope composition with multicollector ICP-MS instruments is also covered in this review.

A simplified implementation of edge detection in MATLAB is faster and more sensitive than fast fourier transform for actin fiber alignment quantification.

PubMed

Kemeny, Steven Frank; Clyne, Alisa Morss

2011-04-01

Fiber alignment plays a critical role in the structure and function of cells and tissues. While fiber alignment quantification is important to experimental analysis and several different methods for quantifying fiber alignment exist, many studies focus on qualitative rather than quantitative analysis perhaps due to the complexity of current fiber alignment methods. Speed and sensitivity were compared in edge detection and fast Fourier transform (FFT) for measuring actin fiber alignment in cells exposed to shear stress. While edge detection using matrix multiplication was consistently more sensitive than FFT, image processing time was significantly longer. However, when MATLAB functions were used to implement edge detection, MATLAB's efficient element-by-element calculations and fast filtering techniques reduced computation cost 100 times compared to the matrix multiplication edge detection method. The new computation time was comparable to the FFT method, and MATLAB edge detection produced well-distributed fiber angle distributions that statistically distinguished aligned and unaligned fibers in half as many sample images. When the FFT sensitivity was improved by dividing images into smaller subsections, processing time grew larger than the time required for MATLAB edge detection. Implementation of edge detection in MATLAB is simpler, faster, and more sensitive than FFT for fiber alignment quantification.

A survey on object detection in optical remote sensing images

NASA Astrophysics Data System (ADS)

Cheng, Gong; Han, Junwei

2016-07-01

Object detection in optical remote sensing images, being a fundamental but challenging problem in the field of aerial and satellite image analysis, plays an important role for a wide range of applications and is receiving significant attention in recent years. While enormous methods exist, a deep review of the literature concerning generic object detection is still lacking. This paper aims to provide a review of the recent progress in this field. Different from several previously published surveys that focus on a specific object class such as building and road, we concentrate on more generic object categories including, but are not limited to, road, building, tree, vehicle, ship, airport, urban-area. Covering about 270 publications we survey (1) template matching-based object detection methods, (2) knowledge-based object detection methods, (3) object-based image analysis (OBIA)-based object detection methods, (4) machine learning-based object detection methods, and (5) five publicly available datasets and three standard evaluation metrics. We also discuss the challenges of current studies and propose two promising research directions, namely deep learning-based feature representation and weakly supervised learning-based geospatial object detection. It is our hope that this survey will be beneficial for the researchers to have better understanding of this research field.

Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies.

PubMed

Liu, Jia; Duffy, Ben A; Bernal-Casas, David; Fang, Zhongnan; Lee, Jin Hyung

2017-02-15

A large number of fMRI studies have shown that the temporal dynamics of evoked BOLD responses can be highly heterogeneous. Failing to model heterogeneous responses in statistical analysis can lead to significant errors in signal detection and characterization and alter the neurobiological interpretation. However, to date it is not clear that, out of a large number of options, which methods are robust against variability in the temporal dynamics of BOLD responses in block-design studies. Here, we used rodent optogenetic fMRI data with heterogeneous BOLD responses and simulations guided by experimental data as a means to investigate different analysis methods' performance against heterogeneous BOLD responses. Evaluations are carried out within the general linear model (GLM) framework and consist of standard basis sets as well as independent component analysis (ICA). Analyses show that, in the presence of heterogeneous BOLD responses, conventionally used GLM with a canonical basis set leads to considerable errors in the detection and characterization of BOLD responses. Our results suggest that the 3rd and 4th order gamma basis sets, the 7th to 9th order finite impulse response (FIR) basis sets, the 5th to 9th order B-spline basis sets, and the 2nd to 5th order Fourier basis sets are optimal for good balance between detection and characterization, while the 1st order Fourier basis set (coherence analysis) used in our earlier studies show good detection capability. ICA has mostly good detection and characterization capabilities, but detects a large volume of spurious activation with the control fMRI data. Copyright © 2016 Elsevier Inc. All rights reserved.

Optical Coherence Tomography Minimum Intensity as an Objective Measure for the Detection of Hydroxychloroquine Toxicity.

PubMed

Allahdina, Ali M; Stetson, Paul F; Vitale, Susan; Wong, Wai T; Chew, Emily Y; Ferris, Fredrick L; Sieving, Paul A; Cukras, Catherine

2018-04-01

As optical coherence tomography (OCT) minimum intensity (MI) analysis provides a quantitative assessment of changes in the outer nuclear layer (ONL), we evaluated the ability of OCT-MI analysis to detect hydroxychloroquine toxicity. Fifty-seven predominantly female participants (91.2% female; mean age, 55.7 ± 10.4 years; mean time on hydroxychloroquine, 15.0 ± 7.5 years) were enrolled in a case-control study and categorized into affected (i.e., with toxicity, n = 19) and unaffected (n = 38) groups using objective multifocal electroretinographic (mfERG) criteria. Spectral-domain OCT scans of the macula were analyzed and OCT-MI values quantitated for each subfield of the Early Treatment Diabetic Retinopathy Study (ETDRS) grid. A two-sample U-test and a cross-validation approach were used to assess the sensitivity and specificity of toxicity detection according to OCT-MI criteria. The medians of the OCT-MI values in all nine of the ETDRS subfields were significantly elevated in the affected group relative to the unaffected group (P < 0.005 for all comparisons), with the largest difference found for the inner inferior subfield (P < 0.0001). The receiver operating characteristic analysis of median MI values of the inner inferior subfields showed high sensitivity and high specificity in the detection of toxicity with area under the curve = 0.99. Retinal changes secondary to hydroxychloroquine toxicity result in increased OCT reflectivity in the ONL that can be detected and quantitated using OCT-MI analysis. Analysis of OCT-MI values demonstrates high sensitivity and specificity for detecting the presence of hydroxychloroquine toxicity in this cohort and may contribute additionally to current screening practices.

Optical Coherence Tomography Minimum Intensity as an Objective Measure for the Detection of Hydroxychloroquine Toxicity

PubMed Central

Allahdina, Ali M.; Stetson, Paul F.; Vitale, Susan; Wong, Wai T.; Chew, Emily Y.; Ferris, Fredrick L.; Sieving, Paul A.

2018-01-01

Purpose As optical coherence tomography (OCT) minimum intensity (MI) analysis provides a quantitative assessment of changes in the outer nuclear layer (ONL), we evaluated the ability of OCT-MI analysis to detect hydroxychloroquine toxicity. Methods Fifty-seven predominantly female participants (91.2% female; mean age, 55.7 ± 10.4 years; mean time on hydroxychloroquine, 15.0 ± 7.5 years) were enrolled in a case-control study and categorized into affected (i.e., with toxicity, n = 19) and unaffected (n = 38) groups using objective multifocal electroretinographic (mfERG) criteria. Spectral-domain OCT scans of the macula were analyzed and OCT-MI values quantitated for each subfield of the Early Treatment Diabetic Retinopathy Study (ETDRS) grid. A two-sample U-test and a cross-validation approach were used to assess the sensitivity and specificity of toxicity detection according to OCT-MI criteria. Results The medians of the OCT-MI values in all nine of the ETDRS subfields were significantly elevated in the affected group relative to the unaffected group (P < 0.005 for all comparisons), with the largest difference found for the inner inferior subfield (P < 0.0001). The receiver operating characteristic analysis of median MI values of the inner inferior subfields showed high sensitivity and high specificity in the detection of toxicity with area under the curve = 0.99. Conclusions Retinal changes secondary to hydroxychloroquine toxicity result in increased OCT reflectivity in the ONL that can be detected and quantitated using OCT-MI analysis. Analysis of OCT-MI values demonstrates high sensitivity and specificity for detecting the presence of hydroxychloroquine toxicity in this cohort and may contribute additionally to current screening practices. PMID:29677357

Series length used during trend analysis affects sensitivity to changes in progression rate in the ocular hypertension treatment study.

PubMed

Gardiner, Stuart K; Demirel, Shaban; De Moraes, Carlos Gustavo; Liebmann, Jeffrey M; Cioffi, George A; Ritch, Robert; Gordon, Mae O; Kass, Michael A

2013-02-15

Trend analysis techniques to detect glaucomatous progression typically assume a constant rate of change. This study uses data from the Ocular Hypertension Treatment Study to assess whether this assumption decreases sensitivity to changes in progression rate, by including earlier periods of stability. Series of visual fields (mean 24 per eye) completed at 6-month intervals from participants randomized initially to observation were split into subseries before and after the initiation of treatment (the "split-point"). The mean deviation rate of change (MDR) was derived using these entire subseries, and using only the window length (W) tests nearest the split-point, for different window lengths of W tests. A generalized estimating equation model was used to detect changes in MDR occurring at the split-point. Using shortened subseries with W = 7 tests, the MDR slowed by 0.142 dB/y upon initiation of treatment (P < 0.001), and the proportion of eyes showing "rapid deterioration" (MDR <-0.5 dB/y with P < 5%) decreased from 11.8% to 6.5% (P < 0.001). Using the entire sequence, no significant change in MDR was detected (P = 0.796), and there was no change in the proportion of eyes progressing (P = 0.084). Window lengths 6 ≤ W ≤ 9 produced similar benefits. Event analysis revealed a beneficial treatment effect in this dataset. This effect was not detected by linear trend analysis applied to entire series, but was detected when using shorter subseries of length between six and nine fields. Using linear trend analysis on the entire field sequence may not be optimal for detecting and monitoring progression. Nonlinear analyses may be needed for long series of fields. (ClinicalTrials.gov number, NCT00000125.).

Detection of Significant Pneumococcal Meningitis Biomarkers by Ego Network.

PubMed

Wang, Qian; Lou, Zhifeng; Zhai, Liansuo; Zhao, Haibin

2017-06-01

To identify significant biomarkers for detection of pneumococcal meningitis based on ego network. Based on the gene expression data of pneumococcal meningitis and global protein-protein interactions (PPIs) data recruited from open access databases, the authors constructed a differential co-expression network (DCN) to identify pneumococcal meningitis biomarkers in a network view. Here EgoNet algorithm was employed to screen the significant ego networks that could accurately distinguish pneumococcal meningitis from healthy controls, by sequentially seeking ego genes, searching candidate ego networks, refinement of candidate ego networks and significance analysis to identify ego networks. Finally, the functional inference of the ego networks was performed to identify significant pathways for pneumococcal meningitis. By differential co-expression analysis, the authors constructed the DCN that covered 1809 genes and 3689 interactions. From the DCN, a total of 90 ego genes were identified. Starting from these ego genes, three significant ego networks (Module 19, Module 70 and Module 71) that could predict clinical outcomes for pneumococcal meningitis were identified by EgoNet algorithm, and the corresponding ego genes were GMNN, MAD2L1 and TPX2, respectively. Pathway analysis showed that these three ego networks were related to CDT1 association with the CDC6:ORC:origin complex, inactivation of APC/C via direct inhibition of the APC/C complex pathway, and DNA strand elongation, respectively. The authors successfully screened three significant ego modules which could accurately predict the clinical outcomes for pneumococcal meningitis and might play important roles in host response to pathogen infection in pneumococcal meningitis.

Distribution of lead in selected organs and its effect on reproduction parameters of pheasants (Phasianus colchicus) after an experimental per oral administration.

PubMed

Gasparik, Jozef; Venglarcik, Jozef; Slamecka, Jaroslav; Kropil, Rudolf; Smehyl, Peter; Kopecky, Jan

2012-01-01

Lead poisoning has been reported in almost every country on earth. In this study the effect of experimental lead pellet intake (2-6 pellets per week [groups B2, B4, B6] and ad libitum [BAD] accessibility for 10 weeks) on its distribution in liver, kidney, pectoral muscle, ovary, eggs and the effect of selected reproductive parameters (egg weight, fertilization, hatchability) was analyzed in breeding pheasants. Lead pellets were force fed to the digestive tract (struma, ingluvies) and the ingestion was controlled. Concentration of lead was detected using the atomic absorption spectrophotometry. Analysis of the lead concentration in liver showed a significantly higher concentration in all group after the lead pellets intake. The increase of the lead concentration was dose-dependent and the concentration detected in group BAD was similar as in group B2. Very similar tendencies were detected for the lead concentration in kidney. The accumulation of lead in pectoral muscle was lower, in comparison with liver and kidney. Compared to lead concentration detected in ovary of the control group a significant increase was detected in all experimental groups, reaching the maximum in the group B6. Similar significant increase of lead concentration was detected in eggs. The average weight of eggs was 32.01 ± 2.71 g in the control group and lower in all experimental groups, but this decrease was significant only in the group B6. The fertilization rate was the highest in the control group and a dose-dependent decrease was detected with the lowest value in the group B6. For egg hatching ratio a significant decrease was detected in groups B4 and B6. Results of this study clearly describe accumulation of lead in the body and a its negative effect on the reproductive parameters. In the ad libitum experimental group the most similar results were found as in group B2, suggesting a rate of "natural" lead pellet intake.

Development of Solid-State Nanopore Technology for Life Detection

NASA Technical Reports Server (NTRS)

Bywaters, K. B.; Schmidt, H.; Vercoutere, W.; Deamer, D.; Hawkins, A. R.; Quinn, R. C.; Burton, A. S.; Mckay, C. P.

2017-01-01

Biomarkers for life on Earth are an important starting point to guide the search for life elsewhere. However, the search for life beyond Earth should incorporate technologies capable of recognizing an array of potential biomarkers beyond what we see on Earth, in order to minimize the risk of false negatives from life detection missions. With this in mind, charged linear polymers may be a universal signature for life, due to their ability to store information while also inherently reducing the tendency of complex tertiary structure formation that significantly inhibit replication. Thus, these molecules are attractive targets for biosignature detection as potential "self-sustaining chemical signatures." Examples of charged linear polymers, or polyelectrolytes, include deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) as well as synthetic polyelectrolytes that could potentially support life, including threose nucleic acid (TNA) and other xenonucleic acids (XNAs). Nanopore analysis is a novel technology that has been developed for singlemolecule sequencing with exquisite single nucleotide resolution which is also well-suited for analysis of polyelectrolyte molecules. Nanopore analysis has the ability to detect repeating sequences of electrical charges in organic linear polymers, and it is not molecule- specific (i.e. it is not restricted to only DNA or RNA). In this sense, it is a better life detection technique than approaches that are based on specific molecules, such as the polymerase chain reaction (PCR), which requires that the molecule being detected be composed of DNA.

Detection of Mouse Cough Based on Sound Monitoring and Respiratory Airflow Waveforms

PubMed Central

Chen, Liyan; Lai, Kefang; Lomask, Joseph Mark; Jiang, Bert; Zhong, Nanshan

2013-01-01

Detection for cough in mice has never yielded clearly audible sounds, so there is still a great deal of debates as to whether mice can cough in response to tussive stimuli. Here we introduce an approach for detection of mouse cough based on sound monitoring and airflow signals. 40 Female BALB/c mice were pretreated with normal saline, codeine, capasazepine or desensitized with capsaicin. Single mouse was put in a plethysmograph, exposed to aerosolized 100 µmol/L capsaicin for 3 min, followed by continuous observation for 3 min. Airflow signals of total 6 min were recorded and analyzed to detect coughs. Simultaneously, mouse cough sounds were sensed by a mini-microphone, monitored manually by an operator. When manual and automatic detection coincided, the cough was positively identified. Sound and sound waveforms were also recorded and filtered for further analysis. Body movements were observed by operator. Manual versus automated counts were compared. Seven types of airflow signals were identified by integrating manual and automated monitoring. Observation of mouse movements and analysis of sound waveforms alone did not produce meaningful data. Mouse cough numbers decreased significantly after all above drugs treatment. The Bland-Altman and consistency analysis between automatic and manual counts was 0.968 and 0.956. The study suggests that the mouse is able to present with cough, which could be detected by sound monitoring and respiratory airflow waveform changes. PMID:23555643

Assessment of low-contrast detectability for compressed digital chest images

NASA Astrophysics Data System (ADS)

Cook, Larry T.; Insana, Michael F.; McFadden, Michael A.; Hall, Timothy J.; Cox, Glendon G.

1994-04-01

The ability of human observers to detect low-contrast targets in screen-film (SF) images, computed radiographic (CR) images, and compressed CR images was measured using contrast detail (CD) analysis. The results of these studies were used to design a two- alternative forced-choice (2AFC) experiment to investigate the detectability of nodules in adult chest radiographs. CD curves for a common screen-film system were compared with CR images compressed up to 125:1. Data from clinical chest exams were used to define a CD region of clinical interest that sufficiently challenged the observer. From that data, simulated lesions were introduced into 100 normal CR chest films, and forced-choice observer performance studies were performed. CR images were compressed using a full-frame discrete cosine transform (FDCT) technique, where the 2D Fourier space was divided into four areas of different quantization depending on the cumulative power spectrum (energy) of each image. The characteristic curve of the CR images was adjusted so that optical densities matched those of the SF system. The CD curves for SF and uncompressed CR systems were statistically equivalent. The slope of the CD curve for each was - 1.0 as predicted by the Rose model. There was a significant degradation in detection found for CR images compressed to 125:1. Furthermore, contrast-detail analysis demonstrated that many pulmonary nodules encountered in clinical practice are significantly above the average observer threshold for detection. We designed a 2AFC observer study using simulated 1-cm lesions introduced into normal CR chest radiographs. Detectability was reduced for all compressed CR radiographs.

How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches.

PubMed

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M; Jonsson, Gudberg K; Anguera, M Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013-First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann-Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training.

How Game Location Affects Soccer Performance: T-Pattern Analysis of Attack Actions in Home and Away Matches

PubMed Central

Diana, Barbara; Zurloni, Valentino; Elia, Massimiliano; Cavalera, Cesare M.; Jonsson, Gudberg K.; Anguera, M. Teresa

2017-01-01

The influence of game location on performance has been widely examined in sport contexts. Concerning soccer, game-location affects positively the secondary and tertiary level of performance; however, there are fewer evidences about its effect on game structure (primary level of performance). This study aimed to detect the effect of game location on a primary level of performance in soccer. In particular, the objective was to reveal the hidden structures underlying the attack actions, in both home and away matches played by a top club (Serie A 2012/2013—First Leg). The methodological approach was based on systematic observation, supported by digital recordings and T-pattern analysis. Data were analyzed with THEME 6.0 software. A quantitative analysis, with nonparametric Mann–Whitney test and descriptive statistics, was carried out to test the hypotheses. A qualitative analysis on complex patterns was performed to get in-depth information on the game structure. This study showed that game tactics were significantly different, with home matches characterized by a more structured and varied game than away matches. In particular, a higher number of different patterns, with a higher level of complexity and including more unique behaviors was detected in home matches than in the away ones. No significant differences were found in the number of events coded per game between the two conditions. THEME software, and the corresponding T-pattern detection algorithm, enhance research opportunities by going further than frequency-based analyses, making this method an effective tool in supporting sport performance analysis and training. PMID:28878712

Applicability of direct total reflection X-ray fluorescence analysis for selenium determination in solutions related to environmental and geochemical studies

NASA Astrophysics Data System (ADS)

Marguí, E.; Floor, G. H.; Hidalgo, M.; Kregsamer, P.; Roman-Ross, G.; Streli, C.; Queralt, I.

2010-12-01

A significant amount of environmental studies related to selenium determination in different environmental compartments have been published in the last years due to the narrow range between the Se nutritious requirement as essential element and toxic effects upon exposure. However, the direct analysis of complex liquid samples like natural waters and extraction solutions presents significant problems related to the low Se concentrations and the complicated matrix of this type of samples. The goal of the present research was to study the applicability of direct TXRF analysis of different type of solutions commonly used in environmental and geochemical studies, confirm the absence or presence of matrix effects and evaluate the limits of detection and accuracy for Se determination in the different matrices. Good analytical results were obtained for the direct analysis of ground and rain water samples with limits of detection for Se two orders of magnitude lower than the permissible Se concentration in drinking waters ([Se] = 10 μg/L) according to the WHO. However, the Se detection limits for more complex liquid samples such as thermal waters and extraction solutions were in the μg/L range due to the presence of high contents of other elements present in the matrix (i.e., Br, Fe, Zn) or the high background of the TXRF spectrum that hamper the Se determination at trace levels. Our results give insight into the possibilities and drawbacks of direct TXRF analysis and to a certain extent the potential applications in the environmental and geochemical field.

Depleted Uranium (DU) Follow-up Program Update

DTIC Science & Technology

2010-11-01

hematology, serum chemistry, neuroendocrine, urinalysis, urine, sem en and blood uranium, renal markers, semen analysis, bone metabolism) • Chromosomal...Clinical Findings • No clinically significant differences detected between low and high uranium exposure groups for – Semen characteristics

Assessment of Prospectively Assigned Likert Scores for Targeted Magnetic Resonance Imaging-Transrectal Ultrasound Fusion Biopsies in Patients with Suspected Prostate Cancer.

PubMed

Costa, Daniel N; Lotan, Yair; Rofsky, Neil M; Roehrborn, Claus; Liu, Alexander; Hornberger, Brad; Xi, Yin; Francis, Franto; Pedrosa, Ivan

2016-01-01

We assess the performance of prospectively assigned magnetic resonance imaging based Likert scale scores for the detection of clinically significant prostate cancer, and analyze the pre-biopsy imaging variables associated with increased cancer detection using targeted magnetic resonance imaging-transrectal ultrasound fusion biopsy. In this retrospective review of prospectively generated data including men with abnormal multiparametric prostate magnetic resonance imaging (at least 1 Likert score 3 or greater lesion) who underwent subsequent targeted magnetic resonance imaging-transrectal ultrasound fusion biopsy, we determined the association between different imaging variables (Likert score, lesion size, lesion location, prostate volume, radiologist experience) and targeted biopsy positivity rate. We also compared the detection of clinically significant cancer according to Likert scale scores. Tumors with high volume (50% or more of any core) Gleason score 3+4 or any tumor with greater Gleason score were considered clinically significant. Each lesion served as the elementary unit for analysis. We used logistic regression for univariate and multivariate (stepwise selection) analysis to assess for an association between targeted biopsy positivity rate and each tested variable. The relationship between Likert scale and Gleason score was evaluated using the Spearman correlation coefficient. A total of 161 men with 244 lesions met the study eligibility criteria. Targeted biopsies diagnosed cancer in 41% (66 of 161) of the men and 41% (99 of 244) of the lesions. The Likert score was the strongest predictor of targeted biopsy positivity (OR 3.7, p <0.0001). Other imaging findings associated with a higher targeted biopsy positivity rate included smaller prostate volume (OR 0.7, p <0.01), larger lesion size (OR 2.2, p <0.001) and anterior location (OR 2.0, p=0.01). On multiple logistic regression analysis Likert score, lesion size and prostate volume were significant predictors of targeted biopsy positivity. Higher Likert scores were also associated with increased detection of clinically significant tumors (p <0.0001). The Likert scale score used to convey the degree of suspicion on multiparametric magnetic resonance imaging is the strongest predictor of targeted biopsy positivity and of the presence of clinically significant tumor. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Meta-Analysis of Infectious Agents and Depression

PubMed Central

Wang, Xiao; Zhang, Liang; Lei, Yang; Liu, Xia; Zhou, Xinyu; Liu, Yiyun; Wang, Mingju; Yang, Liu; Zhang, Lujun; Fan, Songhua; Xie, Peng

2014-01-01

Depression is a debilitating psychiatric disorder and a growing global public health issue. However, the relationships between microbial infections and depression remains uncertain. A computerized literature search of Medline, ISI Web of Knowledge, PsycINFO, and the Cochrane Library was conducted up to May 2013, and 6362 studies were initially identified for screening. Case-control studies detected biomarker of microorganism were included. Based on inclusion and exclusion criteria, 28 studies were finally included to compare the detection of 16 infectious agents in unipolar depressed patients and healthy controls with a positive incident being defined as a positive biochemical marker of microbial infection. A customized form was used for data extraction. Pooled analysis revealed that the majority of the 16 infectious agents were not significantly associated with depression. However, there were statistically significant associations between depression and infection with Borna disease virus, herpes simplex virus-1, varicella zoster virus, Epstein-Barr virus, and Chlamydophila trachomatis. PMID:24681753

Current trends in gamma radiation detection for radiological emergency response

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Sanjoy; Guss, Paul; Maurer, Richard

2011-09-01

Passive and active detection of gamma rays from shielded radioactive materials, including special nuclear materials, is an important task for any radiological emergency response organization. This article reports on the current trends and status of gamma radiation detection objectives and measurement techniques as applied to nonproliferation and radiological emergencies. In recent years, since the establishment of the Domestic Nuclear Detection Office by the Department of Homeland Security, a tremendous amount of progress has been made in detection materials (scintillators, semiconductors), imaging techniques (Compton imaging, use of active masking and hybrid imaging), data acquisition systems with digital signal processing, field programmable gate arrays and embedded isotopic analysis software (viz. gamma detector response and analysis software [GADRAS]1), fast template matching, and data fusion (merging radiological data with geo-referenced maps, digital imagery to provide better situational awareness). In this stride to progress, a significant amount of inter-disciplinary research and development has taken place-techniques and spin-offs from medical science (such as x-ray radiography and tomography), materials engineering (systematic planned studies on scintillators to optimize several qualities of a good scintillator, nanoparticle applications, quantum dots, and photonic crystals, just to name a few). No trend analysis of radiation detection systems would be complete without mentioning the unprecedented strategic position taken by the National Nuclear Security Administration (NNSA) to deter, detect, and interdict illicit trafficking in nuclear and other radioactive materials across international borders and through the global maritime transportation-the so-called second line of defense.

The Use of Neutron Analysis Techniques for Detecting The Concentration And Distribution of Chloride Ions in Archaeological Iron

PubMed Central

Watkinson, D; Rimmer, M; Kasztovszky, Z; Kis, Z; Maróti, B; Szentmiklósi, L

2014-01-01

Chloride (Cl) ions diffuse into iron objects during burial and drive corrosion after excavation. Located under corrosion layers, Cl is inaccessible to many analytical techniques. Neutron analysis offers non-destructive avenues for determining Cl content and distribution in objects. A pilot study used prompt gamma activation analysis (PGAA) and prompt gamma activation imaging (PGAI) to analyse the bulk concentration and longitudinal distribution of Cl in archaeological iron objects. This correlated with the object corrosion rate measured by oxygen consumption, and compared well with Cl measurement using a specific ion meter. High-Cl areas were linked with visible damage to the corrosion layers and attack of the iron core. Neutron techniques have significant advantages in the analysis of archaeological metals, including penetration depth and low detection limits. PMID:26028670

A fractal analysis of pathogen detection by biosensors

NASA Astrophysics Data System (ADS)

Doke, Atul M.; Sadana, Ajit

2006-05-01

A fractal analysis is presented for the detection of pathogens such as Franscisela tularensis, and Yersinia pestis (the bacterium that causes plague) using a CANARY (cellular analysis and notification of antigens risks and yields) biosensor (Rider et al., 2003). In general, the binding and dissociation rate coefficients may be adequately described by either a single- or a dual-fractal analysis. An attempt is made to relate the binding rate coefficient to the degree of heterogeneity (fractal dimension value) present on the biosensor surface. Binding and dissociation rate coefficient values obtained are presented. The kinetics aspects along with the affinity values presented are of interest, and should along with the rate coefficients presented for the binding and the dissociation phase be of significant interest in help designing better biosensors for an application area that is bound to gain increasing importance in the future.

Phenology satellite experiment

NASA Technical Reports Server (NTRS)

Dethier, B. E. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The detection of a phenological event (the Brown Wave-vegetation sensescence) for specific forest and crop types using ERTS-1 imagery is described. Data handling techniques including computer analysis and photointerpretation procedures are explained. Computer analysis of multspectral scanner digital tapes in all bands was used to give the relative changes of spectral reflectance with time of forests and specified crops. These data were obtained for a number of the twenty-four sites located within four north-south corridors across the United States. Analysis of ground observation photography and ERTS-1 imagery for sites in the Appalachian Corridor and Mississippi Valley Corridor indicates that the recession of vegetation development can be detected very well. Tentative conclusions are that specific phenological events such as crop maturity or leaf fall can be mapped for specific sites and possible for different regions. Preliminary analysis based on a number of samples in mixed deciduous hardwood stands indicates that as senescence proceeds both the rate of change and differences in color among species can be detected. The results to data show the feasibility of the development and refinement of phenoclimatic models.

Characterization of the cell growth analysis for detection of immortal cellular impurities in human mesenchymal stem cells.

PubMed

Kono, Ken; Takada, Nozomi; Yasuda, Satoshi; Sawada, Rumi; Niimi, Shingo; Matsuyama, Akifumi; Sato, Yoji

2015-03-01

The analysis of in vitro cell senescence/growth after serial passaging can be one of ways to show the absence of immortalized cells, which are frequently tumorigenic, in human cell-processed therapeutic products (hCTPs). However, the performance of the cell growth analysis for detection of the immortalized cellular impurities has never been evaluated. In the present study, we examined the growth rates of human mesenchymal stem cells (hMSCs, passage 5 (P = 5)) contaminated with various doses of HeLa cells, and compared with that of hMSCs alone. The growth rates of the contaminated hMSCs were comparable to that of hMSCs alone at P = 5, but significantly increased at P = 6 (0.1% and 0.01% HeLa) or P = 7 (0.001% HeLa) within 30 days. These findings suggest that the cell growth analysis is a simple and sensitive method to detect immortalized cellular impurities in hCTPs derived from human somatic cells. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Differences in compassion fatigue, symptoms of posttraumatic stress disorder and relationship satisfaction, including sexual desire and functioning, between male and female detectives who investigate sexual offenses against children: a pilot study.

PubMed

Lane, Eric J; Lating, Jeffrey M; Lowry, Jenny L; Martino, Traci P

2010-01-01

Law enforcement detectives who work with traumatized individuals, especially children who were victims of sexual abuse or assault, are likely to experience job-related emotional distress. The purpose of this study was to examine the relations among compassion fatigue, probable PTSD symptoms, and personal relationship satisfaction, including communication and sexual satisfaction, in a sample of 47 male and female detectives. Responses to the administered questionnaires indicated a relation between compassion fatigue symptoms and probable PTSD symptoms. There also were compelling gender differences. For example, for male detectives, open communication with their spouse or significant other was negatively correlated with burnout, indicating the more open the communication, the lower the reported burnout. However for female detectives there was a negative correlation between open communication with spouse or significant other and compassion satisfaction, suggesting that more open communication was related to lower levels of satisfaction with their ability to be a professional caregiver Furthermore, although stepwise regression analysis indicated that years of service as a detective is independently associated with sexual desire, female detectives evidenced less sexual desire and more difficulty with sexual functioning than did male detectives. Implications of these preliminary findings are discussed and limitations addressed.

Mathematical evaluation of the amino acid and polyphenol content and antioxidant activities of fruits from different apricot cultivars.

PubMed

Sochor, Jiri; Skutkova, Helena; Babula, Petr; Zitka, Ondrej; Cernei, Natalia; Rop, Otakar; Krska, Boris; Adam, Vojtech; Provazník, Ivo; Kizek, Rene

2011-09-01

Functional foods are of interest because of their significant effects on human health, which can be connected with the presence of some biologically important compounds. In this study, we carried out complex analysis of 239 apricot cultivars (Prunus armeniaca L.) cultivated in Lednice (climatic area T4), South Moravia, Czech Republic. Almost all previously published studies have focused only on analysis of certain parameters. However, we focused on detection both primary and secondary metabolites in a selection of apricot cultivars with respect to their biological activity. The contents of thirteen biogenic alpha-L-amino acids (arginine, asparagine, isoleucine, lysine, serine, threonine, valine, leucine, phenylalanine, tryptophan, tyrosine, proline and alanine) were determined using ion exchange chromatography with UV-Vis spectrometry detection. Profile of polyphenols, measured as content of ten polyphenols with significant antioxidant properties (gallic acid, procatechinic acid, p-aminobenzoic acid, chlorogenic acid, caffeic acid, vanillin, p-coumaric acid, rutin, ferrulic acid and quercetrin), was determined by high performance liquid chromatography with spectrometric/electrochemical detection. Moreover, content of total phenolics was determined spectrophotometrically using the Folin-Ciocalteu method. Antioxidant activity was determined using five independent spectrophotometric methods: DPPH assay, DMPD method, ABTS method, FRAP and Free Radicals methods. Considering the complexity of the obtained data, they were processed and correlated using bioinformatics techniques (cluster analysis, principal component analysis). The studied apricot cultivars were clustered according to their common biochemical properties, which has not been done before. The observed similarities and differences were discussed.

Second feature of the matter two-point function

NASA Astrophysics Data System (ADS)

Tansella, Vittorio

2018-05-01

We point out the existence of a second feature in the matter two-point function, besides the acoustic peak, due to the baryon-baryon correlation in the early Universe and positioned at twice the distance of the peak. We discuss how the existence of this feature is implied by the well-known heuristic argument that explains the baryon bump in the correlation function. A standard χ2 analysis to estimate the detection significance of the second feature is mimicked. We conclude that, for realistic values of the baryon density, a SKA-like galaxy survey will not be able to detect this feature with standard correlation function analysis.

A New Reassigned Spectrogram Method in Interference Detection for GNSS Receivers.

PubMed

Sun, Kewen; Jin, Tian; Yang, Dongkai

2015-09-02

Interference detection is very important for Global Navigation Satellite System (GNSS) receivers. Current work on interference detection in GNSS receivers has mainly focused on time-frequency (TF) analysis techniques, such as spectrogram and Wigner-Ville distribution (WVD), where the spectrogram approach presents the TF resolution trade-off problem, since the analysis window is used, and the WVD method suffers from the very serious cross-term problem, due to its quadratic TF distribution nature. In order to solve the cross-term problem and to preserve good TF resolution in the TF plane at the same time, in this paper, a new TF distribution by using a reassigned spectrogram has been proposed in interference detection for GNSS receivers. This proposed reassigned spectrogram method efficiently combines the elimination of the cross-term provided by the spectrogram itself according to its inherent nature and the improvement of the TF aggregation property achieved by the reassignment method. Moreover, a notch filter has been adopted in interference mitigation for GNSS receivers, where receiver operating characteristics (ROCs) are used as metrics for the characterization of interference mitigation performance. The proposed interference detection method by using a reassigned spectrogram is evaluated by experiments on GPS L1 signals in the disturbing scenarios in comparison to the state-of-the-art TF analysis approaches. The analysis results show that the proposed interference detection technique effectively overcomes the cross-term problem and also keeps good TF localization properties, which has been proven to be valid and effective to enhance the interference Sensors 2015, 15 22168 detection performance; in addition, the adoption of the notch filter in interference mitigation has shown a significant acquisition performance improvement in terms of ROC curves for GNSS receivers in jamming environments.

A New Reassigned Spectrogram Method in Interference Detection for GNSS Receivers

PubMed Central

Sun, Kewen; Jin, Tian; Yang, Dongkai

2015-01-01

Interference detection is very important for Global Navigation Satellite System (GNSS) receivers. Current work on interference detection in GNSS receivers has mainly focused on time-frequency (TF) analysis techniques, such as spectrogram and Wigner–Ville distribution (WVD), where the spectrogram approach presents the TF resolution trade-off problem, since the analysis window is used, and the WVD method suffers from the very serious cross-term problem, due to its quadratic TF distribution nature. In order to solve the cross-term problem and to preserve good TF resolution in the TF plane at the same time, in this paper, a new TF distribution by using a reassigned spectrogram has been proposed in interference detection for GNSS receivers. This proposed reassigned spectrogram method efficiently combines the elimination of the cross-term provided by the spectrogram itself according to its inherent nature and the improvement of the TF aggregation property achieved by the reassignment method. Moreover, a notch filter has been adopted in interference mitigation for GNSS receivers, where receiver operating characteristics (ROCs) are used as metrics for the characterization of interference mitigation performance. The proposed interference detection method by using a reassigned spectrogram is evaluated by experiments on GPS L1 signals in the disturbing scenarios in comparison to the state-of-the-art TF analysis approaches. The analysis results show that the proposed interference detection technique effectively overcomes the cross-term problem and also keeps good TF localization properties, which has been proven to be valid and effective to enhance the interference detection performance; in addition, the adoption of the notch filter in interference mitigation has shown a significant acquisition performance improvement in terms of ROC curves for GNSS receivers in jamming environments. PMID:26364637

Rapid detection of pathological mutations and deletions of the haemoglobin beta gene (HBB) by High Resolution Melting (HRM) analysis and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR).

PubMed

Turner, Andrew; Sasse, Jurgen; Varadi, Aniko

2016-10-19

Inherited disorders of haemoglobin are the world's most common genetic diseases, resulting in significant morbidity and mortality. The large number of mutations associated with the haemoglobin beta gene (HBB) makes gene scanning by High Resolution Melting (HRM) PCR an attractive diagnostic approach. However, existing HRM-PCR assays are not able to detect all common point mutations and have only a very limited ability to detect larger gene rearrangements. The aim of the current study was to develop a HBB assay, which can be used as a screening test in highly heterogeneous populations, for detection of both point mutations and larger gene rearrangements. The assay is based on a combination of conventional HRM-PCR and a novel Gene Ratio Analysis Copy Enumeration (GRACE) PCR method. HRM-PCR was extensively optimised, which included the use of an unlabelled probe and incorporation of universal bases into primers to prevent interference from common non-pathological polymorphisms. GRACE-PCR was employed to determine HBB gene copy numbers relative to a reference gene using melt curve analysis to detect rearrangements in the HBB gene. The performance of the assay was evaluated by analysing 410 samples. A total of 44 distinct pathological genotypes were detected. In comparison with reference methods, the assay has a sensitivity of 100 % and a specificity of 98 %. We have developed an assay that detects both point mutations and larger rearrangements of the HBB gene. This assay is quick, sensitive, specific and cost effective making it suitable as an initial screening test that can be used for highly heterogeneous cohorts.

Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.

PubMed

He, Jieyue; Li, Chaojun; Ye, Baoliu; Zhong, Wei

2012-06-25

Most computational algorithms mainly focus on detecting highly connected subgraphs in PPI networks as protein complexes but ignore their inherent organization. Furthermore, many of these algorithms are computationally expensive. However, recent analysis indicates that experimentally detected protein complexes generally contain Core/attachment structures. In this paper, a Greedy Search Method based on Core-Attachment structure (GSM-CA) is proposed. The GSM-CA method detects densely connected regions in large protein-protein interaction networks based on the edge weight and two criteria for determining core nodes and attachment nodes. The GSM-CA method improves the prediction accuracy compared to other similar module detection approaches, however it is computationally expensive. Many module detection approaches are based on the traditional hierarchical methods, which is also computationally inefficient because the hierarchical tree structure produced by these approaches cannot provide adequate information to identify whether a network belongs to a module structure or not. In order to speed up the computational process, the Greedy Search Method based on Fast Clustering (GSM-FC) is proposed in this work. The edge weight based GSM-FC method uses a greedy procedure to traverse all edges just once to separate the network into the suitable set of modules. The proposed methods are applied to the protein interaction network of S. cerevisiae. Experimental results indicate that many significant functional modules are detected, most of which match the known complexes. Results also demonstrate that the GSM-FC algorithm is faster and more accurate as compared to other competing algorithms. Based on the new edge weight definition, the proposed algorithm takes advantages of the greedy search procedure to separate the network into the suitable set of modules. Experimental analysis shows that the identified modules are statistically significant. The algorithm can reduce the computational time significantly while keeping high prediction accuracy.

Could texture features from preoperative CT image be used for predicting occult peritoneal carcinomatosis in patients with advanced gastric cancer?

PubMed

Kim, Hae Young; Kim, Young Hoon; Yun, Gabin; Chang, Won; Lee, Yoon Jin; Kim, Bohyoung

2018-01-01

To retrospectively investigate whether texture features obtained from preoperative CT images of advanced gastric cancer (AGC) patients could be used for the prediction of occult peritoneal carcinomatosis (PC) detected during operation. 51 AGC patients with occult PC detected during operation from January 2009 to December 2012 were included as occult PC group. For the control group, other 51 AGC patients without evidence of distant metastasis including PC, and whose clinical T and N stage could be matched to those of the patients of the occult PC group, were selected from the period of January 2011 to July 2012. Each group was divided into test (n = 41) and validation cohort (n = 10). Demographic and clinical data of these patients were acquired from the hospital database. Texture features including average, standard deviation, kurtosis, skewness, entropy, correlation, and contrast were obtained from manually drawn region of interest (ROI) over the omentum on the axial CT image showing the omentum at its largest cross sectional area. After using Fisher's exact and Wilcoxon signed-rank test for comparison of the clinical and texture features between the two groups of the test cohort, conditional logistic regression analysis was performed to determine significant independent predictor for occult PC. Using the optimal cut-off value from receiver operating characteristic (ROC) analysis for the significant variables, diagnostic sensitivity and specificity were determined in the test cohort. The cut-off value of the significant variables obtained from the test cohort was then applied to the validation cohort. Bonferroni correction was used to adjust P value for multiple comparisons. Between the two groups, there was no significant difference in the clinical features. Regarding the texture features, the occult PC group showed significantly higher average, entropy, standard deviation, and significantly lower correlation (P value < 0.004 for all). Conditional logistic regression analysis demonstrated that entropy was significant independent predictor for occult PC. When the cut-off value of entropy (> 7.141) was applied to the validation cohort, sensitivity and specificity for the prediction of occult PC were 80% and 90%, respectively. For AGC patients whose PC cannot be detected with routine imaging such as CT, texture analysis may be a useful adjunct for the prediction of occult PC.

Integrating Oil Debris and Vibration Measurements for Intelligent Machine Health Monitoring. Degree awarded by Toledo Univ., May 2002

NASA Technical Reports Server (NTRS)

Dempsey, Paula J.

2003-01-01

A diagnostic tool for detecting damage to gears was developed. Two different measurement technologies, oil debris analysis and vibration were integrated into a health monitoring system for detecting surface fatigue pitting damage on gears. This integrated system showed improved detection and decision-making capabilities as compared to using individual measurement technologies. This diagnostic tool was developed and evaluated experimentally by collecting vibration and oil debris data from fatigue tests performed in the NASA Glenn Spur Gear Fatigue Rig. An oil debris sensor and the two vibration algorithms were adapted as the diagnostic tools. An inductance type oil debris sensor was selected for the oil analysis measurement technology. Gear damage data for this type of sensor was limited to data collected in the NASA Glenn test rigs. For this reason, this analysis included development of a parameter for detecting gear pitting damage using this type of sensor. The vibration data was used to calculate two previously available gear vibration diagnostic algorithms. The two vibration algorithms were selected based on their maturity and published success in detecting damage to gears. Oil debris and vibration features were then developed using fuzzy logic analysis techniques, then input into a multi sensor data fusion process. Results show combining the vibration and oil debris measurement technologies improves the detection of pitting damage on spur gears. As a result of this research, this new diagnostic tool has significantly improved detection of gear damage in the NASA Glenn Spur Gear Fatigue Rigs. This research also resulted in several other findings that will improve the development of future health monitoring systems. Oil debris analysis was found to be more reliable than vibration analysis for detecting pitting fatigue failure of gears and is capable of indicating damage progression. Also, some vibration algorithms are as sensitive to operational effects as they are to damage. Another finding was that clear threshold limits must be established for diagnostic tools. Based on additional experimental data obtained from the NASA Glenn Spiral Bevel Gear Fatigue Rig, the methodology developed in this study can be successfully implemented on other geared systems.

Frontiers in In-Situ Cosmic Dust Detection and Analysis

NASA Astrophysics Data System (ADS)

Sternovsky, Zoltán; Auer, Siegfried; Drake, Keith; Grün, Eberhard; Horányi, Mihály; Le, Huy; Srama, Ralf; Xie, Jianfeng

2011-11-01

In-situ cosmic dust instruments and measurements played a critical role in the emergence of the field of dusty plasmas. The major breakthroughs included the discovery of β-meteoroids, interstellar dust particles within the solar system, Jovian stream particles, and the detection and analysis of Enceladus's plumes. The science goals of cosmic dust research require the measurements of the charge, the spatial, size and velocity distributions, and the chemical and isotopic compositions of individual dust particles. In-situ dust instrument technology has improved significantly in the last decade. Modern dust instruments with high sensitivity can detect submicron-sized particles even at low impact velocities. Innovative ion optics methods deliver high mass resolution, m/dm>100, for chemical and isotopic analysis. The accurate trajectory measurement of cosmic dust is made possible even for submicron-sized grains using the Dust Trajectory Sensor (DTS). This article is a brief review of the current capabilities of modern dust instruments, future challenges and opportunities in cosmic dust research.

Analysis of digitized cervical images to detect cervical neoplasia

NASA Astrophysics Data System (ADS)

Ferris, Daron G.

2004-05-01

Cervical cancer is the second most common malignancy in women worldwide. If diagnosed in the premalignant stage, cure is invariably assured. Although the Papanicolaou (Pap) smear has significantly reduced the incidence of cervical cancer where implemented, the test is only moderately sensitive, highly subjective and skilled-labor intensive. Newer optical screening tests (cervicography, direct visual inspection and speculoscopy), including fluorescent and reflective spectroscopy, are fraught with certain weaknesses. Yet, the integration of optical probes for the detection and discrimination of cervical neoplasia with automated image analysis methods may provide an effective screening tool for early detection of cervical cancer, particularly in resource poor nations. Investigative studies are needed to validate the potential for automated classification and recognition algorithms. By applying image analysis techniques for registration, segmentation, pattern recognition, and classification, cervical neoplasia may be reliably discriminated from normal epithelium. The National Cancer Institute (NCI), in cooperation with the National Library of Medicine (NLM), has embarked on a program to begin this and other similar investigative studies.

BMI and breast cancer prognosis benefit: mammography screening reveals differences between normal weight and overweight women.

PubMed

Crispo, Anna; Grimaldi, Maria; D'Aiuto, Massimiliano; Rinaldo, Massimo; Capasso, Immacolata; Amore, Alfonso; D'Aiuto, Giuseppe; Giudice, Aldo; Ciliberto, Gennaro; Montella, Maurizio

2015-02-01

Few studies are available on the potential impact of body weight on breast cancer prognosis in screen-detected patients. Moreover, it is not known whether body mass index (BMI) could have a different prognostic impact in screen-detected versus symptomatic breast cancer patients. To investigate these unsolved issues, we carried out a retrospective study evaluating the effect of BMI on breast cancer prognosis in screen-detected vs symptomatic breast cancer patients. We conducted a follow-up study on 448 women diagnosed with incident, histologically-confirmed breast cancer. Patients were categorized according to their BMI as normal weight, overweight and obese. Disease free survival (DFS), overall survival (OS), and BMI curves were compared according to mode of cancer detection. Among screen-detected patients, higher BMI was associated with a significant lower DFS, whereas no significant difference was observed among symptomatic patients. OS showed similar results. In the multivariate analysis adjusting for age, education, tumor size, nodal status, estrogen receptor (ER), progesterone receptor (PR) and menopausal status, the risk for high level of BMI among screen-detected patients did not reach the statistical significance for either recurrence or survival. Our study highlights the potential impact of high bodyweight in breast cancer prognosis, the findings confirm that obesity plays a role in women breast cancer prognosis independently from diagnosis mode. Copyright © 2014 Elsevier Ltd. All rights reserved.

Alternations of Structure and Functional Activity of Below Ground Microbial Communities at Elevated Atmospheric Carbon Dioxide

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

He, Zhili; Xu, Meiying; Deng, Ye

2010-05-17

The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functionalmore » gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended correspondence analysis (DCA) of all 5001 detected functional gene probes although no significant differences were detected in the overall microbial diversity. A further analysis of 1503 detected functional genes involved in C, N, P, and S cycles showed that a considerable portion (39percent) of them were only detected under either aCO2 (14percent) or eCO2 (25percent), indicating that the functional characteristics of the microbial community were significantly altered by eCO2. Also, for those shared genes (61percent) detected, some significantly (p<0.05) changed their abundance at eCO2. Especially, genes involved in labile C degradation, such as amyA, egl, and ara for starch, cellulose, and hemicelluloses, respectively, C fixation (e.g., rbcL, pcc/acc), N fixation (nifH), and phosphorus utilization (ppx) were significantly increased under eCO2, while those involved in decomposing recalcitrant C, such as glx, lip, and mnp for lignin degradation remained unchanged. This study provides insights into our understanding of belowground microbial communities and their feedbacks to terrestrial ecosystems at eCO2.« less

Luminance level of a monitor: influence on detectability and detection rate of breast cancer in 2D mammography

NASA Astrophysics Data System (ADS)

Bemelmans, Frédéric; Rashidnasab, Alaleh; Chesterman, Frédérique; Kimpe, Tom; Bosmans, Hilde

2016-03-01

Purpose: To evaluate lesion detectability and reading time as a function of luminance level of the monitor. Material and Methods: 3D mass models and microcalcification clusters were simulated into ROIs of for processing mammograms. Randomly selected ROIs were subdivided in three groups according to their background glandularity: high (>30%), medium (15-30%) and low (<15%). 6 non-spiculated masses (9 - 11mm), 6 spiculated masses (5 - 7mm) and 6 microcalcification clusters (2 - 4mm) were scaled in 3D to create a range of sizes. The linear attenuation coefficient (AC) of the masses was adjusted from 100% glandular tissue to 90%, 80%, 70%, to create different contrasts. Six physicists read the full database on Barco's Coronis Uniti monitor for four different luminance levels (300, 800, 1000 and 1200 Cd/m2), using a 4-AFC tool. Percentage correct (PC) and time were computed for all different conditions. A paired t-test was performed to evaluate the effect of luminance on PC and time. A multi-factorial analysis was performed using MANOVA.. Results: Paired t-test indicated a statistically significant difference for the average time per session between 300 and 1200; 800 and 1200; 1000 and 1200 Cd/m2, for all participants combined. There was no effect on PC. MANOVA denoted significantly lower reading times for high glandularity images at 1200 Cd/m2. Both types of masses were significantly faster detected at 1200 Cd/m2, for the contrast study. In the size study, microcalcification clusters and spiculated masses had a significantly higher detection rate at 1200 Cd/m2. Conclusion: These results demonstrate a significant decrease in reading time, while detectability remained constant.

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.

K-Ras mutation detection in liquid biopsy and tumor tissue as prognostic biomarker in patients with pancreatic cancer: a systematic review with meta-analysis.

PubMed

Li, Tao; Zheng, Yuanting; Sun, Hong; Zhuang, Rongyuan; Liu, Jing; Liu, Tianshu; Cai, Weimin

2016-07-01

K-Ras gene mutations have been found in most pancreatic cancers; however, conflicting data on the prognostic value of K-Ras mutations in pancreatic cancer have been published. We conducted a meta-analysis to assess its prognostic significance. Literature searches of PubMed, EMBASE, Cochrane Library, Web of Science and Google Scholar were performed through December 2015 to identify publications exploring the association of K-Ras mutation with overall survival. Forty eligible studies involving 3427 patients with pancreatic cancer were included in the present meta-analysis. Our analysis showed a hazard ratio (HR) of negative association with survival of 1.61 [95 % confidence interval (CI) 1.36-1.90; p < 0.01] in K-Ras mutant pancreatic cancer patients. In subgroup analyses, K-Ras mutations detected in tumor tissues and in liquid biopsies had HRs of 1.37 (95 % CI 1.20-1.57; p < 0.01) and 3.16 (95 % CI 2.1-4.71; p < 0.01), respectively. In addition, the HR was higher when K-Ras mutations were detected in fresh frozen samples (HR = 2.01, 95 % CI 1.28-3.16, p = 0.002) than in formalin-fixed, paraffin-embedded (FFPE) samples (HR = 1.29, 95 % CI 1.12-1.49, p < 0.01). Though K-Ras alterations are more frequent among non-East Asian individuals than East Asian individuals, there were no significant differences in HRs of survival between the two ethnic subgroups. In conclusion, this meta-analysis suggests that K-Ras mutations are associated with a worse overall survival in pancreatic cancer patients, especially when mutations are detected in liquid biopsies or fresh frozen tumor tissue samples.

Prognostic value of circulating tumor cells detected with the CellSearch System in patients with gastric cancer: evidence from a meta-analysis.

PubMed

Yang, Chaogang; Zou, Kun; Yuan, Zewei; Guo, Tangxi; Xiong, Bin

2018-01-01

Circulating tumor cells (CTCs) have been proposed as a marker for predicting the prognosis of cancer. However, the prognostic value of CTCs detected with the CellSearch System in patients with gastric cancer (GC) remains controversial. We performed a meta-analysis of available studies to investigate this topic. Two authors systematically searched the studies independently in PubMed, Science Citation Index, Cochrane Database, Embase, and the references in relevant studies (up to September 2017) using keywords. Our meta-analysis was performed in Stata software, version 12.0 (2011; Stata Corp, College Station, TX, USA), with the risk ratio (RR), hazard ratio (HR), and 95% CI as the effect measures. Subgroup analyses and meta-regression were also conducted. Seven studies (including eight sets of data) containing 579 patients with GC from four countries were included in this meta-analysis. The pooled results showed CTC-positive status detected by the CellSearch System was significantly associated with poor overall survival (HR =2.09, 95% CI [1.71, 2.55], P <0.001, I 2 =31.5%) and progression-free survival (HR =2.11, 95% CI [1.25, 3.57], P =0.005, I 2 =75.6%) of patients with GC, regardless of sampling time. The disease control rate of CTC-positive group was lower than that of CTC-negative group for both baseline and intra-therapy, although no statistical difference existed at both sampling time points (baseline: 69.5% versus 81.8%, RR=0.79, 95% CI [0.54, 1.16], P =0.23, I 2 =68.0%; intra-therapy: 50.0% versus 85.9%, RR=0.24, 95% CI [0.02, 3.13], P =0.28, I 2 =87.4%). Our meta-analysis demonstrated that CTCs detected with the CellSearch System from the peripheral blood had significant prognostic value and might predict poor response to chemotherapy for patients with GC.

Assessing bat detectability and occupancy with multiple automated echolocation detectors

USGS Publications Warehouse

Gorresen, P.M.; Miles, A.C.; Todd, C.M.; Bonaccorso, F.J.; Weller, T.J.

2008-01-01

Occupancy analysis and its ability to account for differential detection probabilities is important for studies in which detecting echolocation calls is used as a measure of bat occurrence and activity. We examined the feasibility of remotely acquiring bat encounter histories to estimate detection probability and occupancy. We used echolocation detectors coupled to digital recorders operating at a series of proximate sites on consecutive nights in 2 trial surveys for the Hawaiian hoary bat (Lasiurus cinereus semotus). Our results confirmed that the technique is readily amenable for use in occupancy analysis. We also conducted a simulation exercise to assess the effects of sampling effort on parameter estimation. The results indicated that the precision and bias of parameter estimation were often more influenced by the number of sites sampled than number of visits. Acceptable accuracy often was not attained until at least 15 sites or 15 visits were used to estimate detection probability and occupancy. The method has significant potential for use in monitoring trends in bat activity and in comparative studies of habitat use. ?? 2008 American Society of Mammalogists.

Detecting deforestation with a spectral change detection approach using multitemporal Landsat data: a case study of Kinabalu Park, Sabah, Malaysia.

PubMed

Phua, Mui-How; Tsuyuki, Satoshi; Furuya, Naoyuki; Lee, Jung Soo

2008-09-01

Tropical deforestation is occurring at an alarming rate, threatening the ecological integrity of protected areas. This makes it vital to regularly assess protected areas to confirm the efficacy of measures that protect that area from clearing. Satellite remote sensing offers a systematic and objective means for detecting and monitoring deforestation. This paper examines a spectral change approach to detect deforestation using pattern decomposition (PD) coefficients from multitemporal Landsat data. Our results show that the PD coefficients for soil and vegetation can be used to detect deforestation using change vector analysis (CVA). CVA analysis demonstrates that deforestation in the Kinabalu area, Sabah, Malaysia has significantly slowed from 1.2% in period 1 (1973 and 1991) to 0.1% in period 2 (1991 and 1996). A comparison of deforestation both inside and outside Kinabalu Park has highlighted the effectiveness of the park in protecting the tropical forest against clearing. However, the park is still facing pressure from the area immediately surrounding the park (the 1 km buffer zone) where the deforestation rate has remained unchanged.

Fast and simultaneous detection of prominent natural antioxidants using analytical microsystems for capillary electrophoresis with a glassy carbon electrode: a new gateway to food environments.

PubMed

Blasco, Antonio Javier; Barrigas, Inés; González, María Cristina; Escarpa, Alberto

2005-12-01

This paper examines for the first time the analytical possibilities of fast and simultaneous detection of prominent natural antioxidants including examples of flavonoids and vitamins using a CE microchip with electrochemical detection (ED). Unpinched injection conditions, zone electrophoretic separation and amperometric detection were carefully assayed and optimised. Analysis involved the zone electrophoretic separation of arbutin, (+)-catechin and ascorbic acid in less than 4 min using a borate buffer (pH 9.0, 50 mM), employing 2 kV as the separation voltage and +1.0 V as the detection potential. In addition, the separation of different 'couples' of natural antioxidants of food significance including (+)-catechin and ascorbic acid, (+)-catechin and rutin, as well as arbutin and phlorizdin is proposed. To demonstrate the potential and future role of CE microsystems, analytical possibilities and a new route in the raw sample analysis are presented. The preliminary results obtained allow the proposal of CE-ED microchips as a real gateway to microanalysis in foods.

Mastery in Goal Scoring, T-Pattern Detection, and Polar Coordinate Analysis of Motor Skills Used by Lionel Messi and Cristiano Ronaldo

PubMed Central

Castañer, Marta; Barreira, Daniel; Camerino, Oleguer; Anguera, M. Teresa; Fernandes, Tiago; Hileno, Raúl

2017-01-01

Research in soccer has traditionally given more weight to players' technical and tactical skills, but few studies have analyzed the motor skills that underpin specific motor actions. The objective of this study was to investigate the style of play of the world's top soccer players, Cristiano Ronaldo and Lionel Messi, and how they use their motor skills in attacking actions that result in a goal. We used and improved the easy-to-use observation instrument (OSMOS-soccer player) with 9 criteria, each one expanded to build 50 categories. Associations between these categories were investigated by T-pattern detection and polar coordinate analysis. T-pattern analysis detects temporal structures of complex behavioral sequences composed of simpler or directly distinguishable events within specified observation periods (time point series). Polar coordinate analysis involves the application of a complex procedure to provide a vector map of interrelated behaviors obtained from prospective and retrospective sequential analysis. The T-patterns showed that for both players the combined criteria were mainly between the different aspects of motor skills, namely the use of lower limbs, contact with the ball using the outside of the foot, locomotion, body orientation with respect to the opponent goal line, and the criteria of technical actions and the right midfield. Polar coordinate analysis detected significant associations between the same criteria included in the T-patterns as well as the criteria of turning the body, numerical equality with no pressure, and relative numerical superiority. PMID:28553245

Mastery in Goal Scoring, T-Pattern Detection, and Polar Coordinate Analysis of Motor Skills Used by Lionel Messi and Cristiano Ronaldo.

PubMed

Castañer, Marta; Barreira, Daniel; Camerino, Oleguer; Anguera, M Teresa; Fernandes, Tiago; Hileno, Raúl

2017-01-01

Research in soccer has traditionally given more weight to players' technical and tactical skills, but few studies have analyzed the motor skills that underpin specific motor actions. The objective of this study was to investigate the style of play of the world's top soccer players, Cristiano Ronaldo and Lionel Messi, and how they use their motor skills in attacking actions that result in a goal. We used and improved the easy-to-use observation instrument (OSMOS-soccer player) with 9 criteria, each one expanded to build 50 categories. Associations between these categories were investigated by T-pattern detection and polar coordinate analysis. T-pattern analysis detects temporal structures of complex behavioral sequences composed of simpler or directly distinguishable events within specified observation periods (time point series). Polar coordinate analysis involves the application of a complex procedure to provide a vector map of interrelated behaviors obtained from prospective and retrospective sequential analysis. The T-patterns showed that for both players the combined criteria were mainly between the different aspects of motor skills, namely the use of lower limbs, contact with the ball using the outside of the foot, locomotion, body orientation with respect to the opponent goal line, and the criteria of technical actions and the right midfield. Polar coordinate analysis detected significant associations between the same criteria included in the T-patterns as well as the criteria of turning the body, numerical equality with no pressure, and relative numerical superiority.

Phylogeography, intraspecific structure and sex-biased dispersal of Dall's porpoise, Phocoenoides dalli, revealed by mitochondrial and microsatellite DNA analyses.

PubMed

Escorza-Treviño, S; Dizon, A E

2000-08-01

Mitochondrial DNA (mtDNA) control-region sequences and microsatellite loci length polymorphisms were used to estimate phylogeographical patterns (historical patterns underlying contemporary distribution), intraspecific population structure and gender-biased dispersal of Phocoenoides dalli dalli across its entire range. One-hundred and thirteen animals from several geographical strata were sequenced over 379 bp of mtDNA, resulting in 58 mtDNA haplotypes. Analysis using F(ST) values (based on haplotype frequencies) and phi(ST) values (based on frequencies and genetic distances between haplotypes) yielded statistically significant separation (bootstrap values P < 0.05) among most of the stocks currently used for management purposes. A minimum spanning network of haplotypes showed two very distinctive clusters, differentially occupied by western and eastern populations, with some common widespread haplotypes. This suggests some degree of phyletic radiation from west to east, superimposed on gene flow. Highly male-biased migration was detected for several population comparisons. Nuclear microsatellite DNA markers (119 individuals and six loci) provided additional support for population subdivision and gender-biased dispersal detected in the mtDNA sequences. Analysis using F(ST) values (based on allelic frequencies) yielded statistically significant separation between some, but not all, populations distinguished by mtDNA analysis. R(ST) values (based on frequencies of and genetic distance between alleles) showed no statistically significant subdivision. Again, highly male-biased dispersal was detected for all population comparisons, suggesting, together with morphological and reproductive data, the existence of sexual selection. Our molecular results argue for nine distinct dalli-type populations that should be treated as separate units for management purposes.

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model.

PubMed

Sun, Xiaoxiao; Dalpiaz, David; Wu, Di; S Liu, Jun; Zhong, Wenxuan; Ma, Ping

2016-08-26

Accurate identification of differentially expressed (DE) genes in time course RNA-Seq data is crucial for understanding the dynamics of transcriptional regulatory network. However, most of the available methods treat gene expressions at different time points as replicates and test the significance of the mean expression difference between treatments or conditions irrespective of time. They thus fail to identify many DE genes with different profiles across time. In this article, we propose a negative binomial mixed-effect model (NBMM) to identify DE genes in time course RNA-Seq data. In the NBMM, mean gene expression is characterized by a fixed effect, and time dependency is described by random effects. The NBMM is very flexible and can be fitted to both unreplicated and replicated time course RNA-Seq data via a penalized likelihood method. By comparing gene expression profiles over time, we further classify the DE genes into two subtypes to enhance the understanding of expression dynamics. A significance test for detecting DE genes is derived using a Kullback-Leibler distance ratio. Additionally, a significance test for gene sets is developed using a gene set score. Simulation analysis shows that the NBMM outperforms currently available methods for detecting DE genes and gene sets. Moreover, our real data analysis of fruit fly developmental time course RNA-Seq data demonstrates the NBMM identifies biologically relevant genes which are well justified by gene ontology analysis. The proposed method is powerful and efficient to detect biologically relevant DE genes and gene sets in time course RNA-Seq data.

Is there an association between flow diverter fish mouthing and delayed-type hypersensitivity to metals?-a case-control study.

PubMed

Kocer, Naci; Mondel, Prabath Kumar; Yamac, Elif; Kavak, Ayse; Kizilkilic, Osman; Islak, Civan

2017-11-01

Flow diverters are increasingly used in the treatment of complex and giant intracranial aneurysms. However, they are associated with complications like late aneurysmal rupture. Additionally, flow diverters show focal structural decrease in luminal diameter without any intimal hyperplasia. This resembles a "fish mouth" when viewed en face. In this pilot study, we tested the hypothesis of a possible association between flow diverter fish-mouthing and delayed-type hypersensitivity to its metal constituents. We retrospectively reviewed patient records from our center between May 2010 and November 2015. A total of nine patients had flow diverter fish mouthing. A control group of 25 patients was selected. All study participants underwent prospective patch test to detect hypersensitivity to flow diverter metal constituents. Analysis was performed using logistic regression analysis and Wilcoxon sign rank sum test. Univariate and multivariate analyses were performed to test variables to predict flow diverter fish mouthing. The association between flow diverter fish mouthing and positive patch test was not statistically significant. In multivariate analysis, history of allergy and maximum aneurysm size category was associated with flow diverter fish mouthing. This was further confirmed on Wilcoxon sign rank sum test. The study showed statistically significant association between flow diverter fish mouthing and history of contact allergy and a small aneurysmal size. Further large-scale studies are needed to detect a statistically significant association between flow diverter fish mouthing and patch test. We recommend early and more frequent follow-up imaging in patients with contact allergy to detect flow diverter fish mouthing and its subsequent evolution.

Identification and Assessment of Cardiac Amyloidosis by Myocardial Strain Analysis of Cardiac Magnetic Resonance Imaging.

PubMed

Oda, Seitaro; Utsunomiya, Daisuke; Nakaura, Takeshi; Yuki, Hideaki; Kidoh, Masafumi; Morita, Kosuke; Takashio, Seiji; Yamamuro, Megumi; Izumiya, Yasuhiro; Hirakawa, Kyoko; Ishida, Toshifumi; Tsujita, Kenichi; Ueda, Mitsuharu; Yamashita, Taro; Ando, Yukio; Hata, Hiroyuki; Yamashita, Yasuyuki

2017-06-23

We explored the usefulness of myocardial strain analysis on cardiac magnetic resonance imaging (CMR) scans for the identification of cardiac amyloidosis.Methods and Results:The 61 patients with systemic amyloidosis underwent 3.0-T CMR, including CMR tagging and late-gadolinium enhanced (LGE) imaging. The circumferential strain (CS) of LGE-positive and LGE-negative patients was measured on midventricular short-axis images and compared. Logistic regression modeling of CMR parameters was performed to detect patients with LGE-positive cardiac amyloidosis. Of the 61 patients with systemic amyloidosis 48 were LGE-positive and 13 were LGE-negative. The peak CS was significantly lower in the LGE-positive than in the LGE-negative patients (-9.5±2.3 vs. -13.3±1.4%, P<0.01). The variability in the peak CS time was significantly greater in the LGE-positive than in the LGE-negative patients (46.1±24.5 vs. 21.2±20.1 ms, P<0.01). The peak CS significantly correlated with clinical biomarkers. The sensitivity, specificity, and accuracy of the diagnostic model using CS parameters for the identification of LGE-positive amyloidosis were 93.8%, 76.9%, and 90.2%, respectively. Myocardial strain analysis by CMR helped detect LGE-positive amyloidosis without the need for contrast medium. The peak CS and variability in the peak CS time may correlate with the severity of cardiac amyloid deposition and may be more sensitive than LGE imaging for the detection of early cardiac disease in patients with amyloidosis.

Laboratory Detection and Analysis of Organic Compounds in Rocks Using HPLC and XRD Methods

NASA Technical Reports Server (NTRS)

Dragoi, D.; Kanik, I.; Bar-Cohen, Y.; Sherrit, S.; Tsapin, A.; Kulleck, J.

2004-01-01

In this work we describe an analytical method for determining the presence of organic compounds in rocks, limestone, and other composite materials. Our preliminary laboratory experiments on different rocks/limestone show that the organic component in mineralogical matrices is a minor phase on order of hundreds of ppm and can be better detected using high precision liquid chromatography (HPLC). The matrix, which is the major phase, plays an important role in embedding and protecting the organic molecules from the harsh Martian environment. Some rocks bear significant amounts of amino acids therefore, it is possible to identify these phases using powder x-ray diffraction (XRD) by crystallizing the organic. The method of detection/analysis of organics, in particular amino acids, that have been associated with life will be shown in the next section.

A retrospective analysis of preoperative staging modalities for oral squamous cell carcinoma.

PubMed

Kähling, Ch; Langguth, T; Roller, F; Kroll, T; Krombach, G; Knitschke, M; Streckbein, Ph; Howaldt, H P; Wilbrand, J-F

2016-12-01

An accurate preoperative assessment of cervical lymph node status is a prerequisite for individually tailored cancer therapies in patients with oral squamous cell carcinoma. The detection of malignant spread and its treatment crucially influence the prognosis. The aim of the present study was to analyze the different staging modalities used among patients with a diagnosis of primary oral squamous cell carcinoma between 2008 and 2015. An analysis of preoperative staging findings, collected by clinical palpation, ultrasound, and computed tomography (CT), was performed. The results obtained were compared with the results of the final histopathological findings of the neck dissection specimens. A statistical analysis using McNemar's test was performed. The sensitivity of CT for the detection of malignant cervical tumor spread was 74.5%. The ultrasound obtained a sensitivity of 60.8%. Both CT and ultrasound demonstrated significantly enhanced sensitivity compared to the clinical palpation with a sensitivity of 37.1%. No significant difference was observed between CT and ultrasound. A combination of different staging modalities increased the sensitivity significantly compared with ultrasound staging alone. No significant difference in sensitivity was found between the combined use of different staging modalities and CT staging alone. The highest sensitivity, of 80.0%, was obtained by a combination of all three staging modalities: clinical palpation, ultrasound and CT. The present study indicates that CT has an essential role in the preoperative staging of patients with oral squamous cell carcinoma. Its use not only significantly increases the sensitivity of cervical lymph node metastasis detection but also offers a preoperative assessment of local tumor spread and resection borders. An additional non-invasive cervical lymph node examination increases the sensitivity of the tumor staging process and reduces the risk of occult metastasis. Copyright © 2016 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Analysis of Eddy Current Capabilities for the Detection of Outer Diameter Stress Corrosion Cracking in Small Bore Metallic Structures

NASA Technical Reports Server (NTRS)

Wincheski, Buzz; Williams, Phillip; Simpson, John

2007-01-01

The use of eddy current techniques for the detection of outer diameter damage in tubing and many complex aerospace structures often requires the use of an inner diameter probe due to a lack of access to the outside of the part. In small bore structures the probe size and orientation are constrained by the inner diameter of the part, complicating the optimization of the inspection technique. Detection of flaws through a significant remaining wall thickness becomes limited not only by the standard depth of penetration, but also geometrical aspects of the probe. Recently, an orthogonal eddy current probe was developed for detection of such flaws in Space Shuttle Primary Reaction Control System (PRCS) Thrusters. In this case, the detection of deeply buried stress corrosion cracking by an inner diameter eddy current probe was sought. Probe optimization was performed based upon the limiting spatial dimensions, flaw orientation, and required detection sensitivity. Analysis of the probe/flaw interaction was performed through the use of finite and boundary element modeling techniques. Experimental data for the flaw detection capabilities, including a probability of detection study, will be presented along with the simulation data. The results of this work have led to the successful deployment of an inspection system for the detection of stress corrosion cracking in Space Shuttle Primary Reaction Control System (PRCS) Thrusters.

Statistical significance of task related deep brain EEG dynamic changes in the time-frequency domain.

PubMed

Chládek, J; Brázdil, M; Halámek, J; Plešinger, F; Jurák, P

2013-01-01

We present an off-line analysis procedure for exploring brain activity recorded from intra-cerebral electroencephalographic data (SEEG). The objective is to determine the statistical differences between different types of stimulations in the time-frequency domain. The procedure is based on computing relative signal power change and subsequent statistical analysis. An example of characteristic statistically significant event-related de/synchronization (ERD/ERS) detected across different frequency bands following different oddball stimuli is presented. The method is used for off-line functional classification of different brain areas.

Biosensing Based on Nanoparticles for Food Allergens Detection

PubMed Central

Gómez-Arribas, Lidia Nazaret; Hurtado-Sánchez, María del Carmen

2018-01-01

Food allergy is one of the major health threats for sensitized individuals all over the world and, over the years, the food industry has made significant efforts and investments to offer safe foods for allergic consumers. The analysis of the concentration of food allergen residues in processing equipment, in raw materials or in the final product, provides analytical information that can be used for risk assessment as well as to ensure that food-allergic consumers get accurate and useful information to make their food choices and purchasing decisions. The development of biosensors based on nanomaterials for applications in food analysis is a challenging area of growing interest in the last years. Research in this field requires the combined efforts of experts in very different areas including food chemistry, biotechnology or materials science. However, the outcome of such collaboration can be of significant impact on the food industry as well as for consumer’s safety. These nanobiosensing devices allow the rapid, selective, sensitive, cost-effective and, in some cases, in-field, online and real-time detection of a wide range of compounds, even in complex matrices. Moreover, they can also enable the design of novel allergen detection strategies. Herein we review the main advances in the use of nanoparticles for the development of biosensors and bioassays for allergen detection, in food samples, over the past few years. Research in this area is still in its infancy in comparison, for instance, to the application of nanobiosensors for clinical analysis. However, it will be of interest for the development of new technologies that reduce the gap between laboratory research and industrial applications. PMID:29617319

Deep UV laser-induced fluorescence detection of unlabeled drugs and proteins in microchip electrophoresis.

PubMed

Schulze, Philipp; Ludwig, Martin; Kohler, Frank; Belder, Detlev

2005-03-01

Deep UV fluorescence detection at 266-nm excitation wavelength has been realized for sensitive detection in microchip electrophoresis. For this purpose, an epifluorescence setup was developed enabling the coupling of a deep UV laser into a commercial fluorescence microscope. Deep UV laser excitation utilizing a frequency quadrupled pulsed laser operating at 266 nm shows an impressive performance for native fluorescence detection of various compounds in fused-silica microfluidic devices. Aromatic low molecular weight compounds such as serotonin, propranolol, a diol, and tryptophan could be detected at low-micromolar concentrations. Deep UV fluorescence detection was also successfully employed for the detection of unlabeled basic proteins. For this purpose, fused-silica chips dynamically coated with hydroxypropylmethyl cellulose were employed to suppress analyte adsorption. Utilizing fused-silica chips permanently coated with poly(vinyl alcohol), it was also possible to separate and detect egg white chicken proteins. These data show that deep UV fluorescence detection significantly widens the application range of fluorescence detection in chip-based analysis techniques.

Survey of Legionella spp. in Mud Spring Recreation Area

NASA Astrophysics Data System (ADS)

Hsu, B.-M.; Ma, P.-H.; Su, I.-Z.; Chen, N.-S.

2009-04-01

Legionella genera are parasites of FLA, and intracellular bacterial replication within the FLA plays a major role in the transmission of disease. At least 13 FLA species—including Acanthamoeba spp., Naegleria spp., and Hartmannella spp.—support intracellular bacterial replication. In the study, Legionellae were detected with microbial culture or by direct DNA extraction and analysis from concentrated water samples or cultured free-living amoebae, combined with molecular methods that allow the taxonomic identification of these pathogens. The water samples were taken from a mud spring recreation area located in a mud-rock-formation area in southern Taiwan. Legionella were detected in 15 of the 34 samples (44.1%). Four of the 34 samples analyzed by Legionella culture were positive for Legionella, five of 34 were positive for Legionella when analyzed by direct DNA extraction and analysis, and 11 of 34 were positive for amoebae-resistant Legionella when analyzed by FLA culture. Ten samples were shown to be positive for Legionella by one analysis method and five samples were shown to be positive by two analysis methods. However, Legionella was detected in no sample by all three analysis methods. This suggests that the three analysis methods should be used together to detect Legionella in aquatic environments. In this study, L. pneumophila serotype 6 coexisted with A. polyphaga, and two uncultured Legionella spp. coexisted with either H. vermiformis or N. australiensis. Of the unnamed Legionella genotypes detected in six FLA culture samples, three were closely related to L. waltersii and the other three were closely related to L. pneumophila serotype 6. Legionella pneumophila serotype 6, L. drancourtii, and L. waltersii are noted endosymbionts of FLA and are categorized as pathogenic bacteria. This is significant for human health because these Legionella exist within FLA and thus come into contact with typically immunocompromised people.

Mobile TNA system to detect explosives and drugs concealed in cars and trucks

NASA Astrophysics Data System (ADS)

Bendahan, Joseph; Gozani, Tsahi

1998-12-01

The drug problem in the U.S. is serious and efforts to fight it are constrained by the lack of adequate means to curb the inflow of smuggled narcotics into the country through cargo containers. Also, events such as the disastrous explosion in Oklahoma City, the IRA bombing in London, and the bombing of the U.S. military residence in Dharan make the development of new tools for the detection of explosives and drugs in vehicles imperative. Thermal neutron analysis (TNA) technology, developed for the detection of explosives in suitcases, and detection of landmines and unexploded ordnance is presently being applied to the nonintrusive detection of significant amounts of explosives and drugs concealed in cars, trucks and large cargo containers. TNA technology is based on the analysis of characteristic gamma rays emitted following thermal neutron capture. A TNA system can be used in a variety of operational scenarios, such as inspection before an unloaded cargo container from a spit is moved to temporary storage, inspection of trucks unloaded from a ferry, or inspection of vehicles parked close to Federal building or military bases. This paper will discuss the detection process and operational scenarios, and will present results from recent simulations and measurements.

Optic disc detection and boundary extraction in retinal images.

PubMed

Basit, A; Fraz, Muhammad Moazam

2015-04-10

With the development of digital image processing, analysis and modeling techniques, automatic retinal image analysis is emerging as an important screening tool for early detection of ophthalmologic disorders such as diabetic retinopathy and glaucoma. In this paper, a robust method for optic disc detection and extraction of the optic disc boundary is proposed to help in the development of computer-assisted diagnosis and treatment of such ophthalmic disease. The proposed method is based on morphological operations, smoothing filters, and the marker controlled watershed transform. Internal and external markers are used to first modify the gradient magnitude image and then the watershed transformation is applied on this modified gradient magnitude image for boundary extraction. This method has shown significant improvement over existing methods in terms of detection and boundary extraction of the optic disc. The proposed method has optic disc detection success rate of 100%, 100%, 100% and 98.9% for the DRIVE, Shifa, CHASE_DB1, and DIARETDB1 databases, respectively. The optic disc boundary detection achieved an average spatial overlap of 61.88%, 70.96%, 45.61%, and 54.69% for these databases, respectively, which are higher than currents methods.

Automatic thermographic image defect detection of composites

NASA Astrophysics Data System (ADS)

Luo, Bin; Liebenberg, Bjorn; Raymont, Jeff; Santospirito, SP

2011-05-01

Detecting defects, and especially reliably measuring defect sizes, are critical objectives in automatic NDT defect detection applications. In this work, the Sentence software is proposed for the analysis of pulsed thermography and near IR images of composite materials. Furthermore, the Sentence software delivers an end-to-end, user friendly platform for engineers to perform complete manual inspections, as well as tools that allow senior engineers to develop inspection templates and profiles, reducing the requisite thermographic skill level of the operating engineer. Finally, the Sentence software can also offer complete independence of operator decisions by the fully automated "Beep on Defect" detection functionality. The end-to-end automatic inspection system includes sub-systems for defining a panel profile, generating an inspection plan, controlling a robot-arm and capturing thermographic images to detect defects. A statistical model has been built to analyze the entire image, evaluate grey-scale ranges, import sentencing criteria and automatically detect impact damage defects. A full width half maximum algorithm has been used to quantify the flaw sizes. The identified defects are imported into the sentencing engine which then sentences (automatically compares analysis results against acceptance criteria) the inspection by comparing the most significant defect or group of defects against the inspection standards.

Home Runs and Humbugs: Comment on Bond and DePaulo (2008)

ERIC Educational Resources Information Center

O'Sullivan, Maureen

2008-01-01

In 2006, C. F. Bond Jr. and B. M. DePaulo provided a meta-analysis of means and concluded that average lie detection accuracy was significantly greater than chance for most people. Now, they have presented an analysis of standard deviations (C. F. Bond Jr. & B. M. DePaulo, 2008), claiming that there are no reliable individual differences in lie…

The use of ultra-high pressure liquid chromatography with tandem mass spectrometric detection of analysis of agrochemical residues and mycotoxines in food - challenges and applications

USDA-ARS?s Scientific Manuscript database

In the field of food contaminant analysis, the most significant development of recent years has been the integration of ultra-high pressure liquid chromatography (UHPLC), coupled to tandem quadrupole mass spectrometry (MS/MS), into analytical applications. In this review, we describe the emergence o...

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

PubMed Central

2010-01-01

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm. PMID:21637426

Determination of N-glycans by high performance liquid chromatography using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate as the glycosylamine labeling reagent.

PubMed

Wu, Yike; Sha, Qiuyue; Du, Juan; Wang, Chang; Zhang, Liang; Liu, Bi-Feng; Lin, Yawei; Liu, Xin

2018-02-02

Robust, efficient identification and accurate quantification of N-glycans are of great significance in N-glycomics analysis. Here, a simple and rapid derivatization method, based on the combination of microwave-assisted deglycosylation and 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC) labeling, was developed for the analysis of N-glycan by high performance liquid chromatography with fluorescence detection (HPLC-FLD). After optimizing various parameters affecting deglycosylation and derivatization by RNase B, the time for N-glycan labeling was shortened to 50 min with ∼10-fold enhancement in detection sensitivity comparing to conventional 2-aminobenzoic acid (2-AA) labeling method. Additionally, the method showed good linearity (correlation coefficients > 0.991) and reproducibility (RSD < 8.7%). These advantages of the proposed method were further validated by the analysis of complex samples, including fetuin and human serum. Investigation of serum N-glycome for preliminary diagnosis of human lung cancer was conducted, where significant changes of several N-glycans corresponding to core-fucosylated, mono- and disialylated glycans have been evidenced by a series of statistical analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Hyperspectral image analysis for plant stress detection

USDA-ARS?s Scientific Manuscript database

Abiotic and disease-induced stress significantly reduces plant productivity. Automated on-the-go mapping of plant stress allows timely intervention and mitigating of the problem before critical thresholds are exceeded, thereby, maximizing productivity. A hyperspectral camera analyzed the spectral ...

Quantitative Ultrasound Assessment of Duchenne Muscular Dystrophy Using Edge Detection Analysis.

PubMed

Koppaka, Sisir; Shklyar, Irina; Rutkove, Seward B; Darras, Basil T; Anthony, Brian W; Zaidman, Craig M; Wu, Jim S

2016-09-01

The purpose of this study was to investigate the ability of quantitative ultrasound (US) using edge detection analysis to assess patients with Duchenne muscular dystrophy (DMD). After Institutional Review Board approval, US examinations with fixed technical parameters were performed unilaterally in 6 muscles (biceps, deltoid, wrist flexors, quadriceps, medial gastrocnemius, and tibialis anterior) in 19 boys with DMD and 21 age-matched control participants. The muscles of interest were outlined by a tracing tool, and the upper third of the muscle was used for analysis. Edge detection values for each muscle were quantified by the Canny edge detection algorithm and then normalized to the number of edge pixels in the muscle region. The edge detection values were extracted at multiple sensitivity thresholds (0.01-0.99) to determine the optimal threshold for distinguishing DMD from normal. Area under the receiver operating curve values were generated for each muscle and averaged across the 6 muscles. The average age in the DMD group was 8.8 years (range, 3.0-14.3 years), and the average age in the control group was 8.7 years (range, 3.4-13.5 years). For edge detection, a Canny threshold of 0.05 provided the best discrimination between DMD and normal (area under the curve, 0.96; 95% confidence interval, 0.84-1.00). According to a Mann-Whitney test, edge detection values were significantly different between DMD and controls (P < .0001). Quantitative US imaging using edge detection can distinguish patients with DMD from healthy controls at low Canny thresholds, at which discrimination of small structures is best. Edge detection by itself or in combination with other tests can potentially serve as a useful biomarker of disease progression and effectiveness of therapy in muscle disorders.

Evaluation of clinical image processing algorithms used in digital mammography.

PubMed

Zanca, Federica; Jacobs, Jurgen; Van Ongeval, Chantal; Claus, Filip; Celis, Valerie; Geniets, Catherine; Provost, Veerle; Pauwels, Herman; Marchal, Guy; Bosmans, Hilde

2009-03-01

Screening is the only proven approach to reduce the mortality of breast cancer, but significant numbers of breast cancers remain undetected even when all quality assurance guidelines are implemented. With the increasing adoption of digital mammography systems, image processing may be a key factor in the imaging chain. Although to our knowledge statistically significant effects of manufacturer-recommended image processings have not been previously demonstrated, the subjective experience of our radiologists, that the apparent image quality can vary considerably between different algorithms, motivated this study. This article addresses the impact of five such algorithms on the detection of clusters of microcalcifications. A database of unprocessed (raw) images of 200 normal digital mammograms, acquired with the Siemens Novation DR, was collected retrospectively. Realistic simulated microcalcification clusters were inserted in half of the unprocessed images. All unprocessed images were subsequently processed with five manufacturer-recommended image processing algorithms (Agfa Musica 1, IMS Raffaello Mammo 1.2, Sectra Mamea AB Sigmoid, Siemens OPVIEW v2, and Siemens OPVIEW v1). Four breast imaging radiologists were asked to locate and score the clusters in each image on a five point rating scale. The free-response data were analyzed by the jackknife free-response receiver operating characteristic (JAFROC) method and, for comparison, also with the receiver operating characteristic (ROC) method. JAFROC analysis revealed highly significant differences between the image processings (F = 8.51, p < 0.0001), suggesting that image processing strongly impacts the detectability of clusters. Siemens OPVIEW2 and Siemens OPVIEW1 yielded the highest and lowest performances, respectively. ROC analysis of the data also revealed significant differences between the processing but at lower significance (F = 3.47, p = 0.0305) than JAFROC. Both statistical analysis methods revealed that the same six pairs of modalities were significantly different, but the JAFROC confidence intervals were about 32% smaller than ROC confidence intervals. This study shows that image processing has a significant impact on the detection of microcalcifications in digital mammograms. Objective measurements, such as described here, should be used by the manufacturers to select the optimal image processing algorithm.

Hepatocellular Carcinoma Screening Associated with Early Tumor Detection and Improved Survival Among Patients with Cirrhosis in the US.

PubMed

Singal, Amit G; Mittal, Sahil; Yerokun, Olutola A; Ahn, Chul; Marrero, Jorge A; Yopp, Adam C; Parikh, Neehar D; Scaglione, Steve J

2017-09-01

Professional societies recommend hepatocellular carcinoma screening in patients with cirrhosis, but high-quality data evaluating its effectiveness to improve early tumor detection and survival in "real world" clinical practice are needed. We aim to characterize the association between hepatocellular carcinoma screening and early tumor detection, curative treatment, and overall survival among patients with cirrhosis. We performed a retrospective cohort study of patients diagnosed with hepatocellular carcinoma between June 2012 and May 2013 at 4 health systems in the US. Patients were categorized in the screening group if hepatocellular carcinoma was detected by imaging performed for screening purposes. Generalized linear models and multivariate Cox regression with frailty adjustment were used to compare early detection, curative treatment, and survival between screen-detected and non-screen-detected patients. Among 374 hepatocellular carcinoma patients, 42% (n = 157) were detected by screening. Screen-detected patients had a significantly higher proportion of early tumors (Barcelona Clinic Liver Cancer stage A 63.1% vs 36.4%, P <.001) and were more likely to undergo curative treatment (31% vs 13%, P = .02). Hepatocellular carcinoma screening was significantly associated with improved survival in multivariate analysis (hazards ratio 0.41; 95% confidence interval, 0.26-0.65) after adjusting for patient demographics, Child-Pugh class, and performance status. Median survival of screen-detected patients was 14.6 months, compared with 6.0 months for non-screen-detected patients, with the difference remaining significant after adjusting for lead-time bias (hazards ratio 0.59, 95% confidence interval, 0.37-0.93). Hepatocellular carcinoma screening is associated with increased early tumor detection and improved survival; however, a minority of hepatocellular carcinoma patients are detected by screening. Interventions to increase screening use in patients with cirrhosis may help curb hepatocellular carcinoma mortality rates. Copyright © 2017 Elsevier Inc. All rights reserved.

A novel multiplex PCR assay for simultaneous detection of nine clinically significant bacterial pathogens associated with bovine mastitis.

PubMed

Ashraf, Aqeela; Imran, Muhammad; Yaqub, Tahir; Tayyab, Muhammad; Shehzad, Wasim; Thomson, Peter C

2017-06-01

For rapid and simultaneous detection of nine bovine mastitic pathogens, a sensitive and specific multiplex PCR assay was developed. The assay was standardized using reference strains and validated on mastitic milk cultures which were identified to species level based on 16S rRNA sequencing. Multiplex PCR assay also efficiently detected the target bacterial strains directly from milk. The detection limit of the assay was up to 50 pg for DNA isolated from pure cultures and 10 4  CFU/ml for spiked milk samples. As estimated by latent class analysis, the assay was sensitive up to 88% and specific up to 98% for targeted mastitic pathogens, compared with the bacterial culture method and the 16S rRNA sequence analysis. This novel molecular assay could be useful for monitoring and maintaining the bovine udder health, ensuring the bacteriological safety of milk, and conducting epidemiological studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the SAR derived alert in the detection of oil spills according to the analysis of the EGEMP.

PubMed

Ferraro, Guido; Baschek, Björn; de Montpellier, Geraldine; Njoten, Ove; Perkovic, Marko; Vespe, Michele

2010-01-01

Satellite services that deliver information about possible oil spills at sea currently use different labels of "confidence" to describe the detections based on radar image processing. A common approach is to use a classification differentiating between low, medium and high levels of confidence. There is an ongoing discussion on the suitability of the existing classification systems of possible oil spills detected by radar satellite images with regard to the relevant significance and correspondence to user requirements. This paper contains a basic analysis of user requirements, current technical possibilities of satellite services as well as proposals for a redesign of the classification system as an evolution towards a more structured alert system. This research work offers a first review of implemented methodologies for the categorisation of detected oil spills, together with the proposal of explorative ideas evaluated by the European Group of Experts on satellite Monitoring of sea-based oil Pollution (EGEMP). Copyright 2009 Elsevier Ltd. All rights reserved.

Performance characteristics and relationship of PSA value/kinetics on carbon-11 acetate PET/CT imaging in biochemical relapse of prostate cancer.

PubMed

Almeida, Fabio D; Yen, Chi-Kwan; Scholz, Mark C; Lam, Richard Y; Turner, Jeffrey; Bans, Larry L; Lipson, Robert

2017-01-01

An elevated serum prostate-specific antigen (PSA) level alone cannot distinguish between local-regional recurrences and distant metastases after treatment with curative intent. With available salvage treatments, it has become important to localize the site of recurrence. 11 C-Acetate PET/CT was performed in patients with rising PSA, with statistical analysis of detection rates, sites/location of detection, PSA kinetics and comparison with other tracers (FDG and Choline). Correlation to biopsy, subsequent imaging and PSA response to focal treatment was also performed. 88% (637) of 721 11 C-Acetate PET/CT scans performed were positive. There was a statistically significant difference in PSA values between the positive and negative scans (P < 0.001 for mean difference) with the percentage of positive scans and PSA having a positive correlation. A PSA of 1.09 ng/mL was found to be an optimal cutoff. PSAdT was significantly correlated with a positive scan only when the PSA was < 1.0 ng/mL. For this subgroup, a PSAdT of < 3.8 months appeared significant (P < 0.05) as an optimal cutoff point. 11 C-Acetate PET/CT demonstrates a high detection rate for the site of recurrence/metastasis in biochemical relapsed prostate cancer (88% overall detection rate, PPV 90.8%). This analysis suggests an optimal PSA threshold of > 1.09 ng/mL or a PSAdT of < 3.8 months when the PSA is below 1.0 ng/mL as independent predictors of positive findings.

Genome-wide gene–gene interaction analysis for next-generation sequencing

PubMed Central

Zhao, Jinying; Zhu, Yun; Xiong, Momiao

2016-01-01

The critical barrier in interaction analysis for next-generation sequencing (NGS) data is that the traditional pairwise interaction analysis that is suitable for common variants is difficult to apply to rare variants because of their prohibitive computational time, large number of tests and low power. The great challenges for successful detection of interactions with NGS data are (1) the demands in the paradigm of changes in interaction analysis; (2) severe multiple testing; and (3) heavy computations. To meet these challenges, we shift the paradigm of interaction analysis between two SNPs to interaction analysis between two genomic regions. In other words, we take a gene as a unit of analysis and use functional data analysis techniques as dimensional reduction tools to develop a novel statistic to collectively test interaction between all possible pairs of SNPs within two genome regions. By intensive simulations, we demonstrate that the functional logistic regression for interaction analysis has the correct type 1 error rates and higher power to detect interaction than the currently used methods. The proposed method was applied to a coronary artery disease dataset from the Wellcome Trust Case Control Consortium (WTCCC) study and the Framingham Heart Study (FHS) dataset, and the early-onset myocardial infarction (EOMI) exome sequence datasets with European origin from the NHLBI's Exome Sequencing Project. We discovered that 6 of 27 pairs of significantly interacted genes in the FHS were replicated in the independent WTCCC study and 24 pairs of significantly interacted genes after applying Bonferroni correction in the EOMI study. PMID:26173972

Dispersal of potato cyst nematodes measured using historical and spatial statistical analyses.

PubMed

Banks, N C; Hodda, M; Singh, S K; Matveeva, E M

2012-06-01

Rates and modes of dispersal of potato cyst nematodes (PCNs) were investigated. Analysis of records from eight countries suggested that PCNs spread a mean distance of 5.3 km/year radially from the site of first detection, and spread 212 km over ≈40 years before detection. Data from four countries with more detailed histories of invasion were analyzed further, using distance from first detection, distance from previous detection, distance from nearest detection, straight line distance, and road distance. Linear distance from first detection was significantly related to the time since the first detection. Estimated rate of spread was 5.7 km/year, and did not differ statistically between countries. Time between the first detection and estimated introduction date varied between 0 and 20 years, and differed among countries. Road distances from nearest and first detection were statistically significantly related to time, and gave slightly higher estimates for rate of spread of 6.0 and 7.9 km/year, respectively. These results indicate that the original site of introduction of PCNs may act as a source for subsequent spread and that this may occur at a relatively constant rate over time regardless of whether this distance is measured by road or by a straight line. The implications of this constant radial rate of dispersal for biosecurity and pest management are discussed, along with the effects of control strategies.

An information-theoretic approach to the gravitational-wave burst detection problem

NASA Astrophysics Data System (ADS)

Katsavounidis, E.; Lynch, R.; Vitale, S.; Essick, R.; Robinet, F.

2016-03-01

The advanced era of gravitational-wave astronomy, with data collected in part by the LIGO gravitational-wave interferometers, has begun as of fall 2015. One potential type of detectable gravitational waves is short-duration gravitational-wave bursts, whose waveforms can be difficult to predict. We present the framework for a new detection algorithm - called oLIB - that can be used in relatively low-latency to turn calibrated strain data into a detection significance statement. This pipeline consists of 1) a sine-Gaussian matched-filter trigger generator based on the Q-transform - known as Omicron -, 2) incoherent down-selection of these triggers to the most signal-like set, and 3) a fully coherent analysis of this signal-like set using the Markov chain Monte Carlo (MCMC) Bayesian evidence calculator LALInferenceBurst (LIB). We optimally extract this information by using a likelihood-ratio test (LRT) to map these search statistics into a significance statement. Using representative archival LIGO data, we show that the algorithm can detect gravitational-wave burst events of realistic strength in realistic instrumental noise with good detection efficiencies across different burst waveform morphologies. With support from the National Science Foundation under Grant PHY-0757058.

Video-processing-based system for automated pedestrian data collection and analysis when crossing the street

NASA Astrophysics Data System (ADS)

Mansouri, Nabila; Watelain, Eric; Ben Jemaa, Yousra; Motamed, Cina

2018-03-01

Computer-vision techniques for pedestrian detection and tracking have progressed considerably and become widely used in several applications. However, a quick glance at the literature shows a minimal use of these techniques in pedestrian behavior and safety analysis, which might be due to the technical complexities facing the processing of pedestrian videos. To extract pedestrian trajectories from a video automatically, all road users must be detected and tracked during sequences, which is a challenging task, especially in a congested open-outdoor urban space. A multipedestrian tracker based on an interframe-detection-association process was proposed and evaluated. The tracker results are used to implement an automatic tool for pedestrians data collection when crossing the street based on video processing. The variations in the instantaneous speed allowed the detection of the street crossing phases (approach, waiting, and crossing). These were addressed for the first time in the pedestrian road security analysis to illustrate the causal relationship between pedestrian behaviors in the different phases. A comparison with a manual data collection method, by computing the root mean square error and the Pearson correlation coefficient, confirmed that the procedures proposed have significant potential to automate the data collection process.

Distribution of major herbicides in ground water of the United States

USGS Publications Warehouse

Barbash, Jack E.; Thelin, Gail P.; Kolpin, Dana W.; Gilliom, Robert J.

1999-01-01

Frequencies of detection at or above 0.01 microgram per liter in shallow ground water beneath agricultural areas during the NAWQA study were significantly correlated with agricultural use in those areas for atrazine, cyanazine, alachlor, and metolachlor (P<0.05; Spearman rank correlations), but not for simazine (P>0.05). In urban areas, overall frequencies of detection of these five herbicides in shallow ground water were positively correlated with their total nonagricultural use nationwide (P=0.026; simple linear correlation). Multivariate statistical analysis indicated that frequencies of detection in shallow ground water beneath agricultural areas were positively correlated with half-lives for transformation in aerobic soil and agricultural use of the compounds (P≤0.0001 for both parameters). Although frequencies of detection were not significantly correlated with their subsurface mobility (Koc; P=0.19) or the median well depths of the sampled networks (P=0.72), the range of Koc values among the five herbicides and the range of well depths were limited.

Prostate cancer localization with endorectal MR imaging and MR spectroscopic imaging: effect of clinical data on reader accuracy.

PubMed

Dhingsa, Rajpal; Qayyum, Aliya; Coakley, Fergus V; Lu, Ying; Jones, Kirk D; Swanson, Mark G; Carroll, Peter R; Hricak, Hedvig; Kurhanewicz, John

2004-01-01

To determine the effect of digital rectal examination findings, sextant biopsy results, and prostate-specific antigen (PSA) levels on reader accuracy in the localization of prostate cancer with endorectal magnetic resonance (MR) imaging and MR spectroscopic imaging. This was a retrospective study of 37 patients (mean age, 57 years) with biopsy-proved prostate cancer. Transverse T1-weighted, transverse high-spatial-resolution, and coronal T2-weighted MR images and MR spectroscopic images were obtained. Two independent readers, unaware of clinical data, recorded the size and location of suspicious peripheral zone tumor nodules on a standardized diagram of the prostate. Readers also recorded their degree of diagnostic confidence for each nodule on a five-point scale. Both readers repeated this interpretation with knowledge of rectal examination findings, sextant biopsy results, and PSA level. Step-section histopathologic findings were the reference standard. Logistic regression analysis with generalized estimating equations was used to correlate tumor detection with clinical data, and alternative free-response receiver operating characteristic (AFROC) curve analysis was used to examine the overall effect of clinical data on all positive results. Fifty-one peripheral zone tumor nodules were identified at histopathologic evaluation. Logistic regression analysis showed awareness of clinical data significantly improved tumor detection rate (P <.02) from 15 to 19 nodules for reader 1 and from 13 to 19 nodules for reader 2 (27%-37% overall) by using both size and location criteria. AFROC analysis showed no significant change in overall reader performance because there was an associated increase in the number of false-positive findings with awareness of clinical data, from 11 to 21 for reader 1 and from 16 to 25 for reader 2. Awareness of clinical data significantly improves reader detection of prostate cancer nodules with endorectal MR imaging and MR spectroscopic imaging, but there is no overall change in reader accuracy, because of an associated increase in false-positive findings. A stricter definition of a true-positive result is associated with reduced sensitivity for prostate cancer nodule detection. Copyright RSNA, 2004

An Optimal Bahadur-Efficient Method in Detection of Sparse Signals with Applications to Pathway Analysis in Sequencing Association Studies.

PubMed

Dai, Hongying; Wu, Guodong; Wu, Michael; Zhi, Degui

2016-01-01

Next-generation sequencing data pose a severe curse of dimensionality, complicating traditional "single marker-single trait" analysis. We propose a two-stage combined p-value method for pathway analysis. The first stage is at the gene level, where we integrate effects within a gene using the Sequence Kernel Association Test (SKAT). The second stage is at the pathway level, where we perform a correlated Lancaster procedure to detect joint effects from multiple genes within a pathway. We show that the Lancaster procedure is optimal in Bahadur efficiency among all combined p-value methods. The Bahadur efficiency,[Formula: see text], compares sample sizes among different statistical tests when signals become sparse in sequencing data, i.e. ε →0. The optimal Bahadur efficiency ensures that the Lancaster procedure asymptotically requires a minimal sample size to detect sparse signals ([Formula: see text]). The Lancaster procedure can also be applied to meta-analysis. Extensive empirical assessments of exome sequencing data show that the proposed method outperforms Gene Set Enrichment Analysis (GSEA). We applied the competitive Lancaster procedure to meta-analysis data generated by the Global Lipids Genetics Consortium to identify pathways significantly associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, triglycerides, and total cholesterol.

Accounting for imperfect detection in ecology: a quantitative review.

PubMed

Kellner, Kenneth F; Swihart, Robert K

2014-01-01

Detection in studies of species abundance and distribution is often imperfect. Assuming perfect detection introduces bias into estimation that can weaken inference upon which understanding and policy are based. Despite availability of numerous methods designed to address this assumption, many refereed papers in ecology fail to account for non-detection error. We conducted a quantitative literature review of 537 ecological articles to measure the degree to which studies of different taxa, at various scales, and over time have accounted for imperfect detection. Overall, just 23% of articles accounted for imperfect detection. The probability that an article incorporated imperfect detection increased with time and varied among taxa studied; studies of vertebrates were more likely to incorporate imperfect detection. Among articles that reported detection probability, 70% contained per-survey estimates of detection that were less than 0.5. For articles in which constancy of detection was tested, 86% reported significant variation. We hope that our findings prompt more ecologists to consider carefully the detection process when designing studies and analyzing results, especially for sub-disciplines where incorporation of imperfect detection in study design and analysis so far has been lacking.

Water-soluble vitamin homeostasis in fasting northern elephant seals (Mirounga angustirostris) measured by metabolomics analysis and standard methods

PubMed Central

Boaz, Segal M.; Champagne, Cory D.; Fowler, Melinda A.; Houser, Dorian H.; Crocker, Daniel E.

2011-01-01

Despite the importance of water-soluble vitamins to metabolism, there is limited knowledge of their serum availability in fasting wildlife. We evaluated changes in water-soluble vitamins in northern elephant seals, a species with an exceptional ability to withstand nutrient deprivation. We used a metabolomics approach to measure vitamins and associated metabolites under extended natural fasts for up to seven weeks in free-ranging lactating or developing seals. Water-soluble vitamins were not detected with this metabolomics platform, but could be measured with standard assays. Concentrations of measured vitamins varied independently, but all were maintained at detectable levels over extended fasts, suggesting that defense of vitamin levels is a component of fasting adaptation in the seals. Metabolomics was not ideal for generating complete vitamin profiles in this species, but gave novel insights into vitamin metabolism by detecting key related metabolites. For example, niacin level reductions in lactating females were associated with significant reductions in precursors suggesting downregulation of the niacin synthetic pathway. The ability to detect individual vitamins using metabolomics may be impacted by the large number of novel compounds detected. Modifications to the analysis platforms and compound detection algorithms used in this study may be required for improving water-soluble vitamin detection in this and other novel wildlife systems. PMID:21983145

Identifying reprioritization response shift in a stroke caregiver population: a comparison of missing data methods.

PubMed

Sajobi, Tolulope T; Lix, Lisa M; Singh, Gurbakhshash; Lowerison, Mark; Engbers, Jordan; Mayo, Nancy E

2015-03-01

Response shift (RS) is an important phenomenon that influences the assessment of longitudinal changes in health-related quality of life (HRQOL) studies. Given that RS effects are often small, missing data due to attrition or item non-response can contribute to failure to detect RS effects. Since missing data are often encountered in longitudinal HRQOL data, effective strategies to deal with missing data are important to consider. This study aims to compare different imputation methods on the detection of reprioritization RS in the HRQOL of caregivers of stroke survivors. Data were from a Canadian multi-center longitudinal study of caregivers of stroke survivors over a one-year period. The Stroke Impact Scale physical function score at baseline, with a cutoff of 75, was used to measure patient stroke severity for the reprioritization RS analysis. Mean imputation, likelihood-based expectation-maximization imputation, and multiple imputation methods were compared in test procedures based on changes in relative importance weights to detect RS in SF-36 domains over a 6-month period. Monte Carlo simulation methods were used to compare the statistical powers of relative importance test procedures for detecting RS in incomplete longitudinal data under different missing data mechanisms and imputation methods. Of the 409 caregivers, 15.9 and 31.3 % of them had missing data at baseline and 6 months, respectively. There were no statistically significant changes in relative importance weights on any of the domains when complete-case analysis was adopted. But statistical significant changes were detected on physical functioning and/or vitality domains when mean imputation or EM imputation was adopted. There were also statistically significant changes in relative importance weights for physical functioning, mental health, and vitality domains when multiple imputation method was adopted. Our simulations revealed that relative importance test procedures were least powerful under complete-case analysis method and most powerful when a mean imputation or multiple imputation method was adopted for missing data, regardless of the missing data mechanism and proportion of missing data. Test procedures based on relative importance measures are sensitive to the type and amount of missing data and imputation method. Relative importance test procedures based on mean imputation and multiple imputation are recommended for detecting RS in incomplete data.

The White-test helps to reduce biliary leakage in liver resection: a systematic review and meta-analysis.

PubMed

Linke, Richard; Ulrich, Frank; Bechstein, Wolf O; Schnitzbauer, Andreas A

2015-01-01

Bile leakage testing may help to detect and reduce the incidence of biliary leakage after hepatic resection. This review was performed to investigate the value of the White-test in identifying intraoperative biliary leakage and avoiding postoperative leakage. A systematic review and meta-analysis was performed. Two researchers performed literature research. Primary outcome measure was the incidence of post-hepatectomy biliary leakage; secondary outcome measure was the ability of detecting intraoperative biliary leakage with the help of the White-test. A total of 4 publications (including original data from our center) were included in the analysis. Evidence levels of the included studies had medium quality of 2b (individual cohort studies including low quality randomized controlled trials). Use of the White-test led to a significant reduction of post-operative biliary leakage [OR: 0.3 (95% CI: 0.14, 0.63), p = 0.002] and led to a significant higher intraoperative detection of biliary leakages [OR: 0.03 (95%CI: 0.02, 0.07), p < 0.00001]. Existing evidence implicates the use of the White-test after hepatic resection to identify bile leaks intraoperatively and thus reduce incidence of post-operative biliary leakage. Nonetheless, there is a requirement for a high-quality randomized controlled trial with adequately powered sample-size to confirm findings from the above described studies and further increase evidence in this field.

The association between the environmental endocrine disruptor bisphenol A and polycystic ovary syndrome: a systematic review and meta-analysis.

PubMed

Hu, Ying; Wen, Shu; Yuan, Dongzhi; Peng, Le; Zeng, Rujun; Yang, Zhilan; Liu, Qi; Xu, Liangzhi; Kang, Deying

2018-05-01

To investigate the association between bisphenol A (BPA) and polycystic ovary syndrome (PCOS). A systematic review and meta-analysis using STATA software for observational studies. Nine studies involving 493 PCOS patients and 440 controls were included in this review. The meta-analysis demonstrated that PCOS patients had significantly higher BPA levels compared with control groups (standardized mean difference (SMD): 2.437, 95% confidence interval (CI): (1.265, 3.609), p < .001). For studies of serum samples detected by enzyme-linked immunosorbent assay (ELISA), subgroup analyses according to ethnicity, body mass index (BMI), sample size, detection method (high-performance liquid chromatography (HPLC) and ELISA), PCOS-to-control ratio and study quality displayed that high BPA levels were significantly associated with Caucasian PCOS patients (SMD: 0.615, 95% CI: (0.308, 0.922), p < .001), high BMI (SMD: 0.512, 95% CI: (0.180, 0.843), p = .002), high quality (SMD: 0.624, 95% CI: (0.391, 0.856), p < .001), and high HOMA-IR (SMD: 0.467, 95% CI: (0.121, 0.813), p = .008). Serum BPA may be positively associated with women with PCOS and BPA might be involved in the insulin-resistance and hyperandrogenism of PCOS. More evidence from high quality studies, advanced detection methods, and larger cohorts for observational trials are needed to further confirm the association between BPA and PCOS.

A New Method for the Fast Analysis of Trihalomethanes in Tap and Recycled Waters Using Headspace Gas Chromatography with Micro-Electron Capture Detection.

PubMed

Alexandrou, Lydon D; Meehan, Barry J; Morrison, Paul D; Jones, Oliver A H

2017-05-15

Chemical disinfection of water supplies brings significant public health benefits by reducing microbial contamination. The process can however, result in the formation of toxic compounds through interactions between disinfectants and organic material in the source water. These new compounds are termed disinfection by-products (DBPs). The most common are the trihalomethanes (THMs) such as trichloromethane (chloroform), dichlorobromomethane, chlorodibromomethane and tribromomethane (bromoform); these are commonly reported as a single value for total trihalomethanes (TTHMs). Analysis of DBPs is commonly performed via time- and solvent-intensive sample preparation techniques such as liquid-liquid and solid phase extraction. In this study, a method using headspace gas chromatography with micro-electron capture detection was developed and applied for the analysis of THMs in drinking and recycled waters from across Melbourne (Victoria, Australia). The method allowed almost complete removal of the sample preparation step whilst maintaining trace level detection limits (>1 ppb). All drinking water samples had TTHM concentrations below the Australian regulatory limit of 250 µg/L but some were above the U.S. EPA limit of 60 µg/L. The highest TTHM concentration was 67.2 µg/L and lowest 22.9 µg/L. For recycled water, samples taken directly from treatment plants held significantly higher concentrations (153.2 µg/L TTHM) compared to samples from final use locations (4.9-9.3 µg/L).

Detectable end of radiation prostate specific antigen assists in identifying men with unfavorable intermediate-risk prostate cancer at high risk of distant recurrence and cancer-specific mortality.

PubMed

Hayman, Jonathan; Phillips, Ryan; Chen, Di; Perin, Jamie; Narang, Amol K; Trieu, Janson; Radwan, Noura; Greco, Stephen; Deville, Curtiland; McNutt, Todd; Song, Daniel Y; DeWeese, Theodore L; Tran, Phuoc T

2018-06-01

Undetectable End of Radiation PSA (EOR-PSA) has been shown to predict improved survival in prostate cancer (PCa). While validating the unfavorable intermediate-risk (UIR) and favorable intermediate-risk (FIR) stratifications among Johns Hopkins PCa patients treated with radiotherapy, we examined whether EOR-PSA could further risk stratify UIR men for survival. A total of 302 IR patients were identified in the Johns Hopkins PCa database (178 UIR, 124 FIR). Kaplan-Meier curves and multivariable analysis was performed via Cox regression for biochemical recurrence free survival (bRFS), distant metastasis free survival (DMFS), and overall survival (OS), while a competing risks model was used for PCa specific survival (PCSS). Among the 235 patients with known EOR-PSA values, we then stratified by EOR-PSA and performed the aforementioned analysis. The median follow-up time was 11.5 years (138 months). UIR was predictive of worse DMFS and PCSS (P = 0.008 and P = 0.023) on multivariable analysis (MVA). Increased radiation dose was significant for improved DMFS (P = 0.016) on MVA. EOR-PSA was excluded from the models because it did not trend towards significance as a continuous or binary variable due to interaction with UIR, and we were unable to converge a multivariable model with a variable to control for this interaction. However, when stratifying by detectable versus undetectable EOR-PSA, UIR had worse DMFS and PCSS among detectable EOR-PSA patients, but not undetectable patients. UIR was significant on MVA among detectable EOR-PSA patients for DMFS (P = 0.021) and PCSS (P = 0.033), while RT dose also predicted PCSS (P = 0.013). EOR-PSA can assist in predicting DMFS and PCSS among UIR patients, suggesting a clinically meaningful time point for considering intensification of treatment in clinical trials of intermediate-risk men. © 2018 Wiley Periodicals, Inc.

Accuracy of Noncycloplegic Retinoscopy, Retinomax Autorefractor, and SureSight Vision Screener for Detecting Significant Refractive Errors

PubMed Central

Kulp, Marjean Taylor; Ying, Gui-shuang; Huang, Jiayan; Maguire, Maureen; Quinn, Graham; Ciner, Elise B.; Cyert, Lynn A.; Orel-Bixler, Deborah A.; Moore, Bruce D.

2014-01-01

Purpose. To evaluate, by receiver operating characteristic (ROC) analysis, the ability of noncycloplegic retinoscopy (NCR), Retinomax Autorefractor (Retinomax), and SureSight Vision Screener (SureSight) to detect significant refractive errors (RE) among preschoolers. Methods. Refraction results of eye care professionals using NCR, Retinomax, and SureSight (n = 2588) and of nurse and lay screeners using Retinomax and SureSight (n = 1452) were compared with masked cycloplegic retinoscopy results. Significant RE was defined as hyperopia greater than +3.25 diopters (D), myopia greater than 2.00 D, astigmatism greater than 1.50 D, and anisometropia greater than 1.00 D interocular difference in hyperopia, greater than 3.00 D interocular difference in myopia, or greater than 1.50 D interocular difference in astigmatism. The ability of each screening test to identify presence, type, and/or severity of significant RE was summarized by the area under the ROC curve (AUC) and calculated from weighted logistic regression models. Results. For detection of each type of significant RE, AUC of each test was high; AUC was better for detecting the most severe levels of RE than for all REs considered important to detect (AUC 0.97–1.00 vs. 0.92–0.93). The area under the curve of each screening test was high for myopia (AUC 0.97–0.99). Noncycloplegic retinoscopy and Retinomax performed better than SureSight for hyperopia (AUC 0.92–0.99 and 0.90–0.98 vs. 0.85–0.94, P ≤ 0.02), Retinomax performed better than NCR for astigmatism greater than 1.50 D (AUC 0.95 vs. 0.90, P = 0.01), and SureSight performed better than Retinomax for anisometropia (AUC 0.85–1.00 vs. 0.76–0.96, P ≤ 0.07). Performance was similar for nurse and lay screeners in detecting any significant RE (AUC 0.92–1.00 vs. 0.92–0.99). Conclusions. Each test had a very high discriminatory power for detecting children with any significant RE. PMID:24481262

Evidence of hemolysis in pigs infected with highly virulent African swine fever virus

PubMed Central

Karalyan, Zaven; Zakaryan, Hovakim; Arakelova, Elina; Aivazyan, Violeta; Tatoyan, Marina; Kotsinyan, Armen; Izmailyan, Roza; Karalova, Elena

2016-01-01

Aim: The research was conducted to understand more profoundly the pathogenetic aspects of the acute form of the African swine fever (ASF). Materials and Methods: A total of 10 pigs were inoculated with ASF virus (ASFV) (genotype II) in the study of the red blood cells (RBCs), blood and urine biochemistry in the dynamics of disease. Results: The major hematological differences observed in ASFV infected pigs were that the mean corpuscular volume, mean corpuscular hemoglobin, and hematocrits were significantly decreased compared to controls, and the levels of erythropoietin were significantly increased. Also were detected the trends of decrease in RBC count at terminal stages of ASF. Analysis of blood biochemistry revealed that during ASF development, besides bilirubinemia significantly elevated levels of lactate dehydrogenase, and aspartate aminotransferase were detected. Analysis of urine biochemistry revealed the presence of bilirubinuria, proteinuria during ASF development. Proteinuria, especially at late stages of the disease reflects a severe kidney damage possible glomerulonefritis. Conclusion: The results of this study indicate the characteristics of developing hemolytic anemia observed in acute ASF (genotype II). PMID:28096614

A matched-pair study comparing whole-brain irradiation alone to radiosurgery or fractionated stereotactic radiotherapy alone in patients irradiated for up to three brain metastases.

PubMed

Rades, Dirk; Janssen, Stefan; Dziggel, Liesa; Blanck, Oliver; Bajrovic, Amira; Veninga, Theo; Schild, Steven E

2017-01-06

This matched-pair study was initiated to validate the results of a retrospective study of 186 patients published in 2007 that compared whole-brain irradiation (WBI) alone and radiosurgery (RS) alone for up to three brain metastases. One-hundred-fifty-two patients receiving WBI alone for up to three brain metastases were matched with 152 patients treated with RS of fractionated stereotactic radiotherapy (FSRT) alone 1:1 for each of eight factors (age, gender, Eastern Oncology Cooperative Group (ECOG)-performance score, nature of tumor, brain metastases number, extra-cerebral spread, period from cancer detection to irradiation of brain metastases, and recursive partitioning analysis (RPA)-class. Groups were analyzed regarding intracerebral control (IC) and overall survival (OS). On univariate analysis of IC, type of irradiation did not significantly affect outcomes (p = 0.84). On Cox regression, brain metastases number (p < 0.001), nature of tumor (p < 0.001) and period from cancer detection to irradiation of brain metastases (p = 0.013) were significantly associated with IC. On univariate analysis of OS, type of irradiation showed no significant association with outcomes (p = 0.63). On multivariate analyses, OS was significantly associated with ECOG performance score (p = 0.011), nature of tumor (p = 0.035), brain metastases number (p = 0.048), extra-cerebral spread (p = 0.002) and RPA-class (p < 0.001). In this matched-pair study, RS/FSRT alone was not superior to WBI alone regarding IC and OS. These results can be considered a revision of the findings from our retrospective previous study without matched-pair design, where RS alone resulted in significantly better IC than WBI alone on multivariate analysis.

A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibility

PubMed Central

Gui, Jiang; Andrew, Angeline S.; Andrews, Peter; Nelson, Heather M.; Kelsey, Karl T.; Karagas, Margaret R.; Moore, Jason H.

2010-01-01

A central goal of human genetics is to identify and characterize susceptibility genes for common complex human diseases. An important challenge in this endeavor is the modeling of gene-gene interaction or epistasis that can result in non-additivity of genetic effects. The multifactor dimensionality reduction (MDR) method was developed as machine learning alternative to parametric logistic regression for detecting interactions in absence of significant marginal effects. The goal of MDR is to reduce the dimensionality inherent in modeling combinations of polymorphisms using a computational approach called constructive induction. Here, we propose a Robust Multifactor Dimensionality Reduction (RMDR) method that performs constructive induction using a Fisher’s Exact Test rather than a predetermined threshold. The advantage of this approach is that only those genotype combinations that are determined to be statistically significant are considered in the MDR analysis. We use two simulation studies to demonstrate that this approach will increase the success rate of MDR when there are only a few genotype combinations that are significantly associated with case-control status. We show that there is no loss of success rate when this is not the case. We then apply the RMDR method to the detection of gene-gene interactions in genotype data from a population-based study of bladder cancer in New Hampshire. PMID:21091664

Characterization of the behavior of three definitions of prostate-specific antigen-based biochemical failure in relation to detection and follow-up biases: comparison with the American Society for Therapeutic Radiology and Oncology consensus definition.

PubMed

Williams, Scott G

2006-03-01

To examine the impact of detection biases on three prostate cancer biochemical failure (bF) definitions in comparison with the existing American Society for Therapeutic Radiology and Oncology Consensus Definition (ACD). Three alternative bF definitions were tested against the ACD: three rises in prostate-specific antigen (PSA) level without backdating, nadir plus 2 ng/mL, and a threshold PSA level of >3 ng/mL, according to data from 1050 men. The mean time between PSA tests (MTBT), regularity of collection, and calendar year of analysis were examined in each bF definition. The MTBT produced a statistically significant difference in the derived hazard ratio for identification of bF in all definitions. The influence of test regularity was statistically significant beyond the median level of regularity in all definitions. The year of analysis impacted greatly on the ACD, whereas the three alternative definitions exhibited minor follow-up duration variations by comparison. The alternative definitions had reliable follow-up when the crude median time to censoring was at least 1.6 times greater than that of failure. Detection biases will always be a significant issue in defining bF. A number of alternative failure definitions have more predictable interactions with these biases than the existing ACD.

Measurement, time-stamping, and analysis of electrodermal activity in fMRI

NASA Astrophysics Data System (ADS)

Smyser, Christopher; Grabowski, Thomas J.; Rainville, Pierre; Bechara, Antione; Razavi, Mehrdad; Mehta, Sonya; Eaton, Brent L.; Bolinger, Lizann

2002-04-01

A low cost fMRI-compatible system was developed for detecting electrodermal activity without inducing image artifact. Subject electrodermal activity was measured on the plantar surface of the foot using a standard recording circuit. Filtered analog skin conductance responses (SCR) were recorded with a general purpose, time-stamping data acquisition system. A conditioning paradigm involving painful thermal stimulation was used to demonstrate SCR detection and investigate neural correlates of conditioned autonomic activity. 128x128 pixel EPI-BOLD images were acquired with a GE 1.5T Signa scanner. Image analysis was performed using voxel-wise multiple linear regression. The covariate of interest was generated by convolving stimulus event onset with a standard hemodynamic response function. The function was time-shifted to determine optimal activation. Significance was tested using the t-statistic. Image quality was unaffected by the device, and conditioned and unconditioned SCRs were successfully detected. Conditioned SCRs correlated significantly with activity in the right anterior insular cortex. The effect was more robust when responses were scaled by SCR amplitude. The ability to measure and time register SCRs during fMRI acquisition enables studies of cognitive processes marked by autonomic activity, including those involving decision-making, pain, emotion, and addiction.

Analysis of hyperspectral fluorescence images for poultry skin tumor inspection

NASA Astrophysics Data System (ADS)

Kong, Seong G.; Chen, Yud-Ren; Kim, Intaek; Kim, Moon S.

2004-02-01

We present a hyperspectral fluorescence imaging system with a fuzzy inference scheme for detecting skin tumors on poultry carcasses. Hyperspectral images reveal spatial and spectral information useful for finding pathological lesions or contaminants on agricultural products. Skin tumors are not obvious because the visual signature appears as a shape distortion rather than a discoloration. Fluorescence imaging allows the visualization of poultry skin tumors more easily than reflectance. The hyperspectral image samples obtained for this poultry tumor inspection contain 65 spectral bands of fluorescence in the visible region of the spectrum at wavelengths ranging from 425 to 711 nm. The large amount of hyperspectral image data is compressed by use of a discrete wavelet transform in the spatial domain. Principal-component analysis provides an effective compressed representation of the spectral signal of each pixel in the spectral domain. A small number of significant features are extracted from two major spectral peaks of relative fluorescence intensity that have been identified as meaningful spectral bands for detecting tumors. A fuzzy inference scheme that uses a small number of fuzzy rules and Gaussian membership functions successfully detects skin tumors on poultry carcasses. Spatial-filtering techniques are used to significantly reduce false positives.

Asynchronous detection of kinesthetic attention during mobilization of lower limbs using EEG measurements.

PubMed

Melinscak, Filip; Montesano, Luis; Minguez, Javier

2016-02-01

Attention is known to modulate the plasticity of the motor cortex, and plasticity is crucial for recovery in motor rehabilitation. This study addresses the possibility of using an EEG-based brain-computer interface (BCI) to detect kinesthetic attention to movement. A novel experiment emulating physical rehabilitation was designed to study kinesthetic attention. The protocol involved continuous mobilization of lower limbs during which participants reported levels of attention to movement-from focused kinesthetic attention to mind wandering. For this protocol an asynchronous BCI detector of kinesthetic attention and deliberate mind wandering was designed. EEG analysis showed significant differences in theta, alpha, and beta bands, related to the attentional state. These changes were further pinpointed to bands relative to the frequency of the individual alpha peak. The accuracy of the designed BCI ranged between 60.8% and 68.4% (significantly above chance level), depending on the used analysis window length, i.e. acceptable detection delay. This study shows it is possible to use self-reporting to study attention-related changes in EEG during continuous mobilization. Such a protocol is used to develop an asynchronous BCI detector of kinesthetic attention, with potential applications to motor rehabilitation.

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

PubMed

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Performance of RVGui sensor and Kodak Ektaspeed Plus film for proximal caries detection.

PubMed

Abreu, M; Mol, A; Ludlow, J B

2001-03-01

A high-resolution charge-coupled device was used to compare the diagnostic performances obtained with Trophy's new RVGui sensor and Kodak Ektaspeed Plus film with respect to caries detection. Three acquisition modes of the Trophy RVGui sensor were compared with Kodak Ektaspeed Plus film. Images of the proximal surfaces of 40 extracted posterior teeth were evaluated by 6 observers. The presence or absence of caries was scored by means of a 5-point confidence scale. The actual caries status of each surface was determined through ground-section histology. Responses were evaluated by means of receiver operating characteristic analysis. Areas under receiver operating characteristic curves (A(Z)) were assessed through analysis of variance. The mean A(Z) scores were 0.85 for film, 0.84 for the high-resolution caries mode, and 0.82 for both the low resolution caries mode and the high-resolution periodontal mode. These differences were not statistically significant (P =.70). The differences among observers also were not statistically significant (P =.23). The performance of the RVGui sensor in high- and low-resolution modes for proximal caries detection is comparable to that of Ektaspeed Plus film.

Detection of Urine Metabolites in a Rat Model of Chronic Fatigue Syndrome before and after Exercise

PubMed Central

Shao, Changzhuan; Ren, Yiming; Wang, Zinan; Kang, Chenzhe

2017-01-01

Purpose. The aim of the present study was to elucidate the metabolic mechanisms associated with chronic fatigue syndrome (CFS) via an analysis of urine metabolites prior to and following exercise in a rat model. Methods. A rat model of CFS was established using restraint-stress, forced exercise, and crowded and noisy environments over a period of 4 weeks. Behavioral experiments were conducted in order to evaluate the model. Urine metabolites were analyzed via gas chromatography-mass spectrometry (GC-MS) in combination with multivariate statistical analysis before and after exercise. Results. A total of 20 metabolites were detected in CFS rats before and after exercise. Three metabolic pathways (TCA cycle; alanine, aspartate, and glutamate metabolism; steroid hormone biosynthesis) were significantly impacted before and after exercise, while sphingolipid metabolism alone exhibited significant alterations after exercise only. Conclusion. In addition to metabolic disturbances involving some energy substances, alterations in steroid hormone biosynthesis and sphingolipid metabolism were detected in CFS rats. Sphingosine and 21-hydroxypregnenolone may be key biomarkers of CFS, potentially offering evidence in support of immune dysfunction and hypothalamic-pituitary-adrenal (HPA) axis hypoactivity in patients with CFS. PMID:28421200

Detecting dryland degradation through the use of Time Series Segmentation and Residual Trend analysis (TSS-RESTREND)

NASA Astrophysics Data System (ADS)

Burrell, A. L.; Evans, J. P.; Liu, Y.

2017-12-01

Dryland degradation is an issue of international significance as dryland regions play a substantial role in global food production. Remotely sensed data provide the only long term, large scale record of changes within dryland ecosystems. The Residual Trend, or RESTREND, method is applied to satellite observations to detect dryland degradation. Whilst effective in most cases, it has been shown that the RESTREND method can fail to identify degraded pixels if the relationship between vegetation and precipitation has broken-down as a result of severe or rapid degradation. This study presents an extended version of the RESTREND methodology that incorporates the Breaks For Additive Seasonal and Trend method to identify step changes in the time series that are related to significant structural changes in the ecosystem, e.g. land use changes. When applied to Australia, this new methodology, termed Time Series Segmentation and Residual Trend analysis (TSS-RESTREND), was able to detect degradation in 5.25% of pixels compared to only 2.0% for RESTREND alone. This modified methodology was then assessed in two regions with known histories of degradation where it was found to accurately capture both the timing and directionality of ecosystem change.

Eye blink detection for different driver states in conditionally automated driving and manual driving using EOG and a driver camera.

PubMed

Schmidt, Jürgen; Laarousi, Rihab; Stolzmann, Wolfgang; Karrer-Gauß, Katja

2018-06-01

In this article, we examine the performance of different eye blink detection algorithms under various constraints. The goal of the present study was to evaluate the performance of an electrooculogram- and camera-based blink detection process in both manually and conditionally automated driving phases. A further comparison between alert and drowsy drivers was performed in order to evaluate the impact of drowsiness on the performance of blink detection algorithms in both driving modes. Data snippets from 14 monotonous manually driven sessions (mean 2 h 46 min) and 16 monotonous conditionally automated driven sessions (mean 2 h 45 min) were used. In addition to comparing two data-sampling frequencies for the electrooculogram measures (50 vs. 25 Hz) and four different signal-processing algorithms for the camera videos, we compared the blink detection performance of 24 reference groups. The analysis of the videos was based on very detailed definitions of eyelid closure events. The correct detection rates for the alert and manual driving phases (maximum 94%) decreased significantly in the drowsy (minus 2% or more) and conditionally automated (minus 9% or more) phases. Blinking behavior is therefore significantly impacted by drowsiness as well as by automated driving, resulting in less accurate blink detection.

Improved detection and false alarm rejection using FLGPR and color imagery in a forward-looking system

NASA Astrophysics Data System (ADS)

Havens, Timothy C.; Spain, Christopher J.; Ho, K. C.; Keller, James M.; Ton, Tuan T.; Wong, David C.; Soumekh, Mehrdad

2010-04-01

Forward-looking ground-penetrating radar (FLGPR) has received a significant amount of attention for use in explosivehazards detection. A drawback to FLGPR is that it results in an excessive number of false detections. This paper presents our analysis of the explosive-hazards detection system tested by the U.S. Army Night Vision and Electronic Sensors Directorate (NVESD). The NVESD system combines an FLGPR with a visible-spectrum color camera. We present a target detection algorithm that uses a locally-adaptive detection scheme with spectrum-based features. The remaining FLGPR detections are then projected into the camera imagery and image-based features are collected. A one-class classifier is then used to reduce the number of false detections. We show that our proposed FLGPR target detection algorithm, coupled with our camera-based false alarm (FA) reduction method, is effective at reducing the number of FAs in test data collected at a US Army test facility.

Genetic analysis of children of atomic bomb survivors.

PubMed Central

Satoh, C; Takahashi, N; Asakawa, J; Kodaira, M; Kuick, R; Hanash, S M; Neel, J V

1996-01-01

Studies are under way for the detection of potential genetic effects of atomic bomb radiation at the DNA level in the children of survivors. In a pilot study, we have examined six minisatellites and five microsatellites in DNA derived from 100 families including 124 children. We detected a total of 28 mutations in three minisatellite loci. The mean mutation rates per locus per gamete in the six minisatellite loci were 1.5% for 65 exposed gametes for which mean parental gonadal dose was 1.9 Sv and 2.0% for 183 unexposed gametes. We detected four mutations in two tetranucleotide repeat sequences but no mutations in three trinucleotide repeat sequences. The mean mutation rate per locus per gamete was o% for the exposed gametes and 0.5% for the unexposed gametes in the five microsatellite loci. No significant differences in the mutation rates between the exposed and the unexposed gametes were detected in these repetitive sequences. Additional loci are being analyzed to increase the power of our study to observe a significant difference in the mutation rates at the 0.05 level of significance. Images Figure 1. Figure 2. Figure 2. Figure 2. Figure 2. Figure 2. Figure 2. PMID:8781374

Cavity-Enhanced Absorption Spectroscopy and Photoacoustic Spectroscopy for Human Breath Analysis

NASA Astrophysics Data System (ADS)

Wojtas, J.; Tittel, F. K.; Stacewicz, T.; Bielecki, Z.; Lewicki, R.; Mikolajczyk, J.; Nowakowski, M.; Szabra, D.; Stefanski, P.; Tarka, J.

2014-12-01

This paper describes two different optoelectronic detection techniques: cavity-enhanced absorption spectroscopy and photoacoustic spectroscopy. These techniques are designed to perform a sensitive analysis of trace gas species in exhaled human breath for medical applications. With such systems, the detection of pathogenic changes at the molecular level can be achieved. The presence of certain gases (biomarkers), at increased concentration levels, indicates numerous human diseases. Diagnosis of a disease in its early stage would significantly increase chances for effective therapy. Non-invasive, real-time measurements, and high sensitivity and selectivity, capable of minimum discomfort for patients, are the main advantages of human breath analysis. At present, monitoring of volatile biomarkers in breath is commonly useful for diagnostic screening, treatment for specific conditions, therapy monitoring, control of exogenous gases (such as bacterial and poisonous emissions), as well as for analysis of metabolic gases.

Detection of heart disease by open access echocardiography: a retrospective analysis of general practice referrals

PubMed Central

Chambers, John; Kabir, Saleha; Cajeat, Eric

2014-01-01

Background Heart disease is difficult to detect clinically and it has been suggested that echocardiography should be available to all patients with possible cardiac symptoms or signs. Aim To analyse the results of 2 years of open access echocardiography for the frequency of structural heart disease according to request. Design and setting Retrospective database analysis in a teaching hospital open access echocardiography service. Method Reports of all open access transthoracic echocardiograms between January 2011 and December 2012 were categorised as normal, having minor abnormalities, or significant abnormalities according to the indication. Results There were 2343 open access echocardiograms performed and there were significant abnormalities in 29%, predominantly valve disease (n = 304, 13%), LV systolic dysfunction (n = 179, 8%), aortic dilatation (n = 80, 3%), or pulmonary hypertension (n = 91, 4%). If echocardiography had been targeted at a high-risk group, 267 with valve disease would have been detected (compared to 127 with murmur alone) and 139 with LV systolic dysfunction (compared to 91 with suspected heart failure alone). Most GP practices requested fewer than 10 studies, but 6 practices requested over 70 studies. Conclusion Open access echocardiograms are often abnormal but structural disease may not be suspected from the clinical request. Uptake by individual practices is patchy. A targeted expansion of echocardiography in patients with a high likelihood of disease is therefore likely to increase the detection of clinically important pathology. PMID:24567615

Detection of heart disease by open access echocardiography: a retrospective analysis of general practice referrals.

PubMed

Chambers, John; Kabir, Saleha; Cajeat, Eric

2014-02-01

Heart disease is difficult to detect clinically and it has been suggested that echocardiography should be available to all patients with possible cardiac symptoms or signs. To analyse the results of 2 years of open access echocardiography for the frequency of structural heart disease according to request. Retrospective database analysis in a teaching hospital open access echocardiography service. Reports of all open access transthoracic echocardiograms between January 2011 and December 2012 were categorised as normal, having minor abnormalities, or significant abnormalities according to the indication. There were 2343 open access echocardiograms performed and there were significant abnormalities in 29%, predominantly valve disease (n = 304, 13%), LV systolic dysfunction (n = 179, 8%), aortic dilatation (n = 80, 3%), or pulmonary hypertension (n = 91, 4%). If echocardiography had been targeted at a high-risk group, 267 with valve disease would have been detected (compared to 127 with murmur alone) and 139 with LV systolic dysfunction (compared to 91 with suspected heart failure alone). Most GP practices requested fewer than 10 studies, but 6 practices requested over 70 studies. Open access echocardiograms are often abnormal but structural disease may not be suspected from the clinical request. Uptake by individual practices is patchy. A targeted expansion of echocardiography in patients with a high likelihood of disease is therefore likely to increase the detection of clinically important pathology.

Characterization of the nasal and oral microbiota of detection dogs.

PubMed

Isaiah, Anitha; Hoffmann, Aline Rodrigues; Kelley, Russ; Mundell, Paul; Steiner, Jörg M; Suchodolski, Jan S

2017-01-01

Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations-Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines.

Characterization of the nasal and oral microbiota of detection dogs

PubMed Central

Hoffmann, Aline Rodrigues; Kelley, Russ; Mundell, Paul; Steiner, Jörg M.

2017-01-01

Little is known about physiological factors that affect the sense of olfaction in dogs. The objectives of this study were to describe the canine nasal and oral microbiota in detection dogs. We sought to determine the bacterial composition of the nasal and oral microbiota of a diverse population of detection canines. Nasal and oral swabs were collected from healthy dogs (n = 81) from four locations—Alabama, Georgia, California, and Texas. Nasal and oral swabs were also collected from a second cohort of detection canines belonging to three different detection job categories: explosive detection dogs (SP-E; n = 22), patrol and narcotics detection dogs (P-NDD; n = 15), and vapor wake dogs (VWD-E; n = 9). To understand if the nasal and oral microbiota of detection canines were variable, sample collection was repeated after 7 weeks in a subset of dogs. DNA was extracted from the swabs and used for 454-pyrosequencing of the16S rRNA genes. Nasal samples had a significantly lower diversity than oral samples (P<0.01). Actinobacteria and Proteobacteria were higher in nasal samples, while Bacteroidetes, Firmicutes, Fusobacteria, and Tenericutes were higher in oral samples. Bacterial diversity was not significantly different based on the detection job. No significant difference in beta diversity was observed in the nasal samples based on the detection job. In oral samples, however, ANOSIM suggested a significant difference in bacterial communities based on job category albeit with a small effect size (R = 0.1079, P = 0.02). Analysis of the composition of bacterial communities using LEfSe showed that within the nasal samples, Cardiobacterium and Riemerella were higher in VWD-E dogs, and Sphingobacterium was higher in the P-NDD group. In the oral samples Enterococcus and Capnocytophaga were higher in the P-NDD group. Gemella and Aggregatibacter were higher in S-PE, and Pigmentiphaga, Chryseobacterium, Parabacteroides amongst others were higher within the VWD-E group. Our initial data also shows that there is a temporal variation in alpha diversity in nasal samples in detection canines. PMID:28934260

Investigating the usefulness of a cluster-based trend analysis to detect visual field progression in patients with open-angle glaucoma.

PubMed

Aoki, Shuichiro; Murata, Hiroshi; Fujino, Yuri; Matsuura, Masato; Miki, Atsuya; Tanito, Masaki; Mizoue, Shiro; Mori, Kazuhiko; Suzuki, Katsuyoshi; Yamashita, Takehiro; Kashiwagi, Kenji; Hirasawa, Kazunori; Shoji, Nobuyuki; Asaoka, Ryo

2017-12-01

To investigate the usefulness of the Octopus (Haag-Streit) EyeSuite's cluster trend analysis in glaucoma. Ten visual fields (VFs) with the Humphrey Field Analyzer (Carl Zeiss Meditec), spanning 7.7 years on average were obtained from 728 eyes of 475 primary open angle glaucoma patients. Mean total deviation (mTD) trend analysis and EyeSuite's cluster trend analysis were performed on various series of VFs (from 1st to 10th: VF1-10 to 6th to 10th: VF6-10). The results of the cluster-based trend analysis, based on different lengths of VF series, were compared against mTD trend analysis. Cluster-based trend analysis and mTD trend analysis results were significantly associated in all clusters and with all lengths of VF series. Between 21.2% and 45.9% (depending on VF series length and location) of clusters were deemed to progress when the mTD trend analysis suggested no progression. On the other hand, 4.8% of eyes were observed to progress using the mTD trend analysis when cluster trend analysis suggested no progression in any two (or more) clusters. Whole field trend analysis can miss local VF progression. Cluster trend analysis appears as robust as mTD trend analysis and useful to assess both sectorial and whole field progression. Cluster-based trend analyses, in particular the definition of two or more progressing cluster, may help clinicians to detect glaucomatous progression in a timelier manner than using a whole field trend analysis, without significantly compromising specificity. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

PubMed

Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

2017-03-09

It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

Comparative Evaluation of Veriflow® Listeria monocytogenes to USDA and AOAC Culture Based Methods for the Detection of Listeria monocytogenes in Food.

PubMed

Joelsson, Adam C; Brown, Ashley S; Puri, Amrita; Keough, Martin P; Gaudioso, Zara E; Siciliano, Nicholas A; Snook, Adam E

2015-01-01

Veriflow® Listeria monocytogenes (LM) is a molecular based assay for the presumptive detection of Listeria monocytogenes from environmental surfaces, dairy, and ready-to-eat (RTE) food matrixes (hot dogs and deli meat). The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 min post PCR amplification and requires only 24 h of enrichment for maximum sensitivity. The Veriflow LM system eliminates the need for sample purification, gel electrophoresis, or fluorophore-based detection of target amplification, and does not require complex data analysis. This Performance Tested Method(SM) validation study demonstrated the ability of the Veriflow LM method to detect low levels of artificially inoculated L. monocytogenes in seven distinct environmental and food matrixes. In each unpaired reference comparison study, probability of detection analysis indicated no significant difference between the Veriflow LM method and the U.S. Department of Agriculture, Food Safety and Inspection Service Microbiology Laboratory Guidebook 8.08 or AOAC 993.12 reference method. Fifty strains of L. monocytogenes were detected in the inclusivity study, while 39 nonspecific organisms were undetected in the exclusivity study. The study results show that Veriflow LM is a sensitive, selective, and robust assay for the presumptive detection of L. monocytogenes sampled from environmental, dairy, or RTE (hot dogs and deli meat) food matrixes.

Phage-protease-peptide: a novel trifecta enabling multiplex detection of viable bacterial pathogens.

PubMed

Alcaine, S D; Tilton, L; Serrano, M A C; Wang, M; Vachet, R W; Nugen, S R

2015-10-01

Bacteriophages represent rapid, readily targeted, and easily produced molecular probes for the detection of bacterial pathogens. Molecular biology techniques have allowed researchers to make significant advances in the bioengineering of bacteriophage to further improve speed and sensitivity of detection. Despite their host specificity, bacteriophages have not been meaningfully leveraged in multiplex detection of bacterial pathogens. We propose a proof-of-principal phage-based scheme to enable multiplex detection. Our scheme involves bioengineering bacteriophage to carry a gene for a specific protease, which is expressed during infection of the target cell. Upon lysis, the protease is released to cleave a reporter peptide, and the signal detected. Here we demonstrate the successful (i) modification of T7 bacteriophage to carry tobacco etch virus (TEV) protease; (ii) expression of TEV protease by Escherichia coli following infection by our modified T7, an average of 2000 units of protease per phage are produced during infection; and (iii) proof-of-principle detection of E. coli in 3 h after a primary enrichment via TEV protease activity using a fluorescent peptide and using a designed target peptide for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (MALDI-TOF MS) analysis. This proof-of-principle can be translated to other phage-protease-peptide combinations to enable multiplex bacterial detection and readily adopted on multiple platforms, like MALDI-TOF MS or fluorescent readers, commonly found in labs.

Optimization of routine KRAS mutation PCR-based testing procedure for rational individualized first-line-targeted therapy selection in metastatic colorectal cancer.

PubMed

Chretien, Anne-Sophie; Harlé, Alexandre; Meyer-Lefebvre, Magali; Rouyer, Marie; Husson, Marie; Ramacci, Carole; Harter, Valentin; Genin, Pascal; Leroux, Agnès; Merlin, Jean-Louis

2013-02-01

KRAS mutation detection represents a crucial issue in metastatic colorectal cancer (mCRC). The optimization of KRAS mutation detection delay enabling rational prescription of first-line treatment in mCRC including anti-EGFR-targeted therapy requires robust and rapid molecular biology techniques. Routine analysis of mutations in codons 12 and 13 on 674 paraffin-embedded tissue specimens of mCRC has been performed for KRAS mutations detection using three molecular biology techniques, that is, high-resolution melting (HRM), polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and allelic discrimination PCR (TaqMan PCR). Discordant cases were assessed with COBAS 4800 KRAS CE-IVD assay. Among the 674 tumor specimens, 1.5% (10/674) had excessive DNA degradation and could not be analyzed. KRAS mutations were detected in 38.0% (256/674) of the analysable specimens (82.4% in codon 12 and 17.6% in codon 13). Among 613 specimens in whom all three techniques were used, 12 (2.0%) cases of discordance between the three techniques were observed. 83.3% (10/12) of the discordances were due to PCR-RFLP as confirmed by COBAS 4800 retrospective analysis. The three techniques were statistically comparable (κ > 0.9; P < 0.001). From these results, optimization of the routine procedure consisted of proceeding to systematic KRAS detection using HRM and TaqMan and PCR-RFLP in case of discordance and allowed significant decrease in delays. The results showed an excellent correlation between the three techniques. Using HRM and TaqMan warrants high-quality and rapid-routine KRAS mutation detection in paraffin-embedded tumor specimens. The new procedure allowed a significant decrease in delays for reporting results, enabling rational prescription of first-line-targeted therapy in mCRC.

New method for enhanced efficiency in detection of gravitational waves from supernovae using coherent network of detectors

NASA Astrophysics Data System (ADS)

Mukherjee, S.; Salazar, L.; Mittelstaedt, J.; Valdez, O.

2017-11-01

Supernovae in our universe are potential sources of gravitational waves (GW) that could be detected in a network of GW detectors like LIGO and Virgo. Core-collapse supernovae are rare, but the associated gravitational radiation is likely to carry profuse information about the underlying processes driving the supernovae. Calculations based on analytic models predict GW energies within the detection range of the Advanced LIGO detectors, out to tens of Mpc for certain types of signals e.g. coalescing binary neutron stars. For supernovae however, the corresponding distances are much less. Thus, methods that can improve the sensitivity of searches for GW signals from supernovae are desirable, especially in the advanced detector era. Several methods have been proposed based on various likelihood-based regulators that work on data from a network of detectors to detect burst-like signals (as is the case for signals from supernovae) from potential GW sources. To address this problem, we have developed an analysis pipeline based on a method of noise reduction known as the harmonic regeneration noise reduction (HRNR) algorithm. To demonstrate the method, sixteen supernova waveforms from the Murphy et al. 2009 catalog have been used in presence of LIGO science data. A comparative analysis is presented to show detection statistics for a standard network analysis as commonly used in GW pipelines and the same by implementing the new method in conjunction with the network. The result shows significant improvement in detection statistics.

DETECTION OF MALNUTRITION IN PATIENTS UNDERGOING MAINTENANCE HAEMODIALYSIS: A QUANTITATIVE DATA ANALYSIS ON 12 PARAMETERS.

PubMed

Nafzger, Sonja; Fleury, Lea-Angelica; Uehlinger, Dominik E; Plüss, Petra; Scura, Ninetta; Kurmann, Silvia

2015-09-01

Protein-energy-malnutrition (PEM) is common in people with end stage kidney disease (ESKD) undergoing maintenance haemodialysis (MHD) and correlates strongly with mortality. To this day, there is no gold standard for detecting PEM in patients on MHD. The aim of this study was to evaluate if Nutritional Risk Screening 2002 (NRS-2002), handgrip strength measurement, mid-upper arm muscle area (MUAMA), triceps skin fold measurement (TSF), serum albumin, normalised protein catabolic rate (nPCR), Kt/V and eKt/V, dry body weight, body mass index (BMI), age and time since start on MHD are relevant for assessing PEM in patients on MHD. The predictive value of the selected parameters on mortality and mortality or weight loss of more than 5% was assessed. Quantitative data analysis of the 12 parameters in the same patients on MHD in autumn 2009 (n = 64) and spring 2011 (n = 40) with paired statistical analysis and multivariate logistic regression analysis was performed. Paired data analysis showed significant reduction of dry body weight, BMI and nPCR. Kt/Vtot did not change, eKt/v and hand grip strength measurements were significantly higher in spring 2011. No changes were detected in TSF, serum albumin, NRS-2002 and MUAMA. Serum albumin was shown to be the only predictor of death and of the combined endpoint "death or weight loss of more than 5%". We now screen patients biannually for serum albumin, nPCR, Kt/V, handgrip measurement of the shunt-free arm, dry body weight, age and time since initiation of MHD. © 2015 European Dialysis and Transplant Nurses Association/European Renal Care Association.

Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.).

PubMed

Yang, Cong; Tang, Dengguo; Qu, Jingtao; Zhang, Ling; Zhang, Lei; Chen, Zhengjie; Liu, Jian

2016-11-01

A set of RIL population was used to detect QTL associated with the sizes of eight consecutive leaves, across different environments, and ten QTL clusters were identified as main QTLs. One of the important parameters of the maize leaf architecture that affects light penetration into the canopy, leaf size, has long attracted breeders' attention for optimizing the plant type of maize and for maximizing the grain yield (GY). In this study, we used 253 RIL lines derived from a cross between B73 and SICAU1212 to investigate the leaf widths (LWs), leaf lengths (LLs), and leaf areas (LAs) of eight consecutive leaves of maize below the tassel and GY across different environments and to identify quantitative traits loci (QTLs) controlling the above-mentioned traits, using inclusive interval mapping for single-environment analysis plus a mixed-model-based composite interval mapping for joint analysis. A total of 171 and 159 putative QTLs were detected through these two mapping methods, respectively. Single-environment mapping revealed that 39 stable QTLs explained more than 10 % of the phenotypic variance, and 35 of the 39 QTLs were also detected by joint analysis. In addition, joint analysis showed that nine of the 159 QTLs exhibited significant QTL × environment interaction and 15 significant epistatic interactions were identified. Approximately 47.17 % of the QTLs for leaf architectural traits in joint analysis were concentrated in ten main chromosomal regions, namely, bins 1.07, 2.02, 3.06, 4.09, 5.01, 5.02, 5.03-5.04, 5.07, 6.07, and 8.05. This study should provide a basis for further fine-mapping of these main genetic regions and improvement of maize leaf architecture.

[Detection rate analysis on neurological sign of workers exposed to different concentrations of carbon disulfide].

PubMed

Li, Kuirong; Zhou, Wenhui; Gu, Guizhen; Zhou, Shiyi; Zheng, Yuxin; Yu, Shanfa

2014-10-01

To study the effects of exposed to different concentrations of carbon disulfide on neurological signs of workers. Collection the information of concentration of carbon disulfide in the workplace or workers individuals exposed of a chemical fiber industry from 2004 to 2011, a total of 3 537 workers exposed to carbon disulfide were detected muscle strength and muscle tone, knee reflex, Achilles tendon reflex, trembling limbs, sensory function, and three chatter. Chi-square test was used for statistical analysis on abnormal neurological signs of workers. Eight hours time-weighted average concentration range of workers exposed to carbon disulfide in this chemical fiber industry was 0.2-41.0 mg/m(3), geometric mean was 2.38 mg/m(3). Concentration of carbon disulfide exposure of 1 771 workers was from 0.2 to 2.5 mg/m3( ≤ 2.5 mg/m(3)), 642 workers was 2.6-4.8 mg/m(3) (< 5.0 mg/m(3)), other 1 051 workers was from 5.1 to 41.0 mg/m(3) ( > 5.0 mg/m(3)) in all subjects. The different detection rates of knee reflex were 3.0% (31/1 045), 3.7% (21/574), 4.8% (16/331), 3.3% (10/305), 5.9% (11/187), 6.7% (68/1 022), the different detection rates of Achilles tendon reflex were 2.2% (23/1 045), 3.7% (21/574), 2.7% (9/331), 2.3% (7/305), 2.1% (4/187), 5.6% (57/1 022), the different detection rates of sensory dysfunction were 0.4% (4/1 045), 0.5% (3/574), 0.6% (2/331), 0.0% (0/305), 2.1% (4/187), 1.7% (17/1 022) in different cumulative amount of contact groups ( ≤ 10.0, 10.1-20.0, 20.1-30.0, 30.1-40.0, 40.1-50.0, >50.0 mg/m(3) per year), and the differences were statistically significant (χ(2) = 19.53, 21.27 and 15.89, all P values were <0.01) . Stratified according to age and gender, in addition to the ≤ 25 years group the difference of detection rate analysis on Achilles tendon reflex was statistically significant in the different concentration group (the ratio of on Achilles tendon reflex in the different groups of concentration of carbon disulfide exposure of 2.5, 2.6-5.0, ≥ 5.0 mg/m(3) were 0.4% (2/511), 1.0% (1/98), 2.1% (7/327), χ(2) = 5.59, P = 0.045) , the difference of detection rate analysis on neurological sign was not statistically significant in the different concentration group on the rest of the age and gender groups (P > 0.05). Within the concentration range of the object of study contact actual, different concentrations of carbon disulfide in addition to individual neurological signs of individual ages influential, it has no significant effect on the various signs of nervous system of workers of most age and gender groups, expect the age below the 25 years old group.

REPPER—repeats and their periodicities in fibrous proteins

PubMed Central

Gruber, Markus; Söding, Johannes; Lupas, Andrei N.

2005-01-01

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins. REPPER is available at . PMID:15980460

Scan statistics with local vote for target detection in distributed system

NASA Astrophysics Data System (ADS)

Luo, Junhai; Wu, Qi

2017-12-01

Target detection has occupied a pivotal position in distributed system. Scan statistics, as one of the most efficient detection methods, has been applied to a variety of anomaly detection problems and significantly improves the probability of detection. However, scan statistics cannot achieve the expected performance when the noise intensity is strong, or the signal emitted by the target is weak. The local vote algorithm can also achieve higher target detection rate. After the local vote, the counting rule is always adopted for decision fusion. The counting rule does not use the information about the contiguity of sensors but takes all sensors' data into consideration, which makes the result undesirable. In this paper, we propose a scan statistics with local vote (SSLV) method. This method combines scan statistics with local vote decision. Before scan statistics, each sensor executes local vote decision according to the data of its neighbors and its own. By combining the advantages of both, our method can obtain higher detection rate in low signal-to-noise ratio environment than the scan statistics. After the local vote decision, the distribution of sensors which have detected the target becomes more intensive. To make full use of local vote decision, we introduce a variable-step-parameter for the SSLV. It significantly shortens the scan period especially when the target is absent. Analysis and simulations are presented to demonstrate the performance of our method.

Real-Time Detection of Rupture Development: Earthquake Early Warning Using P Waves From Growing Ruptures

NASA Astrophysics Data System (ADS)

Kodera, Yuki

2018-01-01

Large earthquakes with long rupture durations emit P wave energy throughout the rupture period. Incorporating late-onset P waves into earthquake early warning (EEW) algorithms could contribute to robust predictions of strong ground motion. Here I describe a technique to detect in real time P waves from growing ruptures to improve the timeliness of an EEW algorithm based on seismic wavefield estimation. The proposed P wave detector, which employs a simple polarization analysis, successfully detected P waves from strong motion generation areas of the 2011 Mw 9.0 Tohoku-oki earthquake rupture. An analysis using 23 large (M ≥ 7) events from Japan confirmed that seismic intensity predictions based on the P wave detector significantly increased lead times without appreciably decreasing the prediction accuracy. P waves from growing ruptures, being one of the fastest carriers of information on ongoing rupture development, have the potential to improve the performance of EEW systems.

Water Vapor Uptake of Ultrathin Films of Biologically Derived Nanocrystals: Quantitative Assessment with Quartz Crystal Microbalance and Spectroscopic Ellipsometry.

PubMed

Niinivaara, Elina; Faustini, Marco; Tammelin, Tekla; Kontturi, Eero

2015-11-10

Despite the relevance of water interactions, explicit analysis of vapor adsorption on biologically derived surfaces is often difficult. Here, a system was introduced to study the vapor uptake on a native polysaccharide surface; namely, cellulose nanocrystal (CNC) ultrathin films were examined with a quartz crystal microbalance with dissipation monitoring (QCM-D) and spectroscopic ellipsometry (SE). A significant mass uptake of water vapor by the CNC films was detected using the QCM-D upon increasing relative humidity. In addition, thickness changes proportional to changes in relative humidity were detected using SE. Quantitative analysis of the results attained indicated that in preference to being soaked by water at the point of hydration each individual CNC in the film became enveloped by a 1 nm thick layer of adsorbed water vapor, resulting in the detected thickness response.

The Chandra Source Catalog

NASA Astrophysics Data System (ADS)

Evans, Ian; Primini, Francis A.; Glotfelty, Kenny J.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Hain, Roger; Hall, Diane M.; Harbo, Peter N.; He, Xiang Qun (Helen); Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph B.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Plummer, David A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta L.; Sundheim, Beth A.; Tibbetts, Michael S.; van Stone, David W.; Winkelman, Sherry L.; Zografou, Panagoula

2009-09-01

The first release of the Chandra Source Catalog (CSC) was published in 2009 March, and includes information about 94,676 X-ray sources detected in a subset of public ACIS imaging observations from roughly the first eight years of the Chandra mission. This release of the catalog includes point and compact sources with observed spatial extents <˜30''.The CSC is a general purpose virtual X-ray astrophysics facility that provides access to a carefully selected set of generally useful quantities for individual X-ray sources, and is designed to satisfy the needs of a broad-based group of scientists, including those who may be less familiar with astronomical data analysis in the X-ray regime.The catalog (1) provides access to the best estimates of the X-ray source properties for detected sources, with good scientific fidelity, and directly supports medium sophistication scientific analysis on using the individual source data; (2) facilitates analysis of a wide range of statistical properties for classes of X-ray sources; (3) provides efficient access to calibrated observational data and ancillary data products for individual X-ray sources, so that users can perform detailed further analysis using existing tools; and (4) includes real X-ray sources detected with flux significance greater than a predefined threshold, while maintaining the number of spurious sources at an acceptable level. For each detected X-ray source, the CSC provides commonly tabulated quantities, including source position, extent, multi-band fluxes, hardness ratios, and variability statistics, derived from the observations in which the source is detected. In addition to these traditional catalog elements, for each X-ray source the CSC includes an extensive set of file-based data products that can be manipulated interactively, including source images, event lists, light curves, and spectra from each observation in which a source is detected.

On the Interpretation of the Fermi-GBM Transient Observed in Coincidence with LIGO Gravitational-wave Event GW150914

NASA Astrophysics Data System (ADS)

Connaughton, V.; Burns, E.; Goldstein, A.; Blackburn, L.; Briggs, M. S.; Christensen, N.; Hui, C. M.; Kocevski, D.; Littenberg, T.; McEnery, J. E.; Racusin, J.; Shawhan, P.; Veitch, J.; Wilson-Hodge, C. A.; Bhat, P. N.; Bissaldi, E.; Cleveland, W.; Giles, M. M.; Gibby, M. H.; von Kienlin, A.; Kippen, R. M.; McBreen, S.; Meegan, C. A.; Paciesas, W. S.; Preece, R. D.; Roberts, O. J.; Stanbro, M.; Veres, P.

2018-01-01

The weak transient detected by the Fermi Gamma-ray Burst Monitor (GBM) 0.4 s after GW150914 has generated much speculation regarding its possible association with the black hole binary merger. Investigation of the GBM data by Connaughton et al. revealed a source location consistent with GW150914 and a spectrum consistent with a weak, short gamma-ray burst. Greiner et al. present an alternative technique for fitting background-limited data in the low-count regime, and call into question the spectral analysis and the significance of the detection of GW150914-GBM presented in Connaughton et al. The spectral analysis of Connaughton et al. is not subject to the limitations of the low-count regime noted by Greiner et al. We find Greiner et al. used an inconsistent source position and did not follow the steps taken in Connaughton et al. to mitigate the statistical shortcomings of their software when analyzing this weak event. We use the approach of Greiner et al. to verify that our original spectral analysis is not biased. The detection significance of GW150914-GBM is established empirically, with a false-alarm rate (FAR) of ∼ {10}-4 Hz. A post-trials false-alarm probability (FAP) of 2.2× {10}-3 (2.9σ ) of this transient being associated with GW150914 is based on the proximity in time to the gravitational-wave event of a transient with that FAR. The FAR and the FAP are unaffected by the spectral analysis that is the focus of Greiner et al.

Statistical comparison of pooled nitrogen washout data of various altitude decompression response groups

NASA Technical Reports Server (NTRS)

Edwards, B. F.; Waligora, J. M.; Horrigan, D. J., Jr.

1985-01-01

This analysis was done to determine whether various decompression response groups could be characterized by the pooled nitrogen (N2) washout profiles of the group members, pooling individual washout profiles provided a smooth time dependent function of means representative of the decompression response group. No statistically significant differences were detected. The statistical comparisons of the profiles were performed by means of univariate weighted t-test at each 5 minute profile point, and with levels of significance of 5 and 10 percent. The estimated powers of the tests (i.e., probabilities) to detect the observed differences in the pooled profiles were of the order of 8 to 30 percent.

Assessing Aircraft Supply Air to Recommend Compounds for Timely Warning of Contamination

NASA Astrophysics Data System (ADS)

Fox, Richard B.

Taking aircraft out of service for even one day to correct fume-in-cabin events can cost the industry roughly $630 million per year in lost revenue. The quantitative correlation study investigated quantitative relationships between measured concentrations of contaminants in bleed air and probability of odor detectability. Data were collected from 94 aircraft engine and auxiliary power unit (APU) bleed air tests from an archival data set between 1997 and 2011, and no relationships were found. Pearson correlation was followed by regression analysis for individual contaminants. Significant relationships of concentrations of compounds in bleed air to probability of odor detectability were found (p<0.05), as well as between compound concentration and probability of sensory irritancy detectability. Study results may be useful to establish early warning levels. Predictive trend monitoring, a method to identify potential pending failure modes within a mechanical system, may influence scheduled down-time for maintenance as a planned event, rather than repair after a mechanical failure and thereby reduce operational costs associated with odor-in-cabin events. Twenty compounds (independent variables) were found statistically significant as related to probability of odor detectability (dependent variable 1). Seventeen compounds (independent variables) were found statistically significant as related to probability of sensory irritancy detectability (dependent variable 2). Additional research was recommended to further investigate relationships between concentrations of contaminants and probability of odor detectability or probability of sensory irritancy detectability for all turbine oil brands. Further research on implementation of predictive trend monitoring may be warranted to demonstrate how the monitoring process might be applied to in-flight application.

DNA Extraction Method Affects the Detection of a Fungal Pathogen in Formalin-Fixed Specimens Using qPCR.

PubMed

Adams, Andrea J; LaBonte, John P; Ball, Morgan L; Richards-Hrdlicka, Kathryn L; Toothman, Mary H; Briggs, Cheryl J

2015-01-01

Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80-90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.

Opportunities and Challenges for Pancreatic Circulating Tumor Cells.

PubMed

Nagrath, Sunitha; Jack, Rhonda M; Sahai, Vaibhav; Simeone, Diane M

2016-09-01

Sensitive and reproducible platforms have been developed for detection, isolation, and enrichment of circulating tumor cells (CTCs)-rare cells that enter the blood from solid tumors, including those of the breast, prostate gland, lung, pancreas, and colon. These might be used as biomarkers in diagnosis or determination of prognosis. CTCs are no longer simply detected and quantified; they are now used in ex vivo studies of anticancer agents and early detection. We review what we have recently learned about CTCs from pancreatic tumors, describing advances in their isolation and analysis and challenges to their clinical utility. We summarize technologies used to isolate CTCs from blood samples of patients with pancreatic cancer, including immunoaffinity and label-free physical attribute-based capture. We explain methods of CTC analysis and how findings from these studies might be used to detect cancer at earlier stages, monitor disease progression, and determine prognosis. We review studies that have expanded CTCs for testing of anticancer agents and how these approaches might be used to personalize treatment. Advances in the detection, isolation, and analysis of CTCs have increased our understanding of the dissemination and progression of pancreatic cancer. However, standardization of methodologies and prospective studies are needed for this emerging technology to have a significant effect on clinical care. Copyright © 2016 AGA Institute. Published by Elsevier Inc. All rights reserved.

Real-time on-line space research laboratory environment monitoring with off-line trend and prediction analysis

NASA Astrophysics Data System (ADS)

Jules, Kenol; Lin, Paul P.

2007-06-01

With the International Space Station currently operational, a significant amount of acceleration data is being down-linked, processed and analyzed daily on the ground on a continuous basis for the space station reduced gravity environment characterization, the vehicle design requirements verification and science data collection. To help understand the impact of the unique spacecraft environment on the science data, an artificial intelligence monitoring system was developed, which detects in near real time any change in the reduced gravity environment susceptible to affect the on-going experiments. Using a dynamic graphical display, the monitoring system allows science teams, at any time and any location, to see the active vibration disturbances, such as pumps, fans, compressor, crew exercise, re-boost and extra-vehicular activities that might impact the reduced gravity environment the experiments are exposed to. The monitoring system can detect both known and unknown vibratory disturbance activities. It can also perform trend analysis and prediction by analyzing past data over many increments (an increment usually lasts 6 months) collected onboard the station for selected disturbances. This feature can be used to monitor the health of onboard mechanical systems to detect and prevent potential systems failures. The monitoring system has two operating modes: online and offline. Both near real-time on-line vibratory disturbance detection and off-line detection and trend analysis are discussed in this paper.

[Clinical value of genome-wide high resolution chromosomal microarray analysis in etiological study of fetuses with congenital heart defects].

PubMed

Wu, Xiaoli; Fu, Fang; Li, Ru; Pan, Min; Han, Jin; Zhen, Li; Yang, Xin; Zhang, Yongling; Li, Fatao; Liao, Can

2014-12-01

To explore the clinical value of genome-wide high resolution chromosomal microarray analysis (CMA) in etiological study of fetuses with congenital heart disease (CHD) diagnosed by fetal echocardiography. A total of 176 fetuses diagnosed CHD by fetal echocardiography were analyzed, and invasive prenatal diagnosis was performed at Guangzhou Women and Children's Medical Center from January 2012 to January 2014. Among them, 158 fetuses were proved to have normal karyotype, and 88 fetuses (50.0%, 88/176) underwent CMA testing. The parental blood specimens were also collected for assisting the diagnosis of variants of uncertain clinical significance (VOUS). The 88 fetuses were divided into two groups: isolated CHD (n = 68) and CHD with extra-cardiac structural abnormalities (n = 20). The phenotypes of the two groups were subclassified. Copy number variations (CNV) were classified as benign CNV, pathogenic CNV (pCNV) or VOUS. (1) 58 fetuses (66%, 58/88) were with simple CHD and 30 fetuses were with complicated CHD (34%, 30/88). In the 45 fetuses with isolated and simple CHD, the pCNV detection rate was 11% (5/45). In the 23 fetuses with isolated and complicated CHD, the pCNV detection rate was 17% (4/23). In the 13 fetuses with simple CHD and extra-cardiac structural abnormalities, the pCNV detection rate was 5/13. In the 7 fetuses with complicated CHD and extra-cardiac structural abnormalities, the pCNV detection rate was 0. (2) The total detection rate for pCNV detection was 16% (14/88) in the 88 fetuses. The pCNV detection rates for isolated CHD and CHD with extra-cardiac structural abnormalities were 13% (9/68) and 25% (5/20), respectively (P > 0.05). The pCNV detection rates for simple and complicated CHD were 17% (10/58) and 13% (4/30), respectively (P > 0.05). (3) Eighteen fetuses (10.2%, 18/176) had abnormal karyotype results. (4) CMA test was performed in 88 fetuses. CNV detected in 8 fetuses were classified as VOUS initially. After parental microarray analysis, CNV in 5 fetuses were inherited and interpreted as benign. CNV in the other 3 fetuses (3%, 3/88) were remained unknown significance. CNV in 14 fetuses (16% ) were interpreted as pCNV. In fetuses with CHD and normal karyotype, the application of CMA could increase the detection rate of pCNV. Genome-wide CMA could be used as a regular tool in the prenatal diagnosis of fetuses with CHD and normal karyotype. This technology may benefit evaluation of fetal prognosis in prenatal genetic counselling.

BAG3 and HIF-1 α coexpression detected by immunohistochemistry correlated with prognosis in hepatocellular carcinoma after liver transplantation.

PubMed

Xiao, Heng; Tong, Rongliang; Cheng, Shaobing; Lv, Zhen; Ding, Chaofeng; Du, Chengli; Xie, Haiyang; Zhou, Lin; Wu, Jian; Zheng, Shusen

2014-01-01

The objective is to determine the effects of BAG3 and HIF-1 α expression on the prognosis of HCC patients after liver transplantation. Samples from 31 patients with HCC receiving liver transplantation were collected for this study. The immunohistochemistry was used to detect the expression of BAG3 and HIF-1 α of HCC samples. According to the immunohistochemistry results, BAG3 and HIF-1 α staining were significantly associated with tumor TNM stage (P = 0.004, P = 0.012). A significant association between high BAG3/HIF-1 α levels and a shorter overall survival was detected, so as the combined BAG3 and HIF-1 α analysis. The results suggested that the expression level of BAG3 and HIF-1 α is efficient prognostic parameters in patients with HCC after liver transplantation.

Phage-display library biopanning and bioinformatic analysis yielded a high-affinity peptide to inflamed vascular endothelium both in vitro and in vivo.

PubMed

Yang, Min; Liu, Chenwu; Niu, Maochang; Hu, Yonghe; Guo, Mingyang; Zhang, Jun; Luo, Yong; Yuan, Weili; Yang, Mei; Yun, Mingdong; Guo, Linling; Yan, Jiao; Liu, Defang; Liu, Jinghua; Jiang, Yong

2014-01-28

Vascular inflammation is considered the primary pathological condition occurring in many chronic diseases. To detect the inflamed endothelium via imaging analysis or guide the drug to target lesions is therefore important for early diagnosis and treatment of vascular inflammatory diseases. In this study, we obtained a novel peptide NTTTH through high throughout biopanning and bioinformatic analysis. In vitro studies indicated that NTTTH homologs could especially target inflamed vascular endothelial cells, as imaging quantitative analysis indicated that the mean of integrated optical density (MIOD) and mean of stained area (MSA) were significantly higher versus control (P<0.05). In vivo studies showed that, after intravenous injection of enhanced green fluorescent protein (EGFP)-labeled NTTTH homologs into the lipopolysaccharide (LPS)-inflamed mice for 30min, NTTTH homologs were distributed in highly vascularized and inflamed organs like liver and kidney. As a control, little fluorescence could be detected in mice injected with EGFP alone. Cryosection showed that NTTTH homologs especially targeted inflamed vasculatures but not normal ones. We did not detect fluorescence signal in either normal or inflamed mice which were injected with EGFP alone. The results suggested the role of NTTTH homologs in guiding the targeted binding of EGFP to inflamed vasculature and the potential usage for imaging detection and drug delivery. Copyright © 2013 Elsevier B.V. All rights reserved.

Differential diagnosis of cardiovascular diseases and T-wave alternans

NASA Astrophysics Data System (ADS)

Ramasamy, Mouli; Varadan, Vijay K.

2016-04-01

T wave alternans (TWA) is the variation of the T-wave in electrocardiogram that is observed between periodic beats. TWA is one of the important precursors used to diagnose sudden cardiac death (SCD). Several clinical studies have tried to determine the significance of using TWA analysis to detect abnormalities that may lead to Ventricular Arrhythmias, as well as establish metrics to perform risk stratification for cardiovascular patients with prior cardiac episodes. The statistical significance of TWA in predicting ventricular arrhythmias has been established in patients across several diagnoses. Studies have also shown the significance of the predictive value of TWA analysis in post myocardial infarction patients, risk of SCD, congestive heart failure, ischemic cardiomyopathy, and Chagas disease.

Power spectrum weighted edge analysis for straight edge detection in images

NASA Astrophysics Data System (ADS)

Karvir, Hrishikesh V.; Skipper, Julie A.

2007-04-01

Most man-made objects provide characteristic straight line edges and, therefore, edge extraction is a commonly used target detection tool. However, noisy images often yield broken edges that lead to missed detections, and extraneous edges that may contribute to false target detections. We present a sliding-block approach for target detection using weighted power spectral analysis. In general, straight line edges appearing at a given frequency are represented as a peak in the Fourier domain at a radius corresponding to that frequency, and a direction corresponding to the orientation of the edges in the spatial domain. Knowing the edge width and spacing between the edges, a band-pass filter is designed to extract the Fourier peaks corresponding to the target edges and suppress image noise. These peaks are then detected by amplitude thresholding. The frequency band width and the subsequent spatial filter mask size are variable parameters to facilitate detection of target objects of different sizes under known imaging geometries. Many military objects, such as trucks, tanks and missile launchers, produce definite signatures with parallel lines and the algorithm proves to be ideal for detecting such objects. Moreover, shadow-casting objects generally provide sharp edges and are readily detected. The block operation procedure offers advantages of significant reduction in noise influence, improved edge detection, faster processing speed and versatility to detect diverse objects of different sizes in the image. With Scud missile launcher replicas as target objects, the method has been successfully tested on terrain board test images under different backgrounds, illumination and imaging geometries with cameras of differing spatial resolution and bit-depth.

A morphometric analysis of the superior cervical ganglion and its surrounding structures.

PubMed

Fazliogullari, Zeliha; Kilic, Cenk; Karabulut, Ahmet Kagan; Yazar, Fatih

2016-04-01

The aim of this cadaveric study was to detect the superior cervical ganglion (SCG) in a topographic manner according to vertebrae and to determine the relationship between the vertebrae, mandibular angle and longus colli muscle through morphometric analysis. The present study was performed on 40 SCG of 20 human cadavers (16 males, 4 females). The level of the SCG was determined based on the vertebrae. Ganglion length, width and thickness were detected. Distance to the adjacent vertebra, the mandibular angle and medial side of the longus colli muscle were measured. The results were evaluated statistically. The SCG existing in all cadavers was detected at the C2 vertebra level in 34 cadavers and at the C3 vertebra level in 6 cadavers. The average length, width and thickness of the SCG were 15.18 ± 1.12, 4.62 ± 0.25, and 1.83 ± 0.10 mm, respectively. No statistically significant difference was detected in terms of the distances between the ganglion and anterior tubercle of transverse processes of the vertebrae as well as the mandibular angle on either side. The distance between the SCG and the medial edge of the longus colli muscle was significantly greater on the left side in both men (p < 0.001) and women (p < 0.01). Recognition of morphometric characteristics of the SCG and detection of its location according to adjacent formations may serve as a guide for nerve blockage studies and help surgeons to preserve the ganglion in both anterior and anterolateral cervical approaches.

Comparison of formant detection methods used in speech processing applications

NASA Astrophysics Data System (ADS)

Belean, Bogdan

2013-11-01

The paper describes time frequency representations of speech signal together with the formant significance in speech processing applications. Speech formants can be used in emotion recognition, sex discrimination or diagnosing different neurological diseases. Taking into account the various applications of formant detection in speech signal, two methods for detecting formants are presented. First, the poles resulted after a complex analysis of LPC coefficients are used for formants detection. The second approach uses the Kalman filter for formant prediction along the speech signal. Results are presented for both approaches on real life speech spectrograms. A comparison regarding the features of the proposed methods is also performed, in order to establish which method is more suitable in case of different speech processing applications.

The Influence of Assay Design, Blinding, and Gymnema sylvestre on Sucrose Detection by Humans.

PubMed

Aleman, Max G; Marconi, Lauren J; Nguyen, Nam H; Park, Jae M; Patino, Maria M; Wang, Yuchi; Watkins, Celeste S; Shelley, Chris

2016-01-01

The detection and grading of tastes corresponding to different taste modalities can be tested in engaging laboratory sessions using students themselves as test subjects. This article describes a series of experiments in which data pertaining to the detection of salty and sweet tastes are obtained, and the ability of the herb Gymnema sylvestre to disrupt the detection of sucrose is quantified. The effects of blinding and different assay designs on EC50 estimation are also investigated. The data obtained allow for substantial data analysis, including non-linear regression using fixed and free parameters to quantify dose-response relationships, and the use of often under-utilized permutation tests to determine significant differences when the underlying data display heteroscedasticity.

The Influence of Assay Design, Blinding, and Gymnema sylvestre on Sucrose Detection by Humans

PubMed Central

Aleman, Max G.; Marconi, Lauren J.; Nguyen, Nam H.; Park, Jae M.; Patino, Maria M.; Wang, Yuchi; Watkins, Celeste S.; Shelley, Chris

2016-01-01

The detection and grading of tastes corresponding to different taste modalities can be tested in engaging laboratory sessions using students themselves as test subjects. This article describes a series of experiments in which data pertaining to the detection of salty and sweet tastes are obtained, and the ability of the herb Gymnema sylvestre to disrupt the detection of sucrose is quantified. The effects of blinding and different assay designs on EC50 estimation are also investigated. The data obtained allow for substantial data analysis, including non-linear regression using fixed and free parameters to quantify dose-response relationships, and the use of often under-utilized permutation tests to determine significant differences when the underlying data display heteroscedasticity. PMID:27980466

A NEW SYSTEM TO MONITOR DATA ANALYSES AND RESULTS OF PHYSICS DATA VALIDATION BETWEEN PULSES AT DIII-D

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

FLANAGAN,A; SCHACHTER,J.M; SCHISSEL,D.P

2003-02-01

A Data Analysis Monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility (http://nssrv1.gat.com:8000/dam). The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded thus increasing the efficiency of experimental time. An example of a consistency check is comparing the experimentally measured neutron rate and the expected neutron emission, RDD0D. A significant difference between these two values could indicate a problem with one ormore » more diagnostics, or the presence of unanticipated phenomena in the plasma. This new system also tracks the progress of MDSplus dispatched data analysis software and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, CLIPS to implement expert system logic, and displays its results to multiple web clients via HTML. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse.« less

System to monitor data analyses and results of physics data validation between pulses at DIII-D

NASA Astrophysics Data System (ADS)

Flanagan, S.; Schachter, J. M.; Schissel, D. P.

2004-06-01

A data analysis monitoring (DAM) system has been developed to monitor between pulse physics analysis at the DIII-D National Fusion Facility (http://nssrv1.gat.com:8000/dam). The system allows for rapid detection of discrepancies in diagnostic measurements or the results from physics analysis codes. This enables problems to be detected and possibly fixed between pulses as opposed to after the experimental run has concluded, thus increasing the efficiency of experimental time. An example of a consistency check is comparing the experimentally measured neutron rate and the expected neutron emission, RDD0D. A significant difference between these two values could indicate a problem with one or more diagnostics, or the presence of unanticipated phenomena in the plasma. This system also tracks the progress of MDSplus dispatched data analysis software and the loading of analyzed data into MDSplus. DAM uses a Java Servlet to receive messages, C Language Integrated Production System to implement expert system logic, and displays its results to multiple web clients via Hypertext Markup Language. If an error is detected by DAM, users can view more detailed information so that steps can be taken to eliminate the error for the next pulse.

Cocaine use during pregnancy assessed by hair analysis in a Canary Islands cohort

PubMed Central

2012-01-01

Background Drug use during pregnancy is difficult to ascertain, and maternal reports are likely to be inaccurate. The aim of this study was to estimate the prevalence of illicit drug use among pregnant women by using maternal hair analysis. Methods A toxicological analysis of hair was used to detect chronic recreational drug use during pregnancy. In 2007, 347 mother-infant dyads were included from the Hospital La Candelaria, Santa Cruz de Tenerife, Canary Islands (Spain). Data on socioeconomic characteristics and on substance misuse during pregnancy were collected using a structured questionnaire. Drugs of abuse: opiates, cocaine, cannabinoids and amphetamines were detected in maternal hair by immunoassay followed by gas chromatography-mass spectrometry for confirmation and quantitation. Results Hair analysis revealed 2.6% positivity for cocaine and its metabolites. Use of cocaine during pregnancy was associated with unusual behaviour with potentially harmful effects on the baby. Conclusions The results of the study demonstrate significant cocaine use by pregnant women in Canary Islands. The data should be used for the purpose of preventive health and policy strategies aimed to detect and possibly to avoid in the future prenatal exposure to drugs of abuse. PMID:22230295

Experimental strain modal analysis for beam-like structure by using distributed fiber optics and its damage detection

NASA Astrophysics Data System (ADS)

Cheng, Liangliang; Busca, Giorgio; Cigada, Alfredo

2017-07-01

Modal analysis is commonly considered as an effective tool to obtain the intrinsic characteristics of structures including natural frequencies, modal damping ratios, and mode shapes, which are significant indicators for monitoring the health status of engineering structures. The complex mode indicator function (CMIF) can be regarded as an effective numerical tool to perform modal analysis. In this paper, experimental strain modal analysis based on the CMIF has been introduced. Moreover, a distributed fiber-optic sensor, as a dense measuring device, has been applied to acquire strain data along a beam surface. Thanks to the dense spatial resolution of the distributed fiber optics, more detailed mode shapes could be obtained. In order to test the effectiveness of the method, a mass lump—considered as a linear damage component—has been attached to the surface of the beam, and damage detection based on strain mode shape has been carried out. The results manifest that strain modal parameters can be estimated effectively by utilizing the CMIF based on the corresponding simulations and experiments. Furthermore, damage detection based on strain mode shapes benefits from the accuracy of strain mode shape recognition and the excellent performance of the distributed fiber optics.

Detection and monitoring of anaerobic rumen fungi using an ARISA method.

PubMed

Denman, S E; Nicholson, M J; Brookman, J L; Theodorou, M K; McSweeney, C S

2008-12-01

To develop an automated ribosomal intergenic spacer region analysis (ARISA) method for the detection of anaerobic rumen fungi and also to demonstrate utility of the technique to monitor colonization and persistence of fungi, and diet-induced changes in community structure. The method could discriminate between three genera of anaerobic rumen fungal isolates, representing Orpinomyces, Piromyces and Neocallimastix species. Changes in anaerobic fungal composition were observed between animals fed a high-fibre diet compared with a grain-based diet. ARISA analysis of rumen samples from animals on grain showed a decrease in fungal diversity with a dominance of Orpinomyces and Piromyces spp. Clustering analysis of ARISA profile patterns grouped animals based on diet. A single strain of Orpinomyces was dosed into a cow and was detectable within the rumen fungal population for several weeks afterwards. The ARISA technique was capable of discriminating between pure cultures at the genus level. Diet composition has a significant influence on the diversity of anaerobic fungi in the rumen and the method can be used to monitor introduced strains. Through the use of ARISA analysis, a better understanding of the effect of diets on rumen anaerobic fungi populations is provided.

Quantitative analysis of sitagliptin using the (19)F-NMR method: a universal technique for fluorinated compound detection.

PubMed

Zhang, Fen-Fen; Jiang, Meng-Hong; Sun, Lin-Lin; Zheng, Feng; Dong, Lei; Shah, Vishva; Shen, Wen-Bin; Ding, Ya

2015-01-07

To expand the application scope of nuclear magnetic resonance (NMR) technology in quantitative analysis of pharmaceutical ingredients, (19)F nuclear magnetic resonance ((19)F-NMR) spectroscopy has been employed as a simple, rapid, and reproducible approach for the detection of a fluorine-containing model drug, sitagliptin phosphate monohydrate (STG). ciprofloxacin (Cipro) has been used as the internal standard (IS). Influential factors, including the relaxation delay time (d1) and pulse angle, impacting the accuracy and precision of spectral data are systematically optimized. Method validation has been carried out in terms of precision and intermediate precision, linearity, limit of detection (LOD) and limit of quantification (LOQ), robustness, and stability. To validate the reliability and feasibility of the (19)F-NMR technology in quantitative analysis of pharmaceutical analytes, the assay result has been compared with that of (1)H-NMR. The statistical F-test and student t-test at 95% confidence level indicate that there is no significant difference between these two methods. Due to the advantages of (19)F-NMR, such as higher resolution and suitability for biological samples, it can be used as a universal technology for the quantitative analysis of other fluorine-containing pharmaceuticals and analytes.

Meta-Analysis of Genome-Wide Scans Provides Evidence for Sex- and Site-Specific Regulation of Bone Mass

PubMed Central

Sham, Pak C; Zintzaras, Elias; Lewis, Cathryn M; Deng, Hong-Wen; Econs, Michael J; Karasik, David; Devoto, Marcella; Kammerer, Candace M; Spector, Tim; Andrew, Toby; Cupples, L Adrienne; Duncan, Emma L; Foroud, Tatiana; Kiel, Douglas P; Koller, Daniel; Langdahl, Bente; Mitchell, Braxton D; Peacock, Munro; Recker, Robert; Shen, Hui; Sol-Church, Katia; Spotila, Loretta D; Uitterlinden, Andre G; Wilson, Scott G; Kung, Annie WC; Ralston, Stuart H

2014-01-01

Several genome-wide scans have been performed to detect loci that regulate BMD, but these have yielded inconsistent results, with limited replication of linkage peaks in different studies. In an effort to improve statistical power for detection of these loci, we performed a meta-analysis of genome-wide scans in which spine or hip BMD were studied. Evidence was gained to suggest that several chromosomal loci regulate BMD in a site-specific and sex-specific manner. Introduction BMD is a heritable trait and an important predictor of osteoporotic fracture risk. Several genome-wide scans have been performed in an attempt to detect loci that regulate BMD, but there has been limited replication of linkage peaks between studies. In an attempt to resolve these inconsistencies, we conducted a collaborative meta-analysis of genome-wide linkage scans in which femoral neck BMD (FN-BMD) or lumbar spine BMD (LS-BMD) had been studied. Materials and Methods Data were accumulated from nine genome-wide scans involving 11,842 subjects. Data were analyzed separately for LS-BMD and FN-BMD and by sex. For each study, genomic bins of 30 cM were defined and ranked according to the maximum LOD score they contained. While various densitometers were used in different studies, the ranking approach that we used means that the results are not confounded by the fact that different measurement devices were used. Significance for high average rank and heterogeneity was obtained through Monte Carlo testing. Results For LS-BMD, the quantitative trait locus (QTL) with greatest significance was on chromosome 1p13.3-q23.3 (p = 0.004), but this exhibited high heterogeneity and the effect was specific for women. Other significant LS-BMD QTLs were on chromosomes 12q24.31-qter, 3p25.3-p22.1, 11p12-q13.3, and 1q32-q42.3, including one on 18p11-q12.3 that had not been detected by individual studies. For FN-BMD, the strongest QTL was on chromosome 9q31.1-q33.3 (p = 0.002). Other significant QTLs were identified on chromosomes 17p12-q21.33, 14q13.1-q24.1, 9q21.32-q31.1, and 5q14.3-q23.2. There was no correlation in average ranks of bins between men and women and the loci that regulated BMD in men and women and at different sites were largely distinct. Conclusions This large-scale meta-analysis provided evidence for replication of several QTLs identified in previous studies and also identified a QTL on chromosome 18p11-q12.3, which had not been detected by individual studies. However, despite the large sample size, none of the individual loci identified reached genome-wide significance. PMID:17228994

[Prognostic value of chosen parameters of mechanical and bioelectrical uterine activity in prediction of threatening preterm labour].

PubMed

Zietek, Jerzy; Sikora, Jerzy; Horoba, Krzysztof; Matonia, Adam; Jezewski, Janusz; Magnucki, Jacek; Kobielska, Lucyna

2009-03-01

To record and analyse bioelectrical activity of the uterine muscle in the course of physiological pregnancy, labour and threatening premature labour; to define which parameters from the analysis of both electrohysterogram and mechanical activity signal allow us to predict threatening premature labour. Material comprised 62 pregnant women: Group I--27 patients in their first physiological pregnancy, Group II--21 patients in their first pregnancy with symptoms of threatening premature labour, and Group III--14 patients in the first labour period. The on-line analysis of the mechanical (TOCO) and electrical (EHG) contraction activity relied on determination of quantitative parameters of detected uterine contractions. The obtained statistical results demonstrated a possibility to differentiate between Group I and II through the amplitude and contraction area for EHG signal, and only the contraction amplitude for TOCO signal. Additionally, significant differentiating parameters for electrohysterogram are: contraction power and its median frequency. Analyzing Group I and III, significant differences were noted for contraction amplitude and area obtained both from EHG and TOCO signals. Similarly, the contraction power (from EHG) enables us to assign the contractions either to records from Group I or to labour type. There was no significant difference noted between Group II and III. Identification of pregnant women at risk of premature labour should lead to their inclusion in rigorous perinatal surveillance. This requires novel, more sensitive methods that are able to detect early symptoms of the uterine contraction activity increase. Electrohysterography provides complete information on principles of bioelectrical uterine activity. Quantitative parameters of EHG analysis enable the detection of records (contractions) with the symptoms of premature uterine contraction activity.

The role of synovial fluid analysis in the detection of periprosthetic hip and knee infections: a systematic review and meta-analysis.

PubMed

De Fine, Marcello; Giavaresi, Gianluca; Fini, Milena; Illuminati, Andrea; Terrando, Silvio; Pignatti, Giovanni

2018-05-01

This study tried to ascertain (1) the accuracy of synovial fluid white blood cell count and polymorphonucleate percentage in the diagnosis of periprosthetic hip and knee infections, (2) which test yielded superior test performance, and (3) the influence on diagnostic accuracy of study characteristics such as patient number, study design, study level, anatomic site, and threshold value. A systematic search was conducted including papers assessing more effective cutoffs for synovial fluid tests, having comparative design, evaluating an exclusive cohort of hip or knee prostheses, including a clear definition of infected cases, and reporting sufficient data for the calculation of true-positive, false-positive, false-negative, and true-negative. A total of 375 articles were collected and, given the inclusion criteria, ten manuscripts were included. These studies assessed 1155 hip prostheses (276 infected cases) and 1235 knee prostheses (401 infected cases). The specificity of synovial fluid white blood cell count was significantly increased by using the threshold value ≥ 3000 cell/μL (p = 0.006); the sensitivity of polymorphonucleate percentage was significantly higher in detecting knee infections (p = 0.034). Both tests had a high specificity and sensitivity in detecting periprosthetic joint infections, and no clear superiority of one over the other existed. Furthermore, cutoff and anatomic site significantly influenced synovial fluid white blood cell count and polymorphonucleate percentage, respectively. Synovial fluid analysis is adequate in differentiating patients with periprosthetic hip and knee infections. Our data confirms international guidelines suggesting the use of 3000 cell/μL as cutoff threshold for synovial fluid white blood cell count. Since an anatomic site effect has been demonstrated, the goal of future studies will be to identify different cutoffs for hip and knee prostheses.

Cluster analysis of fasciolosis in dairy cow herds in Munster province of Ireland and detection of major climatic and environmental predictors of the exposure risk.

PubMed

Selemetas, Nikolaos; Phelan, Paul; O'Kiely, Padraig; de Waal, Theo

2015-03-19

Fasciolosis caused by Fasciola hepatica is a widespread parasitic disease in cattle farms. The aim of this study was to detect clusters of fasciolosis in dairy cow herds in Munster Province, Ireland and to identify significant climatic and environmental predictors of the exposure risk. In total, 1,292 dairy herds across Munster was sampled in September 2012 providing a single bulk tank milk (BTM) sample. The analysis of samples by an in-house antibody-detection enzyme-linked immunosorbent assay (ELISA), showed that 65% of the dairy herds (n = 842) had been exposed to F. hepatica. Using the Getis-Ord Gi* statistic, 16 high-risk and 24 low-risk (P <0.01) clusters of fasciolosis were identified. The spatial distribution of high-risk clusters was more dispersed and mainly located in the northern and western regions of Munster compared to the low-risk clusters that were mostly concentrated in the southern and eastern regions. The most significant classes of variables that could reflect the difference between high-risk and low-risk clusters were the total number of wet-days and rain-days, rainfall, the normalized difference vegetation index (NDVI), temperature and soil type. There was a bigger proportion of well-drained soils among the low-risk clusters, whereas poorly drained soils were more common among the high-risk clusters. These results stress the role of precipitation, grazing, temperature and drainage on the life cycle of F. hepatica in the temperate Irish climate. The findings of this study highlight the importance of cluster analysis for identifying significant differences in climatic and environmental variables between high-risk and low-risk clusters of fasciolosis in Irish dairy herds.

Evaluation of MMP-9 and MMP-2 and their suppressor TIMP-1 and TIMP-2 in adenocarcinoma of esophagogastric junction.

PubMed

Lu, Xiaofei; Duan, Lingling; Xie, Hongqin; Lu, Xiaoxia; Lu, Daolin; Lu, Daopeng; Jiang, Nan; Chen, Yuxin

2016-01-01

Adenocarcinoma of esophagogastric junction (AEG) is a lethal malignancy featured with early metastasis, poor prognosis, and few treatment options. Matrix metalloproteinase (MMP) and metalloproteinase suppressor (TIMP) have been considered to be associated with cancer invasion and metastasis. In our study, we evaluated expressions of MMP-9, MMP-2, TIMP-1, and TIMP-2 in AEG and their correlation with clinicopathological parameters and the overall survival rate. Expressions of MMP-9, MMP-2, TIMP-1, and TIMP-2 in specimens from 120 AEGs were detected by immunohistochemistry. The correlations between expressions of these four proteins and clinicopathological characters were analyzed by chi-square test. Moreover, the prognostic value of these four biomarkers was evaluated by univariate analysis with Kaplan-Meier method and multivariate analysis with Cox regression model. The positive expression rate of MMP-9, MMP-2, TIMP-1, and TIMP-2 was 65%, 53%, 70%, and 49%, respectively, in the detected 120 AEG samples. MMP-9 was significantly associated with poorly histological differentiation (P=0.001), lymph node metastasis (P=0.007), and UICC stage (P=0.008). TIMP-1 showed significantly reversed correlations with histological differentiation (P=0.001), lymph node metastasis (P=0.007), and Union for International Cancer Control stage (P=0.008). Univariate analysis revealed that lymph node metastasis (P=0.002), depth of invasion (P=0.050), and MMP-9+/TIMP-1 phonotype (P<0.001) were significantly associated with the overall survival rate. Multivariate analyses demonstrated that MMP-9+/TIMP-1-phenotype was an independent prognostic factor in AEGs. Detection of MMP-9 and TIMP-1 expression allows stratification of AEG patients into different survival categories and can be useful for precise individual evaluation and survival prediction.

A phantom-based JAFROC observer study of two CT reconstruction methods: the search for optimisation of lesion detection and effective dose

NASA Astrophysics Data System (ADS)

Thompson, John D.; Chakraborty, Dev P.; Szczepura, Katy; Vamvakas, Ioannis; Tootell, Andrew; Manning, David J.; Hogg, Peter

2015-03-01

Purpose: To investigate the dose saving potential of iterative reconstruction (IR) in a computed tomography (CT) examination of the thorax. Materials and Methods: An anthropomorphic chest phantom containing various configurations of simulated lesions (5, 8, 10 and 12mm; +100, -630 and -800 Hounsfield Units, HU) was imaged on a modern CT system over a tube current range (20, 40, 60 and 80mA). Images were reconstructed with (IR) and filtered back projection (FBP). An ATOM 701D (CIRS, Norfolk, VA) dosimetry phantom was used to measure organ dose. Effective dose was calculated. Eleven observers (15.11+/-8.75 years of experience) completed a free response study, localizing lesions in 544 single CT image slices. A modified jackknife alternative free-response receiver operating characteristic (JAFROC) analysis was completed to look for a significant effect of two factors: reconstruction method and tube current. Alpha was set at 0.05 to control the Type I error in this study. Results: For modified JAFROC analysis of reconstruction method there was no statistically significant difference in lesion detection performance between FBP and IR when figures-of-merit were averaged over tube current (F(1,10)=0.08, p = 0.789). For tube current analysis, significant differences were revealed between multiple pairs of tube current settings (F(3,10) = 16.96, p<0.001) when averaged over image reconstruction method. Conclusion: The free-response study suggests that lesion detection can be optimized at 40mA in this phantom model, a measured effective dose of 0.97mSv. In high-contrast regions the diagnostic value of IR, compared to FBP, is less clear.

Quantitative Assessment of the Influence of Cytochrome P450 1A2 Gene Polymorphism and Colorectal Cancer Risk

PubMed Central

Rewuti, Abudouaini; Ma, Yu-Shui; Wang, Xiao-Feng; Xia, Qing; Fu, Da; Han, Yu-Song

2013-01-01

Cytochrome P450 1A2 (CYP1A2) encodes a member of the cytochrome P450 superfamily of enzymes, which play a central role in activating and detoxifying many carcinogens and endogenous compounds thought to be involved in the development of colorectal cancer (CRC). The CYP1A2*C (rs2069514) and CYP1A2*F (rs762551) polymorphism are two of the most commonly studied polymorphisms of the gene for their association with risk of CRC, but the results are conflicting. To derive a more precise estimation of the relationship between CYP1A2 and genetic risk of CRC, we performed a comprehensive meta-analysis which included 7088 cases and 7568 controls from 12 published case-control studies. In a combined analysis, the summary per-allele odds ratio for CRC was 0.91 (95% CI: 0.83–1.00, P = 0.04), and 0.91 (95% CI: 0.68–1.22, P = 0.53), for CYP1A2 *F and *C allele, respectively. In the subgroup analysis by ethnicity, significant associations were found in Asians for CYP1A2*F and CYP1A2*C, while no significant associations were detected among Caucasian populations. Similar results were also observed using dominant genetic model. Potential sources of heterogeneity were explored by subgroup analysis and meta-regression. No significant heterogeneity was detected in most of comparisons. This meta-analysis suggests that the CYP1A2 *F and *C polymorphism is a protective factor against CRC among Asians. PMID:23951174

Strain-Encoded Cardiac Magnetic Resonance Imaging as an Adjunct for Dobutamine Stress Testing. Incremental Value to Conventional Wall Motion Analysis

PubMed Central

Korosoglou, Grigorios; Lossnitzer, Dirk; Schellberg, Dieter; Lewien, Antje; Wochele, Angela; Schaeufele, Tim; Neizel, Mirja; Steen, Henning; Giannitsis, Evangelos; Katus, Hugo A.; Osman, Nael F.

2009-01-01

Background High-dose dobutamine stress magnetic resonance imaging (DS-MRI) is safe and feasible for the diagnosis of coronary artery disease (CAD) in humans. However, the assessment of cine scans relies on the visual interpretation of regional wall motion, which is subjective. Recently, Strain-Encoded MRI (SENC) has been proposed for the direct color-coded visualization of myocardial strain. The purpose of our study was to compare the diagnostic value of SENC to that provided by conventional wall motion analysis for the detection of inducible ischemia during DS-MRI. Methods and Results Stress induced ischemia was assessed by wall motion analysis and by SENC in 101 patients with suspected or known CAD and in 17 healthy volunteers who underwent DS-MRI in a clinical 1.5T scanner. Quantitative coronary angiography deemed as the standard reference for the presence or absence of significant CAD (≥50% diameter stenosis). On a coronary vessel level, SENC detected inducible ischemia in 86/101 versus 71/101 diseased coronary vessels (p<0.01 versus cine), and showed normal strain response in 189/202 versus 194/202 vessels with <50% stenosis (p=NS versus cine). On a patient level, SENC detected inducible ischemia in 63/64 versus 55/64 patients with CAD (p<0.05 versus cine), and showed normal strain response in 32/37 versus 34/37 patients without CAD (p=NS versus cine).Quantification analysis demonstrated a significant correlation between strain rate reserve (SRreserve) and coronary artery stenosis severity (r²=0.56, p<0.001), and a cut-off value of SRreserve=1.64 deemed as a highly accurate marker for the detection of stenosis≥50% (AUC=0.96, SE=0.01, 95% CI = 0.94–0.98, p<0.001). Conclusions The direct color-coded visualization of strain on MR-images is a useful adjunct for DS-MRI, which provides incremental value for the detection of CAD compared to conventional wall motion readings on cine images. PMID:19808579

Strain-encoded cardiac MRI as an adjunct for dobutamine stress testing: incremental value to conventional wall motion analysis.

PubMed

Korosoglou, Grigorios; Lossnitzer, Dirk; Schellberg, Dieter; Lewien, Antje; Wochele, Angela; Schaeufele, Tim; Neizel, Mirja; Steen, Henning; Giannitsis, Evangelos; Katus, Hugo A; Osman, Nael F

2009-03-01

High-dose dobutamine stress MRI is safe and feasible for the diagnosis of coronary artery disease (CAD) in humans. However, the assessment of cine scans relies on the visual interpretation of regional wall motion, which is subjective. Recently, strain-encoded MRI (SENC) has been proposed for the direct color-coded visualization of myocardial strain. The purpose of our study was to compare the diagnostic value of SENC with that provided by conventional wall motion analysis for the detection of inducible ischemia during dobutamine stress MRI. Stress-induced ischemia was assessed by wall motion analysis and by SENC in 101 patients with suspected or known CAD and in 17 healthy volunteers who underwent dobutamine stress MRI in a clinical 1.5-T scanner. Quantitative coronary angiography deemed as the standard reference for the presence or absence of significant CAD (> or =50% diameter stenosis). On a coronary vessel level, SENC detected inducible ischemia in 86 of 101 versus 71 of 101 diseased coronary vessels (P<0.01 versus cine) and showed normal strain response in 189 of 202 versus 194 of 202 vessels with <50% stenosis (P=NS versus cine). On a patient level, SENC detected inducible ischemia in 63 of 64 versus 55 of 64 patients with CAD (P<0.05 versus cine) and showed normal strain response in 32 of 37 versus 34 of 37 patients without CAD (P=NS versus cine). Quantification analysis demonstrated a significant correlation between strain rate reserve and coronary artery stenosis severity (r(2)=0.56, P<0.001), and a cutoff value of strain rate reserve of 1.64 was deemed as a highly accurate marker for the detection of > or =50% stenosis (area under the curve, 0.96; SE, 0.01; 95% CI, 0.94 to 0.98; P<0.001). The direct color-coded visualization of strain on MR images is a useful adjunct for dobutamine stress MRI, which provides incremental value for the detection of CAD compared with conventional wall motion readings on cine images.

Diagnostic performance of 68Ga-PSMA-11 (HBED-CC) PET/CT in patients with recurrent prostate cancer: evaluation in 1007 patients.

PubMed

Afshar-Oromieh, Ali; Holland-Letz, Tim; Giesel, Frederik L; Kratochwil, Clemens; Mier, Walter; Haufe, Sabine; Debus, Nils; Eder, Matthias; Eisenhut, Michael; Schäfer, Martin; Neels, Oliver; Hohenfellner, Markus; Kopka, Klaus; Kauczor, Hans-Ulrich; Debus, Jürgen; Haberkorn, Uwe

2017-08-01

Since the clinical introduction of 68 Ga-PSMA-11 PET/CT, this imaging method has rapidly spread and is now regarded as a significant step forward in the diagnosis of recurrent prostate cancer (PCa). The aim of this study was to analyse the influence of several variables with possible influence on PSMA ligand uptake in a large cohort. We performed a retrospective analysis of 1007 consecutive patients who were scanned with 68 Ga-PSMA-11 PET/CT (1 h after injection) from January 2014 to January 2017 to detect recurrent disease. Patients with untreated primary PCa or patients referred for PSMA radioligand therapy were excluded. The possible effects of different variables including PSA level and PSA doubling time (PSA DT ), PSA velocity (PSA Vel ), Gleason score (GSC, including separate analysis of GSC 7a and 7b), ongoing androgen deprivation therapy (ADT), patient age and amount of injected activity were evaluated. In 79.5% of patients at least one lesion with characteristics suggestive of recurrent PCa was detected. A pathological (positive) PET/CT scan was associated with PSA level and ADT. GSC, amount of injected activity, patient age, PSA DT and PSA Vel were not associated with a positive PET/CT scan in multivariate analysis. 68 Ga-PSMA-11 PET/CT detects tumour lesions in a high percentage of patients with recurrent PCa. Tumour detection is clearly associated with PSA level and ADT. Only a tendency for an association without statistical significance was found between higher GSC and a higher probability of a pathological PET/CT scan. No associations were found between a pathological 68 Ga-PSMA-11 PET/CT scan and patient age, amount of injected activity, PSA DT or PSA Vel.

MCP-1 in urine as biomarker of disease activity in Systemic Lupus Erythematosus.

PubMed

Barbado, Julia; Martin, Debora; Vega, Luisa; Almansa, Raquel; Gonçalves, Lisbeth; Nocito, Mercedes; Jimeno, Antonio; Ortiz de Lejarazu, Raúl; Bermejo-Martin, Jesus F

2012-11-01

Conventional clinical parameters are not sensitive or specific enough for detecting ongoing disease activity in the Systemic Lupus Erythematosus (SLE). Measurement of cytokines in urine is an encouraging approach to detection of early flares in this disease. Here we have profiled 27 different cytokines, chemokines and celular growth factors in the urine of 48 patients previously diagnosed of SLE as potential biomarkers of disease activity. Correlation analysis with Bonferroni correction showed that MCP-1 was the only immune mediator which levels in urine correlated directly with the SLE Disease Activity Index 2000 (SLEDAI-2K) score (correlation coefficient, p): MCP-1 (0.45,0.003). MCP-1 correlated inversely with levels of C3 complement protein in serum (-0.50,0.001). MCP-1 showed significant higher levels in patients with severe disease activity in comparison with those exhibiting mild activity. Levels of this chemokine were also higher in patients with severe disease activity in comparison with patients with inactive disease and healthy controls. Areas under receiver operating characteristic curves (AUROC) for detection of severe disease (SLEDAI⩾8) was as follows for MCP-1: [AUROC, (IC95%), p]: [0.81 (0.65-0.96) 0.003]. In addition, MCP-1 showed a good result in the AUROC analysis for detecting renal involvement [0.70 (0.52-0.87) 0.050]. When correlation analysis were repeated excluding those patients with active renal disease (n=14), levels of MCP-1 in urine kept on showing a significant positive association with SLEDAI-2K score. In conclusion, multiplex-based cytokine profiling in urine demonstrated the superiority of MCP-1 over a wide range of cytokines as biomarker of disease activity in SLE. Copyright © 2012 Elsevier Ltd. All rights reserved.

Subtle abnormalities of gait detected early in vitamin B6 deficiency in aged and weanling rats with hind leg gait analysis.

PubMed

Schaeffer, M C; Cochary, E F; Sadowski, J A

1990-04-01

Motor abnormalities have been observed in every species made vitamin B6 deficient, and have been detected and quantified early in vitamin B6 deficiency in young adult female Long-Evans rats with hind leg gait analysis. Our objective was to determine if hind leg gait analysis could be used to detect vitamin B6 deficiency in weanling (3 weeks) and aged (23 months) Fischer 344 male rats. Rats (n = 10 per group) were fed: the control diet ad libitum (AL-CON); the control diet devoid of added pyridoxine hydrochloride (DEF); or the control diet pair-fed to DEF (PF-CON). At 10 weeks, plasma pyridoxal phosphate concentration confirmed deficiency in both age groups. Gait abnormalities were detected in the absence of gross motor disturbances in both aged and weanling DEF rats at 2-3 weeks. Width of step was significantly reduced (16%, p less than 0.003) in DEF aged rats compared to AL- and PF-CON. This pattern of response was similar to that reported previously in young adult rats. In weanling rats, pair feeding alone reduced mean width of step (+/- SEM) by 25% compared to ad libitum feeding (2.7 +/- 0.1 vs 3.6 +/- 0.1 cm for PF- vs AL-CON, respectively, p less than 0.05). In DEF weanling rats, width (3.0 +/- 0.1 cm) was increased compared to PF-CON (11%, p less than 0.05) but decreased compared to AL-CON (16%, p less than 0.05). Width of step was significantly altered early in B6 deficiency in rats of different ages and strains and in both sexes.(ABSTRACT TRUNCATED AT 250 WORDS)

Fundamental deficits of auditory perception in Wernicke's aphasia.

PubMed

Robson, Holly; Grube, Manon; Lambon Ralph, Matthew A; Griffiths, Timothy D; Sage, Karen

2013-01-01

This work investigates the nature of the comprehension impairment in Wernicke's aphasia (WA), by examining the relationship between deficits in auditory processing of fundamental, non-verbal acoustic stimuli and auditory comprehension. WA, a condition resulting in severely disrupted auditory comprehension, primarily occurs following a cerebrovascular accident (CVA) to the left temporo-parietal cortex. Whilst damage to posterior superior temporal areas is associated with auditory linguistic comprehension impairments, functional-imaging indicates that these areas may not be specific to speech processing but part of a network for generic auditory analysis. We examined analysis of basic acoustic stimuli in WA participants (n = 10) using auditory stimuli reflective of theories of cortical auditory processing and of speech cues. Auditory spectral, temporal and spectro-temporal analysis was assessed using pure-tone frequency discrimination, frequency modulation (FM) detection and the detection of dynamic modulation (DM) in "moving ripple" stimuli. All tasks used criterion-free, adaptive measures of threshold to ensure reliable results at the individual level. Participants with WA showed normal frequency discrimination but significant impairments in FM and DM detection, relative to age- and hearing-matched controls at the group level (n = 10). At the individual level, there was considerable variation in performance, and thresholds for both FM and DM detection correlated significantly with auditory comprehension abilities in the WA participants. These results demonstrate the co-occurrence of a deficit in fundamental auditory processing of temporal and spectro-temporal non-verbal stimuli in WA, which may have a causal contribution to the auditory language comprehension impairment. Results are discussed in the context of traditional neuropsychology and current models of cortical auditory processing. Copyright © 2012 Elsevier Ltd. All rights reserved.

In situ spectroradiometric quantification of ERTS data

NASA Technical Reports Server (NTRS)

Yost, E. (Principal Investigator)

1972-01-01

The author has identified the following significant results. Additive color photographic analysis of ERTS-1 multispectral imagery indicates that the presence of soil moisture in playas (desert dry lakes) can be readily detected from space. Time sequence additive color presentations in which 600-700 nm bands taken at three successive 18-day cycles show that changes in soil moisture of playas with time can be detected as unique color signatures and can probably be quantitatively measured using photographic images of multispectral scanner data.

Quantitative Analysis of Cell Migration Using Optical Flow

PubMed Central

Boric, Katica; Orio, Patricio; Viéville, Thierry; Whitlock, Kathleen

2013-01-01

Neural crest cells exhibit dramatic migration behaviors as they populate their distant targets. Using a line of zebrafish expressing green fluorescent protein (sox10:EGFP) in neural crest cells we developed an assay to analyze and quantify cell migration as a population, and use it here to characterize in detail the subtle defects in cell migration caused by ethanol exposure during early development. The challenge was to quantify changes in the in vivo migration of all Sox10:EGFP expressing cells in the visual field of time-lapse movies. To perform this analysis we used an Optical Flow algorithm for motion detection and combined the analysis with a fit to an affine transformation. Through this analysis we detected and quantified significant differences in the cell migrations of Sox10:EGFP positive cranial neural crest populations in ethanol treated versus untreated embryos. Specifically, treatment affected migration by increasing the left-right asymmetry of the migrating cells and by altering the direction of cell movements. Thus, by applying this novel computational analysis, we were able to quantify the movements of populations of cells, allowing us to detect subtle changes in cell behaviors. Because cranial neural crest cells contribute to the formation of the frontal mass these subtle differences may underlie commonly observed facial asymmetries in normal human populations. PMID:23936049

Cumulative meta-analysis: a new tool for detection of temporal trends and publication bias in ecology.

PubMed Central

Leimu, Roosa; Koricheva, Julia

2004-01-01

Temporal changes in the magnitude of research findings have recently been recognized as a general phenomenon in ecology, and have been attributed to the delayed publication of non-significant results and disconfirming evidence. Here we introduce a method of cumulative meta-analysis which allows detection of both temporal trends and publication bias in the ecological literature. To illustrate the application of the method, we used two datasets from recently conducted meta-analyses of studies testing two plant defence theories. Our results revealed three phases in the evolution of the treatment effects. Early studies strongly supported the hypothesis tested, but the magnitude of the effect decreased considerably in later studies. In the latest studies, a trend towards an increase in effect size was observed. In one of the datasets, a cumulative meta-analysis revealed publication bias against studies reporting disconfirming evidence; such studies were published in journals with a lower impact factor compared to studies with results supporting the hypothesis tested. Correlation analysis revealed neither temporal trends nor evidence of publication bias in the datasets analysed. We thus suggest that cumulative meta-analysis should be used as a visual aid to detect temporal trends and publication bias in research findings in ecology in addition to the correlative approach. PMID:15347521

[HPLC fingerprint of flavonoids in Sophora flavescens and determination of five components].

PubMed

Ma, Hong-Yan; Zhou, Wan-Shan; Chu, Fu-Jiang; Wang, Dong; Liang, Sheng-Wang; Li, Shao

2013-08-01

A simple and reliable method of high-performance liquid chromatography with photodiode array detection (HPLC-DAD) was developed to evaluate the quality of a traditional Chinese medicine Sophora flavescens through establishing chromatographic fingerprint and simultaneous determination of five flavonoids, including trifolirhizin, maackiain, kushenol I, kurarinone and sophoraflavanone G. The optimal conditions of separation and detection were achieved on an ULTIMATE XB-C18 column (4.6 mm x 250 mm, 5 microm) with a gradient of acetonitrile and water, detected at 295 nm. In the chromatographic fingerprint, 13 peaks were selected as the characteristic peaks to assess the similarities of different samples collected from different origins in China according to similarity evaluation for chromatographic fingerprint of traditional chinese medicine (2004AB) and principal component analysis (PCA) were used in data analysis. There were significant differences in the fingerprint chromatograms between S. flavescens and S. tonkinensis. Principal component analysis showed that kurarinone and sophoraflavanone G were the most important component. In quantitative analysis, the five components showed good regression (R > 0.999) with linear ranges, and their recoveries were in the range of 96.3% - 102.3%. This study indicated that the combination of quantitative and chromatographic fingerprint analysis can be readily utilized as a quality control method for S. flavescens and its related traditional Chinese medicinal preparations.

Detecting the Intention to Move Upper Limbs from Electroencephalographic Brain Signals.

PubMed

Gudiño-Mendoza, Berenice; Sanchez-Ante, Gildardo; Antelis, Javier M

2016-01-01

Early decoding of motor states directly from the brain activity is essential to develop brain-machine interfaces (BMI) for natural motor control of neuroprosthetic devices. Hence, this study aimed to investigate the detection of movement information before the actual movement occurs. This information piece could be useful to provide early control signals to drive BMI-based rehabilitation and motor assisted devices, thus providing a natural and active rehabilitation therapy. In this work, electroencephalographic (EEG) brain signals from six healthy right-handed participants were recorded during self-initiated reaching movements of the upper limbs. The analysis of these EEG traces showed that significant event-related desynchronization is present before and during the execution of the movements, predominantly in the motor-related α and β frequency bands and in electrodes placed above the motor cortex. This oscillatory brain activity was used to continuously detect the intention to move the limbs, that is, to identify the motor phase prior to the actual execution of the reaching movement. The results showed, first, significant classification between relax and movement intention and, second, significant detection of movement intention prior to the onset of the executed movement. On the basis of these results, detection of movement intention could be used in BMI settings to reduce the gap between mental motor processes and the actual movement performed by an assisted or rehabilitation robotic device.

Soil carbon inventories under a bioenergy crop (switchgrass): Measurement limitations

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

Garten, C.T. Jr.; Wullschleger, S.D.

Approximately 5 yr after planting, coarse root carbon (C) and soil organic C (SOC) inventories were compared under different types of plant cover at four switchgrass (Panicum virgatum L.) production field trials in the southeastern USA. There was significantly more coarse root C under switchgrass (Alamo variety) and forest cover than tall fescue (Festuca arundinacea Schreb.), corn (Zea mays L.), or native pastures of mixed grasses. Inventories of SOC under switchgrass were not significantly greater than SOC inventories under other plant covers. At some locations the statistical power associated with ANOVA of SOC inventories was low, which raised questions aboutmore » whether differences in SOC could be detected statistically. A minimum detectable difference (MDD) for SOC inventories was calculated. The MDD is the smallest detectable difference between treatment means once the variation, significance level, statistical power, and sample size are specified. The analysis indicated that a difference of {approx}50 mg SOC/cm{sup 2} or 5 Mg SOC/ha, which is {approx}10 to 15% of existing SOC, could be detected with reasonable sample sizes and good statistical power. The smallest difference in SOC inventories that can be detected, and only with exceedingly large sample sizes, is {approx}2 to 3%. These measurement limitations have implications for monitoring and verification of proposals to ameliorate increasing global atmospheric CO{sub 2} concentrations by sequestering C in soils.« less

Diagnostic power of longitudinal strain at rest for the detection of obstructive coronary artery disease in patients with type 2 diabetes mellitus.

PubMed

Zuo, Houjuan; Yan, Jiangtao; Zeng, Hesong; Li, Wenyu; Li, Pengcheng; Liu, Zhengxiang; Cui, Guanglin; Lv, Jiagao; Wang, Daowen; Wang, Hong

2015-01-01

Global longitudinal strain (GLS) measured by 2-D speckle-tracking echocardiography (2-D STE) at rest has been recognized as a sensitive parameter in the detection of significant coronary artery disease (CAD). However, the diagnostic power of 2-D STE in the detection of significant CAD in patients with diabetes mellitus is unknown. Two-dimensional STE features were studied in total of 143 consecutive patients who underwent echocardiography and coronary angiography. Left ventricular global and segmental peak systolic longitudinal strains (PSLSs) were quantified by speckle-tracking imaging. In the presence of obstructive CAD (defined as stenosis ≥75%), global PSLS was significantly lower in patients with diabetes mellitus than in patients without (16.65 ± 2.29% vs. 17.32 ± 2.27%, p < 0.05). Receiver operating characteristic analysis revealed that global PSLS could effectively detect obstructive CAD in patients without diabetes mellitus (cutoff value: -18.35%, sensitivity: 78.8%, specificity: 77.5%). However, global PSLS could detect obstructive CAD in diabetic patients at a lower cutoff value with inadequate sensitivity and specificity (cutoff value: -17.15%; sensitivity: 61.1%, specificity: 52.9%). In addition, the results for segmental PSLS were similar to those for global PSLS. In conclusion, global and segmental PSLSs at rest were significantly lower in patients with both obstructive CAD and diabetes mellitus than in patients with obstructive CAD only; thus, PSLSs at rest might not be a useful parameter in the detection of obstructive CAD in patients with diabetes mellitus. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Real-Time Detection and Monitoring of Acute Brain Injury Utilizing Evoked Electroencephalographic Potentials.

PubMed

Fisher, Jonathan A N; Huang, Stanley; Ye, Meijun; Nabili, Marjan; Wilent, W Bryan; Krauthamer, Victor; Myers, Matthew R; Welle, Cristin G

2016-09-01

Rapid detection and diagnosis of a traumatic brain injury (TBI) can significantly improve the prognosis for recovery. Helmet-mounted sensors that detect impact severity based on measurements of acceleration or pressure show promise for aiding triage and transport decisions in active, field environments such as professional sports or military combat. The detected signals, however, report on the mechanics of an impact rather than directly indicating the presence and severity of an injury. We explored the use of cortical somatosensory evoked electroencephalographic potentials (SSEPs) to detect and track, in real-time, neural electrophysiological abnormalities within the first hour following head injury in an animal model. To study the immediate electrophysiological effects of injury in vivo, we developed an experimental paradigm involving focused ultrasound that permits continuous, real-time measurements and minimizes mechanical artifact. Injury was associated with a dramatic reduction of amplitude over the damaged hemisphere directly after the injury. The amplitude systematically improved over time but remained significantly decreased at one hour, compared with baseline. In contrast, at one hour there was a concomitant enhancement of the cortical SSEP amplitude evoked from the uninjured hemisphere. Analysis of the inter-trial electroencephalogram (EEG) also revealed significant changes in low-frequency components and an increase in EEG entropy up to 30 minutes after injury, likely reflecting altered EEG reactivity to somatosensory stimuli. Injury-induced alterations in SSEPs were also observed using noninvasive epidermal electrodes, demonstrating viability of practical implementation. These results suggest cortical SSEPs recorded at just a few locations by head-mounted sensors and associated multiparametric analyses could potentially be used to rapidly detect and monitor brain injury in settings that normally present significant levels of mechanical and electrical noise.

Lower and reduced expression of EphA4 is associated with advanced TNM stage, lymph node metastasis, and poor survival in breast carcinoma.

PubMed

Sun, Yuejun; Qian, Jianzhong; Lu, Min; Xu, Hongming

2016-09-01

The expression of EphA4 has been well documented in the development of nerve and in certain types of human cancer. Few studies of EphA4, however, have focused on breast carcinoma. In this study, a set of breast carcinomas was subjected to immunohistochemical staining. In normal luminal cells, EphA4 was weakly detected in 11 (14.3 %), moderately detected in 15 (19.5 %) and highly detected in 51 out of 77 (66.2 %) samples, while in breast carcinoma cells, EphA4 was weakly detected in 42 (54.5 %), moderately detected in 19 (24.7 %) and highly detected in 16 out of 77 (20.8 %) samples (P < 0.001). The expression of EphA4 protein was significantly reduced in 68.8 % of breast carcinoma samples comparing with normal cells. The expression of EphA4 was significantly associated with tumor grade (P = 0.003), TNM stage (P = 0.034), lymph node metastasis (P = 0.034) and Ki-67 (P < 0.001). No significant relationship was found between the expression of EphA4 and age, molecular subtypes, and HER2 status. Survival analysis showed that significant association of low expression of EphA4 in tumor cells with short overall survival (P = 0.048) and disease-free survival (P = 0.051). Our data show that EphA4 was reduced in breast carcinoma, which is associated with high grade, advanced TNM stage, lymph node metastasis, and poor outcome of patients. © 2016 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

[Bacterial contamination of mobile phones shared in hospital wards and the consciousness and behavior of nurses about biological cleanliness].

PubMed

Morioka, Ikuharu; Tabuchi, Yuna; Takahashi, Yuko; Oda, Yuriko; Nakai, Masami; Yanase, Aki; Watazu, Chiyoko

2011-01-01

The purpose of this study was to clarify the contamination of mobile phones shared in hospital wards and its relationship with the consciousness and behavior of nurses about biological cleanliness. Samples from mobile phones were cultured to detect viable bacteria (n=110) and Staphylococcus aureus (n=54). A questionnaire survey was conducted on 110 nurses carrying mobile phones on the day of sampling. Viable bacteria were detected on 79.1% of the mobile phones, whereas S. aureus was detected on 68.6%. All the nurses were aware of hand washing with water or alcohol after regular work, but 33.6% of the nurses were not conscious of hand washing with water or alcohol after using a mobile phone. There was a significant positive relationship between the frequency of using mobile phones and the number of hand washings with water or alcohol. A significant negative relationship was found between the detection of viable bacteria and the number of hand washings with alcohol. The results of logistic regression analysis showed that the detection of viable bacteria was related significantly with the number of hand washings with alcohol (Odds ratio, 0.350; 95%CI, 0.143-0.857) and that the detection of S. aureus was related significantly with the frequency of using mobile phones (Odds ratio, 0.183; 95%CI, 0.036-0.933). It is important to be conscious of the fact that mobile phones shared in hospital wards are easily contaminated. Because hand washing with water or alcohol prevents the contamination of the mobile phones, nurses should take standard precautions after using mobile phones.

A New M Dwarf Debris Disk Candidate in a Young Moving Group Discovered with Disk Detective

NASA Technical Reports Server (NTRS)

Silverberg, Steven M.; Kuchner, Marc J.; Wisniewski, John P.; Gagne, Jonathan; Bans, Alissa S.; Bhattacharjee, Shambo; Currie, Thayne R.; Debes, John R.; Biggs, Joseph R; Bosch, Milton

2016-01-01

We used the Disk Detective citizen science project and the BANYAN II Bayesian analysis tool to identify a new candidate member of a nearby young association with infrared excess. WISE J080822.18-644357.3, an M5.5-type debris disk system with significant excess at both 12 and 22 microns, is a likely member (approx.90% BANYAN II probability) of the approx.45 Myr old Carina association. Since this would be the oldest M dwarf debris disk detected in a moving group, this discovery could be an important constraint on our understanding of M dwarf debris disk evolution.

Serial 3-dimensional computed tomography and a novel method of volumetric analysis for the evaluation of the osteo-odonto-keratoprosthesis.

PubMed

Sipkova, Zuzana; Lam, Fook Chang; Francis, Ian; Herold, Jim; Liu, Christopher

2013-04-01

To assess the use of serial computed tomography (CT) in the detection of osteo-odonto-lamina resorption in osteo-odonto-keratoprosthesis (OOKP) and to investigate the use of new volumetric software, Advanced Lung Analysis software (3D-ALA; GE Healthcare), for detecting changes in OOKP laminar volume. A retrospective assessment of the radiological databases and hospital records was performed for 22 OOKP patients treated at the National OOKP referral center in Brighton, United Kingdom. Three-dimensional surface reconstructions of the OOKP laminae were performed using stored CT data. For the 2-dimensional linear analysis, the linear dimensions of the reconstructed laminae were measured, compared with original measurements taken at the time of surgery, and then assigned a CT grade based on a predetermined resorption grading scale. The volumetric analysis involved calculating the laminar volumes using 3D-ALA. The effectiveness of 2-dimensional linear analysis, volumetric analysis, and clinical examination in detecting laminar resorption was compared. The mean change in laminar volume between the first and second scans was -6.67% (range, +10.13% to -24.86%). CT grades assigned to patients based on laminar dimension measurements remained the same, despite significant changes in laminar volumes. Clinical examination failed to identify 60% of patients who were found to have resorption on volumetric analysis. Currently, the detection of laminar resorption relies on clinical examination and the measurement of laminar dimensions on the 2- and 3-dimensional radiological images. Laminar volume measurement is a useful new addition to the armamentarium. It provides an objective tool that allows for a precise and reproducible assessment of laminar resorption.

Sputum, sex and scanty smears: new case definition may reduce sex disparities in smear-positive tuberculosis.

PubMed

Ramsay, A; Bonnet, M; Gagnidze, L; Githui, W; Varaine, F; Guérin, P J

2009-05-01

Urban clinic, Nairobi. To evaluate the impact of specimen quality and different smear-positive tuberculosis (TB) case (SPC) definitions on SPC detection by sex. Prospective study among TB suspects. A total of 695 patients were recruited: 644 produced > or =1 specimen for microscopy. The male/female sex ratio was 0.8. There were no significant differences in numbers of men and women submitting three specimens (274/314 vs. 339/380, P = 0.43). Significantly more men than women produced a set of three 'good' quality specimens (175/274 vs. 182/339, P = 0.01). Lowering thresholds for definitions to include scanty smears resulted in increases in SPC detection in both sexes; the increase was significantly higher for women. The revised World Health Organization (WHO) case definition was associated with the highest detection rates in women. When analysis was restricted only to patients submitting 'good' quality specimen sets, the difference in detection between sexes was on the threshold for significance (P = 0.05). Higher SPC notification rates in men are commonly reported by TB control programmes. The revised WHO SPC definition may reduce sex disparities in notification. This should be considered when evaluating other interventions aimed at reducing these. Further study is required on the effects of the human immuno-deficiency virus and instructed specimen collection on sex-specific impact of new SPC definition.

Spectroscopic signatures of PETN in contact with sand particles

NASA Astrophysics Data System (ADS)

Ballesteros, Luz M.; Herrera, Gloria M.; Castro, Miguel E.; Briano, Julio; Mina, Nairmen; Hernandez-Rivera, Samuel P.

2005-06-01

The detection of explosive materials is not only important as an issue in landmines but also for global security reasons, unexploded ordnance, and Improvised Explosive Devices detection. In such areas, explosives detection has played a central role in ensuring the safety of the lives of citizens in many countries. Raman Spectroscopy is a well established tool for vibrational spectroscopic analysis and can be applied to the field of explosives identification and detection. The analysis of PETN is important because it is used in laminar form or mixed with RDX to manufacture Semtex plastic explosive and in the fabrication of Improvised Explosive Devices (IEDs). Our investigation is focused on the study of spectroscopic signatures of PETN in contact with soil. Ottawa sand mixed in different proportions with PETN together with the study of the influence of pH, temperature, humidity, and UV light on the vibrational signatures of the mixtures constitute the core of the investigation. The results reveal that the characteristic bands of PETN are not significantly shifted but rather appear constant with respect of the ubiquitous band of sand (~463 cm-1). These results will make possible the development of highly sensitive sensors for detection of explosives materials and IDEs.

Sweet-spot training for early esophageal cancer detection

NASA Astrophysics Data System (ADS)

van der Sommen, Fons; Zinger, Svitlana; Schoon, Erik J.; de With, Peter H. N.

2016-03-01

Over the past decade, the imaging tools for endoscopists have improved drastically. This has enabled physicians to visually inspect the intestinal tissue for early signs of malignant lesions. Besides this, recent studies show the feasibility of supportive image analysis for endoscopists, but the analysis problem is typically approached as a segmentation task where binary ground truth is employed. In this study, we show that the detection of early cancerous tissue in the gastrointestinal tract cannot be approached as a binary segmentation problem and it is crucial and clinically relevant to involve multiple experts for annotating early lesions. By employing the so-called sweet spot for training purposes as a metric, a much better detection performance can be achieved. Furthermore, a multi-expert-based ground truth, i.e. a golden standard, enables an improved validation of the resulting delineations. For this purpose, besides the sweet spot we also propose another novel metric, the Jaccard Golden Standard (JIGS) that can handle multiple ground-truth annotations. Our experiments involving these new metrics and based on the golden standard show that the performance of a detection algorithm of early neoplastic lesions in Barrett's esophagus can be increased significantly, demonstrating a 10 percent point increase in the resulting F1 detection score.

Detection frequency of human herpesviruses-6A, -6B, and -7 genomic sequences in central nervous system DNA samples from post-mortem individuals with unspecified encephalopathy.

PubMed

Chapenko, Svetlana; Roga, Silvija; Skuja, Sandra; Rasa, Santa; Cistjakovs, Maksims; Svirskis, Simons; Zaserska, Zane; Groma, Valerija; Murovska, Modra

2016-08-01

In this autopsy-based study, human herpesvirus-6 (HHV-6) and -7 (HHV-7) genomic sequence frequency, HHV-6 variants, HHV-6 load and the expression of HHV-6 antigens in brain samples from the individuals, with and without unspecified encephalopathy (controls), using nested and real-time polymerase chain reactions, restriction endonuclease, and immunohistochemical analysis were examined. GraphPad Prism 6.0 Mann-Whitney nonparametric and chi-square test and Fisher's exact test were used for statistical analysis. The encephalopathy diagnoses were shown by magnetic resonance imaging made during their lifetime and macro- and microscopically studied autopsy tissue materials. Widespread HHV-6 and/or HHV-7 positivity was detected in the brain tissue of various individuals with encephalopathy, as well as in controls (51/57, 89.4 % and 35/51, 68.6 %, respectively; p = 0.009). Significantly higher detection frequency of single HHV-6 and concurrent HHV-6 + HHV-7 DNA was found in pia mater meninges, frontal lobe, temporal lobe, and olfactory tract DNAs in individuals with encephalopathy compared to the control group. HHV-6 load and higher frequency of the viral load >10 copies/10(6) cells significantly differed in samples from individuals with and without encephalopathy. The expression of HHV-6 antigens was revealed in different neural cell types with strong predominance in the encephalopathy group. In all HHV-6-positive autopsy samples of individuals with and without encephalopathy, HHV-6B was revealed. Significantly higher detection frequency of beta-herpesvirus DNA, more often detected HHV-6 load >10 copies/10(6) cells, as well as the expression of HHV-6 antigens in different brain tissue samples from individuals with encephalopathy in comparison with control group indicate on potential involvement of these viruses in encephalopathy development.

Effects of visual erotic stimulation on vibrotactile detection thresholds in men.

PubMed

Jiao, Chuanshu; Knight, Peter K; Weerakoon, Patricia; Turman, A Bulent

2007-12-01

This study examined the effects of sexual arousal on vibration detection thresholds in the right index finger of 30 healthy, heterosexual males who reported no sexual dysfunction. Vibrotactile detection thresholds at frequencies of 30, 60, and 100 Hz were assessed before and after watching erotic and control videos using a forced-choice, staircase method. A mechanical stimulator was used to produce the vibratory stimulus. Results were analyzed using repeated measures analysis of variance. After watching the erotic video, the vibrotactile detection thresholds at 30, 60, and 100 Hz were significantly reduced (p < .01). No changes in thresholds were detected at any frequency following exposure to the non-erotic stimulus. The results show that sexual arousal resulted in an increase in vibrotactile sensitivity to low frequency stimuli in the index finger of sexually functional men.

Fault Detection and Diagnosis of Railway Point Machines by Sound Analysis

PubMed Central

Lee, Jonguk; Choi, Heesu; Park, Daihee; Chung, Yongwha; Kim, Hee-Young; Yoon, Sukhan

2016-01-01

Railway point devices act as actuators that provide different routes to trains by driving switchblades from the current position to the opposite one. Point failure can significantly affect railway operations, with potentially disastrous consequences. Therefore, early detection of anomalies is critical for monitoring and managing the condition of rail infrastructure. We present a data mining solution that utilizes audio data to efficiently detect and diagnose faults in railway condition monitoring systems. The system enables extracting mel-frequency cepstrum coefficients (MFCCs) from audio data with reduced feature dimensions using attribute subset selection, and employs support vector machines (SVMs) for early detection and classification of anomalies. Experimental results show that the system enables cost-effective detection and diagnosis of faults using a cheap microphone, with accuracy exceeding 94.1% whether used alone or in combination with other known methods. PMID:27092509

Benford's law gives better scaling exponents in phase transitions of quantum XY models.

PubMed

Rane, Ameya Deepak; Mishra, Utkarsh; Biswas, Anindya; Sen De, Aditi; Sen, Ujjwal

2014-08-01

Benford's law is an empirical law predicting the distribution of the first significant digits of numbers obtained from natural phenomena and mathematical tables. It has been found to be applicable for numbers coming from a plethora of sources, varying from seismographic, biological, financial, to astronomical. We apply this law to analyze the data obtained from physical many-body systems described by the one-dimensional anisotropic quantum XY models in a transverse magnetic field. We detect the zero-temperature quantum phase transition and find that our method gives better finite-size scaling exponents for the critical point than many other known scaling exponents using measurable quantities like magnetization, entanglement, and quantum discord. We extend our analysis to the same system but at finite temperature and find that it also detects the finite-temperature phase transition in the model. Moreover, we compare the Benford distribution analysis with the same obtained from the uniform and Poisson distributions. The analysis is furthermore important in that the high-precision detection of the cooperative physical phenomena is possible even from low-precision experimental data.

Identification of aldolase A as a potential diagnostic biomarker for colorectal cancer based on proteomic analysis using formalin-fixed paraffin-embedded tissue.

PubMed

Yamamoto, Tetsushi; Kudo, Mitsuhiro; Peng, Wei-Xia; Takata, Hideyuki; Takakura, Hideki; Teduka, Kiyoshi; Fujii, Takenori; Mitamura, Kuniko; Taga, Atsushi; Uchida, Eiji; Naito, Zenya

2016-10-01

Colorectal cancer (CRC) is one of the most common cancers worldwide, and many patients are already at an advanced stage when they are diagnosed. Therefore, novel biomarkers for early detection of colorectal cancer are required. In this study, we performed a global shotgun proteomic analysis using formalin-fixed and paraffin-embedded (FFPE) CRC tissue. We identified 84 candidate proteins whose expression levels were differentially expressed in cancer and non-cancer regions. A label-free semiquantitative method based on spectral counting and gene ontology (GO) analysis led to a total of 21 candidate proteins that could potentially be detected in blood. Validation studies revealed cyclophilin A, annexin A2, and aldolase A mRNA and protein expression levels were significantly higher in cancer regions than in non-cancer regions. Moreover, an in vitro study showed that secretion of aldolase A into the culture medium was clearly suppressed in CRC cells compared to normal colon epithelium. These findings suggest that decreased aldolase A in blood may be a novel biomarker for the early detection of CRC.

Assessment of Gamma-Ray Spectra Analysis Method Utilizing the Fireworks Algorithm for various Error Measures

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

Alamaniotis, Miltiadis; Tsoukalas, Lefteri H.

2018-01-01

Significant role in enhancing nuclear nonproliferation plays the analysis of obtained data and the inference of the presence or not of special nuclear materials in them. Among various types of measurements, gamma-ray spectra is the widest used type of data utilized for analysis in nonproliferation. In this chapter, a method that employs the fireworks algorithm (FWA) for analyzing gamma-ray spectra aiming at detecting gamma signatures is presented. In particular FWA is utilized to fit a set of known signatures to a measured spectrum by optimizing an objective function, with non-zero coefficients expressing the detected signatures. FWA is tested on amore » set of experimentally obtained measurements and various objective functions -MSE, RMSE, Theil-2, MAE, MAPE, MAP- with results exhibiting its potential in providing high accuracy and high precision of detected signatures. Furthermore, FWA is benchmarked against genetic algorithms, and multiple linear regression with results exhibiting its superiority over the rest tested algorithms with respect to precision for MAE, MAPE and MAP measures.« less

Analysis of small-bowel capsule endoscopy reading by using Quickview mode: training assistants for reading may produce a high diagnostic yield and save time for physicians.

PubMed

Shiotani, Akiko; Honda, Keisuke; Kawakami, Makiko; Kimura, Yoshiki; Yamanaka, Yoshiyuki; Fujita, Minoru; Matsumoto, Hiroshi; Tarumi, Ken-ichi; Manabe, Noriaki; Haruma, Ken

2012-01-01

The aim was to investigate the clinical utility of RAPID Access 6.5 Quickview software and to evaluate whether preview of the capsule endoscopy video by a trained nurse could detect significant lesions accurately compared with endoscopists. As reading capsule endoscopy is time consuming, one possible cost-effective strategy could be the use of trained nonphysicians or newly available software to preread and identify potentially important capsule images. The 100 capsule images of a variety of significant lesions from 87 patients were investigated. The minimum percentages for settings of sensitivity that could pick up the selected images and the detection rate for significant lesions by a well-trained nurse, two endoscopists with limited experience in reading, and one well-trained physician were examined. The frequency of the selected lesions picked up by Quickview mode using percentages for sensitivity settings of 5%, 15%, 25%, and 35% were 61%, 74%, 93%, and 98%, respectively. The percentages for sensitivity significantly correlated (r=0.78, P<0.001) with the reading time. The detection rate by the nurse or the well-trained physician was significantly higher than that by the physician with limited capsule experience (87% and 84.1% vs. 62.7%; P<0.01). The clinical use of Quickview at 25% did not significantly improve the detection rate. Quickview mode can reduce reading time but has an unacceptably miss rate for potentially important lesions. Use of a trained nonphysician assistant can reduce physician's time and improve diagnostic yield.

Clinical utility of transperineal template-guided mapping biopsy of the prostate after negative magnetic resonance imaging-guided transrectal biopsy.

PubMed

Sivaraman, Arjun; Sanchez-Salas, Rafael; Ahmed, Hashim U; Barret, Eric; Cathala, Nathalie; Mombet, Annick; Uriburu Pizarro, Facundo; Carneiro, Arie; Doizi, Steeve; Galiano, Marc; Rozet, Francois; Prapotnich, Dominique; Cathelineau, Xavier

2015-07-01

We evaluated the prostate cancer detection with transperineal template-guided mapping biopsy in patients with elevated prostate-specific antigen and negative magnetic resonance imaging (MRI)-guided biopsy. Totally 75 patients underwent transperineal template-guided mapping biopsy for prior negative MRI-guided (cognitive registration) biopsy during April 2013 to August 2014. Primary objective was to report clinically significant cancer detection in this cohort of patients. Significant cancer was defined using varying thresholds of MCL or Gleason grade 3+4 or greater or both. Cancers with more than 80% of positive core length anterior to the level of urethra were termed anterior zone cancer. Secondary objective was to evaluate the potential clinical and radiological predictors for significant cancer detection. The mean age was 61.6 ± 6.5 years and median prostate-specific antigen was 10.4 ng/dl (7.9-18) with a mean MRI target size of 7.2mm (4-11). Transperineal template-guided mapping biopsy identified cancer in 36% (27/75) patients and 66.6% (18/27) of them were anterior zone cancers. The rates of detection of clinically significant and insignificant cancer according to the several definitions used range from 22.7% to 30.7% and 5.3% to 13.3%, respectively. Multivariate analysis did not identify any predictors for finding clinically significant and anterior cancers in this group of patients. Transperineal template-guided mapping biopsy appears to be an excellent biopsy protocol for downstream management following negative MRI-guided biopsy. Most of the cancers detected were predominantly anterior tumors. Copyright © 2015 Elsevier Inc. All rights reserved.

Tolerance of image enhancement brightness and contrast in lateral cephalometric digital radiography for Steiner analysis

NASA Astrophysics Data System (ADS)

Rianti, R. A.; Priaminiarti, M.; Syahraini, S. I.

2017-08-01

Image enhancement brightness and contrast can be adjusted on lateral cephalometric digital radiographs to improve image quality and anatomic landmarks for measurement by Steiner analysis. To determine the limit value for adjustments of image enhancement brightness and contrast in lateral cephalometric digital radiography for Steiner analysis. Image enhancement brightness and contrast were adjusted on 100 lateral cephalometric radiography in 10-point increments (-30, -20, -10, 0, +10, +20, +30). Steiner analysis measurements were then performed by two observers. Reliabilities were tested by the Interclass Correlation Coefficient (ICC) and significance tested by ANOVA or the Kruskal Wallis test. No significant differences were detected in lateral cephalometric analysis measurements following adjustment of the image enhancement brightness and contrast. The limit value of adjustments of the image enhancement brightness and contrast associated with incremental 10-point changes (-30, -20, -10, 0, +10, +20, +30) does not affect the results of Steiner analysis.

Hyperspectral image analysis for water stress detection of apple trees

USDA-ARS?s Scientific Manuscript database

Plant stress significantly reduces plant productivity. Automated on-the-go mapping of plant stress would allow for a timely intervention and mitigation of the problem before critical thresholds are exceeded, thereby maximizing productivity. The spectral signature of plant leaves was analyzed by a ...

Impact of compressed breast thickness and dose on lesion detectability in digital mammography: FROC study with simulated lesions in real mammograms

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

Salvagnini, Elena, E-mail: elena.salvagnini@gmail.

Purpose: The aim of this work was twofold: (1) to examine whether, with standard automatic exposure control (AEC) settings that maintain pixel values in the detector constant, lesion detectability in clinical images decreases as a function of breast thickness and (2) to verify whether a new AEC setup can increase lesion detectability at larger breast thicknesses. Methods: Screening patient images, acquired on two identical digital mammography systems, were collected over a period of 2 yr. Mammograms were acquired under standard AEC conditions (part 1) and subsequently with a new AEC setup (part 2), programmed to use the standard AEC settingsmore » for compressed breast thicknesses ≤49 mm, while a relative dose increase was applied above this thickness. The images were divided into four thickness groups: T1 ≤ 29 mm, T2 = 30–49 mm, T3 = 50–69 mm, and T4 ≥ 70 mm, with each thickness group containing 130 randomly selected craniocaudal lesion-free images. Two measures of density were obtained for every image: a BI-RADS score and a map of volumetric breast density created with a software application (VolparaDensity, Matakina, NZ). This information was used to select subsets of four images, containing one image from each thickness group, matched to a (global) BI-RADS score and containing a region with the same (local) VOLPARA volumetric density value. One selected lesion (a microcalcification cluster or a mass) was simulated into each of the four images. This process was repeated so that, for a given thickness group, half the images contained a single lesion and half were lesion-free. The lesion templates created and inserted in groups T3 and T4 for the first part of the study were then inserted into the images of thickness groups T3 and T4 acquired with higher dose settings. Finally, all images were visualized using the ViewDEX software and scored by four radiologists performing a free search study. A statistical jackknife-alternative free-response receiver operating characteristic analysis was applied. Results: For part 1, the alternative free-response receiver operating characteristic curves for the four readers were 0.80, 0.65, 0.55 and 0.56 in going from T1 to T4, indicating a decrease in detectability with increasing breast thickness. P-values and the 95% confidence interval showed no significant difference for the T3-T4 comparison (p = 0.78) while all the other differences were significant (p < 0.05). Separate analysis of microcalcification clusters presented the same results while for mass detection, the only significant difference came when comparing T1 to the other thickness groups. Comparing the scores of part 1 and part 2, results for the T3 group acquired with the new AEC setup and T3 group at standard AEC doses were significantly different (p = 0.0004), indicating improved detection. For this group a subanalysis for microcalcification detection gave the same results while no significant difference was found for mass detection. Conclusions: These data using clinical images confirm results found in simple QA tests for many mammography systems that detectability falls as breast thickness increases. Results obtained with the AEC setup for constant detectability above 49 mm showed an increase in lesion detection with compressed breast thickness, bringing detectability of lesions to the same level.« less

Determining the linkage of disease-resistance genes to molecular markers: the LOD-SCORE method revisited with regard to necessary sample sizes.

PubMed

Hühn, M

1995-05-01

Some approaches to molecular marker-assisted linkage detection for a dominant disease-resistance trait based on a segregating F2 population are discussed. Analysis of two-point linkage is carried out by the traditional measure of maximum lod score. It depends on (1) the maximum-likelihood estimate of the recombination fraction between the marker and the disease-resistance gene locus, (2) the observed absolute frequencies, and (3) the unknown number of tested individuals. If one replaces the absolute frequencies by expressions depending on the unknown sample size and the maximum-likelihood estimate of recombination value, the conventional rule for significant linkage (maximum lod score exceeds a given linkage threshold) can be resolved for the sample size. For each sub-population used for linkage analysis [susceptible (= recessive) individuals, resistant (= dominant) individuals, complete F2] this approach gives a lower bound for the necessary number of individuals required for the detection of significant two-point linkage by the lod-score method.

Flow cytometry, morphometry and histopathology as biomarkers of benzo[a]pyrene exposure in brown bullheads (ameiurus nebulosus)

USGS Publications Warehouse

Grady, Andrew W.; McLaughlin, Ronald M.; Caldwell, Charles W.; Schmitt, Christopher J.; Stalling, David L.

1992-01-01

Brown bullheads were given a single intraperitoneal dose of 0, 5, 25 or 125 mg kg−1 benzo[a]pyrene (BaP), a carcinogenic polycyclic aromatic hydrocarbon, and evaluated over 18 months. Flow cytometric analyses of hepatocyte DNA content indicated an increase in DNA synthesis in BaP-exposed fish prior to day 14 post-exposure. Thereafter, all flow cytometric variables returned to initial levels. Histopathological evaluation of livers from fish sampled at 18 months revealed significant differences among treatments in the amount of hepatic macrophage ceroid pigmentation and basophilic staining intensity. No neoplasms or changes in blood cell DNA content were detected. Significant morphometric variations existed among fish, but differences between sexes overshadowed differences attributable to dose. Flow cytometry yielded no evidence of long-term DNA alterations from a single exposure to BaP; however, the differences detected by DNA analysis shortly after the toxic event suggest that flow cytometric cell cycle analysis may be useful for documenting continuing exposures.

Kit receptor tyrosine kinase dysregulations in feline splenic mast cell tumours.

PubMed

Sabattini, S; Barzon, G; Giantin, M; Lopparelli, R M; Dacasto, M; Prata, D; Bettini, G

2017-09-01

This study investigated Kit receptor dysregulations (cytoplasmic immunohistochemical expression and/or c-KIT mutations) in cats affected with splenic mast cell tumours. Twenty-two cats were included. Median survival time was 780 days (range: 1-1219). An exclusive splenic involvement was significantly (P = 0.042) associated with longer survival (807 versus 120 days). Eighteen tumours (85.7%) showed Kit cytoplasmic expression (Kit pattern 2, 3). Mutation analysis was successful in 20 cases. Fourteen missense mutations were detected in 13 out of 20 tumours (65%). Eleven (78.6%) were located in exon 8, and three (21.6%) in exon 9. No mutations were detected in exons 11 and 17. Seven mutations corresponded to the same internal tandem duplication in exon 8 (c.1245_1256dup). Although the association between Kit cytoplasmic expression and mutations was significant, immunohistochemistry cannot be considered a surrogate marker for mutation analysis. No correlation was observed between c-Kit mutations and tumour differentiation, mitotic activity or survival. © 2016 John Wiley & Sons Ltd.

Detecting Eating Psychopathology in Female Athletes by Asking About Exercise: Use of the Compulsive Exercise Test.

PubMed

Plateau, Carolyn R; Arcelus, Jon; Meyer, Caroline

2017-11-01

The present study assessed the suitability of the Compulsive Exercise Test (athlete version; CET-A) for identifying female athletes with clinically significant features related to or comparable with eating psychopathology. Three hundred and sixty-one female athletes (including 12 with a clinically diagnosed eating disorder) completed the Eating Disorders Examination Questionnaire and the CET-A. Receiver operating curve analysis was employed to identify a cut-off value on the CET-A, which could indicate clinically significant features related to or comparable with eating psychopathology among female athletes. The analysis demonstrated that a CET-A score of 10 successfully discriminated female athletes with a current eating disorder. The results suggest that the CET-A may be a suitable tool for detecting eating psychopathology in female athletes. Additional longitudinal research is needed to evaluate the predictive value of the CET-A. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.

Seismo-ionospheric anomalies in DEMETER observationsduring the Wenchuan M7.9 earthquake

NASA Astrophysics Data System (ADS)

Huang, C. C.; Liu, J. Y. G.

2014-12-01

This paper examines pre-earthquake ionospheric anomalies (PEIAs) observed by the French satellite DEMETER (Detection of Electro-Magnetic Emissions Transmitted from Earthquake Regions) during the 12 May 2008 M7.9 Wenchuan earthquake. Both daytime and nighttime electron density (Ne), electron temperature (Te), ion density (Ni) and ion temperature (Ti) are investigated. A statistical analysis of the box-and-whisker method is utilized to see if the four DEMETER datasets 1-6 days before and after the earthquake are significantly different. The analysis is employed to investigate the epicenter and three reference areas along the same magnetic latitude and to discriminate the earthquake-related anomalies from global effects. Results show that the nighttime Ne and Ni over the epicenter significantly decrease 1-6 days before the earthquake. The ionospheric total electron content (TEC) of global ionosphere map (GIM) over the epicenter is further inspected to find the sensitive local time for detecting the PEIAs of the M7.9 Wenchuan earthquake.

Modulation by EEG features of BOLD responses to interictal epileptiform discharges

PubMed Central

LeVan, Pierre; Tyvaert, Louise; Gotman, Jean

2013-01-01

Introduction EEG-fMRI of interictal epileptiform discharges (IEDs) usually assumes a fixed hemodynamic response function (HRF). This study investigates HRF variability with respect to IED amplitude fluctuations using independent component analysis (ICA), with the goal of improving the specificity of EEG-fMRI analyses. Methods We selected EEG-fMRI data from 10 focal epilepsy patients with a good quality EEG. IED amplitudes were calculated in an average reference montage. The fMRI data were decomposed by ICA and a deconvolution method identified IED-related components by detecting time courses with a significant HRF time-locked to the IEDs (F-test, p<0.05). Individual HRF amplitudes were then calculated for each IED. Components with a significant HRF/IED amplitude correlation (Spearman test, p< 0.05) were compared to the presumed epileptogenic focus and to results of a general linear model (GLM) analysis. Results In 7 patients, at least one IED-related component was concordant with the focus, but many IED-related components were at distant locations. When considering only components with a significant HRF/IED amplitude correlation, distant components could be discarded, significantly increasing the relative proportion of activated voxels in the focus (p=0.02). In the 3 patients without concordant IED-related components, no HRF/IED amplitude correlations were detected inside the brain. Integrating IED-related amplitudes in the GLM significantly improved fMRI signal modeling in the epileptogenic focus in 4 patients (p< 0.05). Conclusion Activations in the epileptogenic focus appear to show significant correlations between HRF and IED amplitudes, unlike distant responses. These correlations could be integrated in the analysis to increase the specificity of EEG-fMRI studies in epilepsy. PMID:20026222

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Clinical and histopathological results of the adult patients with unilateral cryptorchidism

PubMed Central

Ateş, Ferhat; Soydan, Hasan; Okçelik, Sezgin; Çırakoğlu, Abdullah; Yılmaz, İsmail; Malkoç, Ercan; Karademir, Kenan

2016-01-01

Objective To evaluate the clinical and histopathological results of adult unilateral cryptorchidism patients. Material and methods Data from adult unilateral cryptorchidism patients that underwent orchiectomy in our clinic between between January 2004 and March 2013 were retrospectively evaluated. Patients were divided into three groups as intra-abdominal, inguinal canal and superficial inguinal region according to the location of the undescended testes. Patients were also grouped according to their testicular volume (<4 cc, 4.1–12 cc, and >12 cc). Histopathology results of orchiectomy specimens were classified as follows: 1. Sertoli cells only, testicular atrophy and vanished testis (anorchia) 2. Hypospermatogenesis, and 3. Maturation arrest. Patients were grouped as normospermia, azoospermia and oligo/astheno/teratospermia groups according to semen analysis results. Correlations between testicular localization, testicular size, semen analysis and pathology results were evaluated. Incidental tumor detection rates were also calculated. Results Two hundred and forty-four adult unilateral cryptorchidism patients underwent orchiectomy in our clinic. There was no a significant relationship between location of the testis and testicular pathology results (p=0.707). Most common semen analysis results was normospermia in patients with high testicular volume group however azoospermia and oligoasthenospermia observed commonly in patients with low testicular volume group. There was a significant relationship between testicular volume and semen analysis results (p=0.023). No significant relationship was observed between semen analysis and pathological results (p=0.929). After an evaluation of all factors with possible effects on the semen analysis results, only testicular volume (p=0.036) was found to have a significant impact. Only one case (0.4%) was incidentally diagnosed seminoma after a review of 233 patients with available histopathological results on record. Conclusion Adult unilateral cryptorchidism has a minimal effect on male fertility or even this effect can be overlooked. Low detection rates of incidental germ cell tumors also make an orchiectomy decision questionable in such cases. PMID:27274891

Auditory backup alarms: distance-at-first-detection via in-situ experimentation on alarm design and hearing protection effects.

PubMed

Alali, Khaled; Casali, John G

2012-01-01

The purpose of this study was to assess normal hearing listeners' performance in detecting a stationary backup alarm signal and to quantify the linear distance at detection point. Detection distances for 12 participants with normal hearing were measured while they were fitted with 7 hearing protectors and while they were unoccluded (open ear). A standard (narrowband) backup alarm signal and a broadband (pulsed white noise) backup alarm signal from Brigade[1] were used. The method of limits, with distance as the physical measurement variable and threshold detection as the task, was employed to find at which distance the participant could first detect the backup alarms. A within-subject Analysis of Variance (ANOVA) revealed a significant main effect of the listening conditions on the detection distance in feet. Post hoc analyses indicated that the Bilsom L3HV conventional passive earmuff (at 1132.2 ft detection distance) was significantly poorer compared to all other HPDs and the open ear in detection distance achieved, and that there were no statistically-significant differences between the unoccluded ear (1652.3 ft), EB-15-Lo BlastPLGTM (1546.2 ft), EB-15-Hi BlastPLGTM (1543.4 ft), E-A-R/3M Combat ArmsTM earplug-nonlinear, level-dependent state (1507.8 ft), E-A-R/3M HiFiTM earplug (1497.7 ft), and Bilsom ImpactTM dichotic electronic earmuff (1567.2 ft). In addition, the E-A-R/3M Combat ArmsTM earplug-passive steady state resulted in significantly longer detection distances than only the open ear condition, at 1474.1 ft versus 1652.3 ft for the open ear. ANOVA also revealed a significant main effect of the backup alarm type on detection distance. The means were 1600.9 ft for the standard (narrowband) backup alarm signal, and a significantly closer 1379.4 ft was required for the Brigade broadband backup alarm signal. For on-ground workers, it is crucial to detect backup alarm signals as far away as possible rather than at close distances since this will provide them more time to react to approaching vehicles. The results of this study suggest that as the attenuation of the hearing protectors increases, precautions should be considered by safety professionals. This is because, as it was the case with the Bilsom passive earmuff and E-A-R/3M Combat ArmsTM earplug-passive steady state, high attenuation minimizes the detection distance and as a result on-foot workers will have less time to react to any approaching vehicle. The main effects of the type of backup alarm signal demonstrated a statistically-significant advantage of the standard backup alarm over the broadband backup alarm on detection distance in feet. The magnitude of the improvement produced by the standard backup alarm was 221.5 feet, a very large margin. For example, with a vehicle backing at 10 mph, the 221.5 ft decrease in detection distance with the Brigade alarm equates to the vehicle arriving 15 seconds sooner at the worker from the point at which its alarm was first heard.

Identifying Key Actors in Heterogeneous Networks

DTIC Science & Technology

2017-11-29

analysis (SNA) and game theory (GT) to improve accuracy for detecting significant or “powerful” actors within a total actor space when both resource...coalesce in order to achieve a desired outcome. Cooperative game theory (CGT) models of coalition formation are based on two limiting assumptions: that...demonstration of a new approach for synthesizing social network analysis and game theory. The ultimate goal of this research agenda is to generalize

Ultrahigh-Sensitivity Piezoresistive Pressure Sensors for Detection of Tiny Pressure.

PubMed

Li, Hongwei; Wu, Kunjie; Xu, Zeyang; Wang, Zhongwu; Meng, Yancheng; Li, Liqiang

2018-06-20

High-sensitivity pressure sensors are crucial for the ultrasensitive touch technology and E-skin, especially at the tiny-pressure range below 100 Pa. However, it is highly challenging to substantially promote sensitivity beyond the current level at several to 200 kPa -1 and to improve the detection limit lower than 0.1 Pa, which is significant for the development of pressure sensors toward ultrasensitive and highly precise detection. Here, we develop an efficient strategy to greatly improve the sensitivity near to 2000 kPa -1 using short-channel coplanar device structure and sharp microstructure, which is systematically proposed for the first time and rationalized by the mathematic calculation and analysis. Significantly, benefiting from the ultrahigh sensitivity, the detection limit is improved to be as small as 0.075 Pa. The sensitivity and detection limit are both superior to the current levels and far surpass the function of human skin. Furthermore, the sensor shows fast response time (50 μs), excellent reproducibility and stability, and low power consumption. Remarkably, the sensor shows excellent detection capacity in the tiny-pressure range, including light-emitting diode switching with a pressure of 7 Pa, ringtone (2-20 Pa) recognition, and ultrasensitive (0.1 Pa) electronic glove. This work represents a performance and strategic progress in the field of pressure sensing.

The ALMA Spectroscopic Survey in the Hubble Ultra Deep Field: Search for [CII] Line and Dust Emission in 6

NASA Astrophysics Data System (ADS)

Aravena, M.; Decarli, R.; Walter, F.; Bouwens, R.; Oesch, P. A.; Carilli, C. L.; Bauer, F. E.; Da Cunha, E.; Daddi, E.; Gónzalez-López, J.; Ivison, R. J.; Riechers, D. A.; Smail, I.; Swinbank, A. M.; Weiss, A.; Anguita, T.; Bacon, R.; Bell, E.; Bertoldi, F.; Cortes, P.; Cox, P.; Hodge, J.; Ibar, E.; Inami, H.; Infante, L.; Karim, A.; Magnelli, B.; Ota, K.; Popping, G.; van der Werf, P.; Wagg, J.; Fudamoto, Y.

2016-12-01

We present a search for [C II] line and dust continuum emission from optical dropout galaxies at z > 6 using ASPECS, our Atacama Large Millimeter submillimeter Array Spectroscopic Survey in the Hubble Ultra-deep Field (UDF). Our observations, which cover the frequency range of 212-272 GHz, encompass approximately the range of 6 < z < 8 for [C II] line emission and reach a limiting luminosity of L [C II] ˜ (1.6-2.5) × 108 L ⊙. We identify 14 [C II] line emitting candidates in this redshift range with significances >4.5σ, two of which correspond to blind detections with no optical counterparts. At this significance level, our statistical analysis shows that about 60% of our candidates are expected to be spurious. For one of our blindly selected [C II] line candidates, we tentatively detect the CO(6-5) line in our parallel 3 mm line scan. None of the line candidates are individually detected in the 1.2 mm continuum. A stack of all [C II] candidates results in a tentative detection with S 1.2 mm = 14 ± 5 μJy. This implies a dust-obscured star-formation rate (SFR) of (3 ± 1) M ⊙ yr-1. We find that the two highest-SFR objects have candidate [C II] lines with luminosities that are consistent with the low-redshift L [C II] versus SFR relation. The other candidates have significantly higher [C II] luminosities than expected from their UV-based SFR. At the current sensitivity, it is unclear whether the majority of these sources are intrinsically bright [C II] emitters, or spurious sources. If only one of our line candidates was real (a scenario greatly favored by our statistical analysis), we find a source density for [C II] emitters at 6 < z < 8 that is significantly higher than predicted by current models and some extrapolations from galaxies in the local universe.

Analysis of spatial and temporal rainfall trends in Sicily during the 1921-2012 period

NASA Astrophysics Data System (ADS)

Liuzzo, Lorena; Bono, Enrico; Sammartano, Vincenzo; Freni, Gabriele

2016-10-01

Precipitation patterns worldwide are changing under the effects of global warming. The impacts of these changes could dramatically affect the hydrological cycle and, consequently, the availability of water resources. In order to improve the quality and reliability of forecasting models, it is important to analyse historical precipitation data to account for possible future changes. For these reasons, a large number of studies have recently been carried out with the aim of investigating the existence of statistically significant trends in precipitation at different spatial and temporal scales. In this paper, the existence of statistically significant trends in rainfall from observational datasets, which were measured by 245 rain gauges over Sicily (Italy) during the 1921-2012 period, was investigated. Annual, seasonal and monthly time series were examined using the Mann-Kendall non-parametric statistical test to detect statistically significant trends at local and regional scales, and their significance levels were assessed. Prior to the application of the Mann-Kendall test, the historical dataset was completed using a geostatistical spatial interpolation technique, the residual ordinary kriging, and then processed to remove the influence of serial correlation on the test results, applying the procedure of trend-free pre-whitening. Once the trends at each site were identified, the spatial patterns of the detected trends were examined using spatial interpolation techniques. Furthermore, focusing on the 30 years from 1981 to 2012, the trend analysis was repeated with the aim of detecting short-term trends or possible changes in the direction of the trends. Finally, the effect of climate change on the seasonal distribution of rainfall during the year was investigated by analysing the trend in the precipitation concentration index. The application of the Mann-Kendall test to the rainfall data provided evidence of a general decrease in precipitation in Sicily during the 1921-2012 period. Downward trends frequently occurred during the autumn and winter months. However, an increase in total annual precipitation was detected during the period from 1981 to 2012.

Increased detection of Barrett’s esophagus and esophageal dysplasia with adjunctive use of wide-area transepithelial sample with three-dimensional computer-assisted analysis (WATS)

PubMed Central

Gross, Seth A; Smith, Michael S; Kaul, Vivek

2017-01-01

Background Barrett’s esophagus (BE) and esophageal dysplasia (ED) are frequently missed during screening and surveillance esophagoscopy because of sampling error associated with four-quadrant random forceps biopsy (FB). Aim The aim of this article is to determine if wide-area transepithelial sampling with three-dimensional computer-assisted analysis (WATS) used adjunctively with FB can increase the detection of BE and ED. Methods In this multicenter prospective trial, patients screened for suspected BE and those with known BE undergoing surveillance were enrolled. Patients at 25 community-based practices underwent WATS adjunctively to targeted FB and random four-quadrant FB. Results Of 4203 patients, 594 were diagnosed with BE by FB alone, and 493 additional cases were detected by adding WATS, increasing the overall detection of BE by 83% (493/594, 95% CI 74%–93%). Low-grade dysplasia (LGD) was diagnosed in 26 patients by FB alone, and 23 additional cases were detected by adding WATS, increasing the detection of LGD by 88.5% (23/26, 95% CI 48%–160%). Conclusions Adjunctive use of WATS to FB significantly improves the detection of both BE and ED. Sampling error, an inherent limitation associated with screening and surveillance, can be improved with WATS allowing better informed decisions to be made about the management and subsequent treatment of these patients. PMID:29881608

Water-soluble vitamin homeostasis in fasting northern elephant seals (Mirounga angustirostris) measured by metabolomics analysis and standard methods.

PubMed

Boaz, Segal M; Champagne, Cory D; Fowler, Melinda A; Houser, Dorian H; Crocker, Daniel E

2012-02-01

Despite the importance of water-soluble vitamins to metabolism, there is limited knowledge of their serum availability in fasting wildlife. We evaluated changes in water-soluble vitamins in northern elephant seals, a species with an exceptional ability to withstand nutrient deprivation. We used a metabolomics approach to measure vitamins and associated metabolites under extended natural fasts for up to 7 weeks in free-ranging lactating or developing seals. Water-soluble vitamins were not detected with this metabolomics platform, but could be measured with standard assays. Concentrations of measured vitamins varied independently, but all were maintained at detectable levels over extended fasts, suggesting that defense of vitamin levels is a component of fasting adaptation in the seals. Metabolomics was not ideal for generating complete vitamin profiles in this species, but gave novel insights into vitamin metabolism by detecting key related metabolites. For example, niacin level reductions in lactating females were associated with significant reductions in precursors suggesting downregulation of the niacin synthetic pathway. The ability to detect individual vitamins using metabolomics may be impacted by the large number of novel compounds detected. Modifications to the analysis platforms and compound detection algorithms used in this study may be required for improving water-soluble vitamin detection in this and other novel wildlife systems. Copyright © 2011 Elsevier Inc. All rights reserved.

Predictive criteria for prostate cancer detection in men with serum PSA concentration of 2.0 to 4.0 ng/mL.

PubMed

Kravchick, Sergey; Peled, Ronit; Dorfman, Dov; Agulansky, Leonid; Ben-Dor, David; Cytron, Shmuel

2005-09-01

To assess the usefulness of measuring testosterone, free testosterone, and the free/total (f/t) prostate-specific antigen (PSA) ratio with the intention of reducing the number of unnecessary biopsies in the patients with PSA values between 2.0 and 4.0 ng/mL. Cancer detection is not rare among patients with PSA values between 2.0 and 4.0 ng/mL. A total of 171 men with serum PSA levels of 2.0 to 4.0 ng/mL were enrolled in this study. The f/t PSA ratio and total and free testosterone levels were quantified. All patients underwent transrectal ultrasound-guided biopsy. The cancer detection rate, clinical and pathologic features of the cancers detected, and the probability of cancer detection in relation to the f/t PSA ratio and total and free testosterone levels were estimated. Two-step statistical analysis was used for descriptive purposes and in the detection of cancer predictors. Statistical significance was set at P < or = 0.05. The mean patient age was 63.3 years. Cancer was detected in 39 (22.8%) of the 171 patients. Only 15.4% of our patients had insignificant cancer. The f/t PSA ratio and total and free testosterone levels were significantly lower in the patients with prostate cancer (19.3%, 13.68 nmol/L, and 28.4 pmol/L, respectively; P < 0.001). The f/t PSA ratio and free testosterone were the strongest predictors of cancer detection (P < 0.001). The results of our study have shown that an important number of cancers could be detected in the PSA range of 2.0 to 4.0 ng/mL. The great majority of cancers detected have the features of medically significant tumors. The combination of the f/t PSA ratio and free testosterone measurements may reveal those patients who require biopsy.

Detecting discordance enrichment among a series of two-sample genome-wide expression data sets.

PubMed

Lai, Yinglei; Zhang, Fanni; Nayak, Tapan K; Modarres, Reza; Lee, Norman H; McCaffrey, Timothy A

2017-01-25

With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene set enrichment analysis have been frequently conducted. Integrative analysis can be conducted when multiple data sets are available. In practice, discordant molecular behaviors among a series of data sets can be of biological and clinical interest. In this study, a statistical method is proposed for detecting discordance gene set enrichment. Our method is based on a two-level multivariate normal mixture model. It is statistically efficient with linearly increased parameter space when the number of data sets is increased. The model-based probability of discordance enrichment can be calculated for gene set detection. We apply our method to a microarray expression data set collected from forty-five matched tumor/non-tumor pairs of tissues for studying pancreatic cancer. We divided the data set into a series of non-overlapping subsets according to the tumor/non-tumor paired expression ratio of gene PNLIP (pancreatic lipase, recently shown it association with pancreatic cancer). The log-ratio ranges from a negative value (e.g. more expressed in non-tumor tissue) to a positive value (e.g. more expressed in tumor tissue). Our purpose is to understand whether any gene sets are enriched in discordant behaviors among these subsets (when the log-ratio is increased from negative to positive). We focus on KEGG pathways. The detected pathways will be useful for our further understanding of the role of gene PNLIP in pancreatic cancer research. Among the top list of detected pathways, the neuroactive ligand receptor interaction and olfactory transduction pathways are the most significant two. Then, we consider gene TP53 that is well-known for its role as tumor suppressor in cancer research. The log-ratio also ranges from a negative value (e.g. more expressed in non-tumor tissue) to a positive value (e.g. more expressed in tumor tissue). We divided the microarray data set again according to the expression ratio of gene TP53. After the discordance enrichment analysis, we observed overall similar results and the above two pathways are still the most significant detections. More interestingly, only these two pathways have been identified for their association with pancreatic cancer in a pathway analysis of genome-wide association study (GWAS) data. This study illustrates that some disease-related pathways can be enriched in discordant molecular behaviors when an important disease-related gene changes its expression. Our proposed statistical method is useful in the detection of these pathways. Furthermore, our method can also be applied to genome-wide expression data collected by the recent RNA-seq technology.

Clinical experience with a computer-aided diagnosis system for automatic detection of pulmonary nodules at spiral CT of the chest

NASA Astrophysics Data System (ADS)

Wormanns, Dag; Fiebich, Martin; Saidi, Mustafa; Diederich, Stefan; Heindel, Walter

2001-05-01

The purpose of the study was to evaluate a computer aided diagnosis (CAD) workstation with automatic detection of pulmonary nodules at low-dose spiral CT in a clinical setting for early detection of lung cancer. Two radiologists in consensus reported 88 consecutive spiral CT examinations. All examinations were reviewed using a UNIX-based CAD workstation with a self-developed algorithm for automatic detection of pulmonary nodules. The algorithm was designed to detect nodules with at least 5 mm diameter. The results of automatic nodule detection were compared to the consensus reporting of two radiologists as gold standard. Additional CAD findings were regarded as nodules initially missed by the radiologists or as false positive results. A total of 153 nodules were detected with all modalities (diameter: 85 nodules <5mm, 63 nodules 5-9 mm, 5 nodules >= 10 mm). Reasons for failure of automatic nodule detection were assessed. Sensitivity of radiologists for nodules >=5 mm was 85%, sensitivity of CAD was 38%. For nodules >=5 mm without pleural contact sensitivity was 84% for radiologists at 45% for CAD. CAD detected 15 (10%) nodules not mentioned in the radiologist's report but representing real nodules, among them 10 (15%) nodules with a diameter $GREW5 mm. Reasons for nodules missed by CAD include: exclusion because of morphological features during region analysis (33%), nodule density below the detection threshold (26%), pleural contact (33%), segmentation errors (5%) and other reasons (2%). CAD improves detection of pulmonary nodules at spiral CT significantly and is a valuable second opinion in a clinical setting for lung cancer screening. Optimization of region analysis and an appropriate density threshold have a potential for further improvement of automatic nodule detection.

Chapter 5: Modulation Excitation Spectroscopy with Phase-Sensitive Detection for Surface Analysis

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

Shulda, Sarah; Richards, Ryan M.

Advancements in in situ spectroscopic techniques have led to significant progress being made in elucidating heterogeneous reaction mechanisms. The potential of these progressive methods is often limited only by the complexity of the system and noise in the data. Short-lived intermediates can be challenging, if not impossible, to identify with conventional spectra analysis means. Often equally difficult is separating signals that arise from active and inactive species. Modulation excitation spectroscopy combined with phase-sensitive detection analysis is a powerful tool for removing noise from the data while simultaneously revealing the underlying kinetics of the reaction. A stimulus is applied at amore » constant frequency to the reaction system, for example, a reactant cycled with an inert phase. Through mathematical manipulation of the data, any signal contributing to the overall spectra but not oscillating with the same frequency as the stimulus will be dampened or removed. With phase-sensitive detection, signals oscillating with the stimulus frequency but with various lag times are amplified providing valuable kinetic information. In this chapter, some examples are provided from the literature that have successfully used modulation excitation spectroscopy with phase-sensitive detection to uncover previously unobserved reaction intermediates and kinetics. Examples from a broad range of spectroscopic methods are included to provide perspective to the reader.« less

A micro-Raman spectroscopic investigation of leukemic U-937 cells in aged cultures

NASA Astrophysics Data System (ADS)

Fazio, Enza; Trusso, Sebastiano; Franco, Domenico; Nicolò, Marco Sebastiano; Allegra, Alessandro; Neri, Fortunato; Musolino, Caterina; Guglielmino, Salvatore P. P.

2016-04-01

Recently it has been shown that micro-Raman spectroscopy combined with multivariate analysis is able to discriminate among different types of tissues and tumoral cells by the detection of significant alterations and/or reorganizations of complex biological molecules, such as nucleic acids, lipids and proteins. Moreover, its use, being in principle a non-invasive technique, appears an interesting clinical tool for the evaluation of the therapeutical effects and of the disease progression. In this work we analyzed molecular changes in aged cultures of leukemia model U937 cells with respect to fresh cultures of the same cell line. In fact, structural variations of individual neoplastic cells on aging may lead to a heterogeneous data set, therefore falsifying confidence intervals, increasing error levels of analysis and consequently limiting the use of Raman spectroscopy analysis. We found that the observed morphological changes of U937 cells corresponded to well defined modifications of the Raman contributions in selected spectral regions, where markers of specific functional groups, useful to characterize the cell state, are present. A detailed subcellular analysis showed a change in cellular organization as a function of time, and correlated to a significant increase of apoptosis levels. Besides the aforementioned study, Raman spectra were used as input for principal component analysis (PCA) in order to detect and classify spectral changes among U937 cells.

A population study of hot Jupiter atmospheres

NASA Astrophysics Data System (ADS)

Tsiaras, A.; Waldmann, I. P.; Zingales, T.; Rocchetto, M.; Damiano, M.; Karpouzas, K.; Tinetti, G.; McKemmish, L. K.; Tennyson, J.; Yrchenko, S. N.

2017-09-01

In the past two decades, we have learnt that every star hosts more than one planet. While the hunt for new exoplanets is on-going, the current sample of more than 3500 confirmed planets reveals a wide spectrum of planetary characteristics. While small planets appear to be the most common, the big and gaseous planets play a key role in the process of planetary formation. We present here the analysis of 30 gaseous extra-solar planets, with temperatures between 600 and 2400 K and radii between 0.35 and 1.9 Jupiter radii. These planets were spectroscopically observed with the Wide Field Camera 3 on-board the Hubble Space Telescope, which is currently one of the most successful instruments for observing exoplanetary atmospheres. The quality of the HST/WFC3 spatially-scanned data combined with our specialised analysis tools, allows us to create the largest and most self-consistent sample of exoplanetary transmission spectra to date and study the collective behaviour of warm and hot gaseous planets rather than isolated case-studies. We define a new metric, the Atmospheric Detectability Index (ADI) to evaluate the statistical significance of an atmospheric detection and find statistically significant atmospheres around 16 planets. For most of the Jupiters in our sample we find the detectability of their atmospheres to be dependent on the planetary radius but not on the planetary mass. This indicates that planetary gravity is a secondary factor in the evolution of planetary atmospheres. We detect the presence of water vapour in all the statistically detectable atmospheres and we cannot rule out its presence in the atmospheres of the others. In addition, TiO and/or VO signatures are detected with 4σ confidence in WASP-76 b, and they are most likely present on WASP-121 b. We find no correlation between expected signal-to-noise and atmospheric detectability for most targets. This has important implications for future large-scale surveys.

Detection of myocardial ischemia by automated, motion-corrected, color-encoded perfusion maps compared with visual analysis of adenosine stress cardiovascular magnetic resonance imaging at 3 T: a pilot study.

PubMed

Doesch, Christina; Papavassiliu, Theano; Michaely, Henrik J; Attenberger, Ulrike I; Glielmi, Christopher; Süselbeck, Tim; Fink, Christian; Borggrefe, Martin; Schoenberg, Stefan O

2013-09-01

The purpose of this study was to compare automated, motion-corrected, color-encoded (AMC) perfusion maps with qualitative visual analysis of adenosine stress cardiovascular magnetic resonance imaging for detection of flow-limiting stenoses. Myocardial perfusion measurements applying the standard adenosine stress imaging protocol and a saturation-recovery temporal generalized autocalibrating partially parallel acquisition (t-GRAPPA) turbo fast low angle shot (Turbo FLASH) magnetic resonance imaging sequence were performed in 25 patients using a 3.0-T MAGNETOM Skyra (Siemens Healthcare Sector, Erlangen, Germany). Perfusion studies were analyzed using AMC perfusion maps and qualitative visual analysis. Angiographically detected coronary artery (CA) stenoses greater than 75% or 50% or more with a myocardial perfusion reserve index less than 1.5 were considered as hemodynamically relevant. Diagnostic performance and time requirement for both methods were compared. Interobserver and intraobserver reliability were also assessed. A total of 29 CA stenoses were included in the analysis. Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy for detection of ischemia on a per-patient basis were comparable using the AMC perfusion maps compared to visual analysis. On a per-CA territory basis, the attribution of an ischemia to the respective vessel was facilitated using the AMC perfusion maps. Interobserver and intraobserver reliability were better for the AMC perfusion maps (concordance correlation coefficient, 0.94 and 0.93, respectively) compared to visual analysis (concordance correlation coefficient, 0.73 and 0.79, respectively). In addition, in comparison to visual analysis, the AMC perfusion maps were able to significantly reduce analysis time from 7.7 (3.1) to 3.2 (1.9) minutes (P < 0.0001). The AMC perfusion maps yielded a diagnostic performance on a per-patient and on a per-CA territory basis comparable with the visual analysis. Furthermore, this approach demonstrated higher interobserver and intraobserver reliability as well as a better time efficiency when compared to visual analysis.

Prospective randomized controlled trial evaluating cap-assisted colonoscopy vs standard colonoscopy

PubMed Central

Tee, Hoi-Poh; Corte, Crispin; Al-Ghamdi, Hamdan; Prakoso, Emilia; Darke, John; Chettiar, Raman; Rahman, Wassim; Davison, Scott; Griffin, Sean P; Selby, Warwick S; Kaffes, Arthur J

2010-01-01

AIM: To study the significance of cap-fitted colonoscopy in improving cecal intubation time and polyp detection rate. METHODS: This study was a prospective randomized controlled trial conducted from March 2008 to February 2009 in a tertiary referral hospital at Sydney. The primary end point was cecal intubation time and the secondary endpoint was polyp detection rate. Consecutive cases of total colonoscopy over a 1-year period were recruited. Randomization into either standard colonoscopy (SC) or cap-assisted colonoscopy (CAC) was performed after consent was obtained. For cases randomized to CAC, one of the three sizes of cap was used: D-201-15004 (with a diameter of 15.3 mm), D-201-14304 (14.6 mm) and D-201-12704 (13.0 mm). All of these caps were produced by Olympus Medical Systems, Japan. Independent predictors for faster cecal time and better polyp detection rate were also determined from this study. RESULTS: There were 200 cases in each group. There was no significant difference in terms of demographic characteristics between the two groups. CAC, when compared to the SC group, had no significant difference in terms of cecal intubation rate (96.0% vs 97.0%, P = 0.40) and time (9.94 ± 7.05 min vs 10.34 ± 6.82 min, P = 0.21), or polyp detection rate (32.8% vs 31.3%, P = 0.75). On the subgroup analysis, there was no significant difference in terms of cecal intubation time by trainees (88.1% vs 84.8%, P = 0.40), ileal intubation rate (82.5% vs 79.0%, P = 0.38) or total colonoscopy time (23.24 ± 13.95 min vs 22.56 ± 9.94 min, P = 0.88). On multivariate analysis, the independent determinants of faster cecal time were consultant-performed procedures (P < 0.001), male patients (P < 0.001), non-usage of hyoscine (P < 0.001) and better bowel preparation (P = 0.01). The determinants of better polyp detection rate were older age (P < 0.001), no history of previous abdominal surgery (P = 0.04), patients not having esophagogastroduodenoscopy in the same setting (P = 0.003), trainee-performed procedures (P = 0.01), usage of hyoscine (P = 0.01) and procedures performed for polyp follow-up (P = 0.01). The limitations of the study were that it was a single-center experience, no blinding was possible, and there were a large number of endoscopists. CONCLUSION: CAC did not significantly different from SC in term of cecal intubation time and polyp detection rate. PMID:20712051

Validation of whole-blood transcriptome signature during microdose recombinant human erythropoietin (rHuEpo) administration.

PubMed

Wang, Guan; Durussel, Jérôme; Shurlock, Jonathan; Mooses, Martin; Fuku, Noriyuki; Bruinvels, Georgie; Pedlar, Charles; Burden, Richard; Murray, Andrew; Yee, Brendan; Keenan, Anne; McClure, John D; Sottas, Pierre-Edouard; Pitsiladis, Yannis P

2017-11-14

Recombinant human erythropoietin (rHuEpo) can improve human performance and is therefore frequently abused by athletes. As a result, the World Anti-Doping Agency (WADA) introduced the Athlete Biological Passport (ABP) as an indirect method to detect blood doping. Despite this progress, challenges remain to detect blood manipulations such as the use of microdoses of rHuEpo. Forty-five whole-blood transcriptional markers of rHuEpo previously derived from a high-dose rHuEpo administration trial were used to assess whether microdoses of rHuEpo could be detected in 14 trained subjects and whether these markers may be confounded by exercise (n = 14 trained subjects) and altitude training (n = 21 elite runners and n = 4 elite rowers, respectively). Differential gene expression analysis was carried out following normalisation and significance declared following application of a 5% false discovery rate (FDR) and a 1.5 fold-change. Adaptive model analysis was also applied to incorporate these markers for the detection of rHuEpo. ALAS2, BCL2L1, DCAF12, EPB42, GMPR, SELENBP1, SLC4A1, TMOD1 and TRIM58 were differentially expressed during and throughout the post phase of microdose rHuEpo administration. The CD247 and TRIM58 genes were significantly up- and down-regulated, respectively, immediately following exercise when compared with the baseline both before and after rHuEpo/placebo. No significant gene expression changes were found 30 min after exercise in either rHuEpo or placebo groups. ALAS2, BCL2L1, DCAF12, SLC4A1, TMOD1 and TRIM58 tended to be significantly expressed in the elite runners ten days after arriving at altitude and one week after returning from altitude (FDR > 0.059, fold-change varying from 1.39 to 1.63). Following application of the adaptive model, 15 genes showed a high sensitivity (≥ 93%) and specificity (≥ 71%), with BCL2L1 and CSDA having the highest sensitivity (93%) and specificity (93%). Current results provide further evidence that transcriptional biomarkers can strengthen the ABP approach by significantly prolonging the detection window and improving the sensitivity and specificity of blood doping detection. Further studies are required to confirm, and if necessary, integrate the confounding effects of altitude training on blood doping.

[G6PD deficiency among children under 7 years old from Yunnan with unique ethnic minority origin].

PubMed

Yao, Li-qin; Zou, Tuan-biao; Wang, Xing-tian; Quan, Xing; Chen, Qian; Yang, Fa-bin; Hu, Li-sha; Fan, Li-mei; Wang, Min; Feng, Xi-yun; Liu, Jin-tao; Zhao, Zhong-ming

2013-04-01

To investigate the epidemiological status of glucose-6-phosphate dehydrogenase (G6PD) deficiency among children from Yunnan with unique ethnic origins. DNA samples from 11759 children were tested with fluorescent spot test, G6PD/6PGD quantitative ratio assay and hemoglobin electrophoresis. The detection rate of G6PD deficiency was 2.5%, for which boys were significantly greater than girls (3.5% vs. 1.4%, P<0.05). Significant differences were also detected among children from different ethnic groups and different regions. For ethnic Han Chinese, the detection rate was 0.7%, which was lower than the majority of ethnic minorities. By regression analysis, altitude of residence and family history both have significant influence on the calculated rate. Occurrence of G6PD deficiency seems to be influenced by gender. It also varies substantially between different ethnic groups as well as regions, e.g., more common in south. It also showed a declining trend after years of diagnosis and intervention. This survey may provide a valuable basis for counseling of G6PD deficiency in Yunnan.

Temporal changes and variability in temperature series over Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Suhaila, Jamaludin

2015-02-01

With the current concern over climate change, the descriptions on how temperature series changed over time are very useful. Annual mean temperature has been analyzed for several stations over Peninsular Malaysia. Non-parametric statistical techniques such as Mann-Kendall test and Theil-Sen slope estimation are used primarily for assessing the significance and detection of trends, while a nonparametric Pettitt's test and sequential Mann-Kendall test are adopted to detect any abrupt climate change. Statistically significance increasing trends for annual mean temperature are detected for almost all studied stations with the magnitude of significant trend varied from 0.02°C to 0.05°C per year. The results shows that climate over Peninsular Malaysia is getting warmer than before. In addition, the results of the abrupt changes in temperature using Pettitt's and sequential Mann-Kendall test reveal the beginning of trends which can be related to El Nino episodes that occur in Malaysia. In general, the analysis results can help local stakeholders and water managers to understand the risks and vulnerabilities related to climate change in terms of mean events in the region.

Methodological Approaches for Monitoring Opportunistic Pathogens in Premise Plumbing: A Review

PubMed Central

Wang, Hong; Bedard, Emilie; Prevost, Michele; Camper, Anne K.; Hill, Vincent R.; Pruden, Amy

2017-01-01

Opportunistic pathogens inhabiting premise (i.e., building) plumbing (OPPPs, e.g., L. pneumophila, M. avium complex, P. aeruginosa, Acanthamoeba, and N. fowleri) are a significant and growing source of disease. Because OPPPs establish and grow as part of the native drinking water microbiota, they do not correspond to fecal indicators, presenting a significant challenge to common and effective monitoring strategies. Further, different OPPPs present distinct requirements for sampling, preservation, and analysis, creating a significant impediment to their parallel detection. The aim of this critical review is to synthesize the state of the science of monitoring OPPPs and to identify a path forward for their simultaneous detection and quantification in a manner commensurate with the need for reliable data to inform risk assessment and mitigation. Water and biofilm sampling procedures, as well as factors influencing sample representativeness and detection sensitivity, are critically evaluated with respect to the five representative bacterial and amoebal OPPPs noted above. Available culturing and molecular approaches are discussed in terms of their advantages, limitations, and applicability. Knowledge gaps and research needs are identified. PMID:28390237

Human Deception Detection from Whole Body Motion Analysis

DTIC Science & Technology

2015-12-01

9.3.2. Prediction Probability The output reports from SPSS detail the stepwise procedures for each series of analyses using Wald statistic values for... statistical significance in determining replication, but instead used a combination of significance and direction of means to determine partial or...and the independents need not be unbound. All data were analyzed utilizing the Statistical Package for Social Sciences ( SPSS , v.19.0, Chicago, IL

Hepatozoon caimani in Caiman crocodilus yacare (Crocodylia, Alligatoridae) from North Pantanal, Brazil.

PubMed

Bouer, Andréa; André, Marcos Rogério; Gonçalves, Luiz Ricardo; Luzzi, Mayara de Cássia; Oliveira, Juliana Paula de; Rodrigues, Adriana Carlos; Varani, Alessandro de Melo; Miranda, Vitor Fernandes Oliveira de; Perles, Lívia; Werther, Karin; Machado, Rosangela Zacarias

2017-01-01

Hepatozoon species are the most common intracellular hemoparasite found in reptiles. Hepatozoon caimani, whose vectors are Culex mosquitoes, has been detected in a high prevalence among caimans in Brazil by blood smears examinations. The present work aimed to detect and characterize the Hepatozoon spp. found in 33 caimans (24 free-ranging and 9 captive; 28 males and 5 females) (Caiman crocodilus yacare) sampled at Poconé, North Pantanal, state of Mato Grosso, Brazil, using blood smears examinations and molecular techniques. Hepatozoon spp.-gametocytes were found in 70.8% (17/24) and 88.8% (8/9) of blood smears from free-ranging and captive caimans, respectively. Hepatozoon spp. 18S rRNA DNA was found in 79.2% (19/24) and 88.8% (8/9) of free-ranging and captive caimans, respectively. Comparative analysis of parasitized and non-parasitized erythrocytes showed that all analyzed features were significantly different (P<0.05) for both linear and area dimensions. Phylogenetic analysis based on 18S rRNA sequences grouped the Hepatozoon spp. sequences detected in the present study together with H. caimani, recently detected in caimans in southern Pantanal.

Detection of the Spermicide Nonoxynol-9 Via GC-MS

NASA Astrophysics Data System (ADS)

Musah, Rabi A.; Vuong, Angela L.; Henck, Colin; Shepard, Jason R. E.

2012-05-01

The spermicide nonoxynol-9 is actually a complex mixture of dozens of closely related amphiphilic compounds, and the chemical properties of this assortment significantly hamper its characterization by GC-MS. The inability to perform routine GC-MS testing on nonoxynol-9 has limited its evidentiary value in forensic casework, which relies heavily on this technique for analysis. A disturbing trend in sexual assault is the use of condoms by assailants, to avoid leaving behind DNA evidence that can connect a perpetrator to a victim. This observation necessitates the development of alternative methods for the analysis of trace evidence that can show causal links between a victim and a suspect. Detection of lubricants associated with sexual assault is one such way to establish this connection. The development of GC-MS methods that permit facile detection of both nonoxynol-9 alone and nonoxynol-9 extracted from other complex matrices that have potential as trace evidence in sexual assault is reported. A detection limit of 2.14 μg of nonoxynol-9 is demonstrated, and a detailed mass spectral profile that elaborates on what is known of its structure is provided.

[Analysis of phthalates in aromatic and deodorant aerosol products and evaluation of exposure risk].

PubMed

Sato, Yoshiki; Sugaya, Naeko; Nakagawa, Tomoo; Morita, Masatoshi

2015-01-01

We established an analytical method for the detection of seven phthalates, dimethyl phthalate, diethyl phthalate (DEP), benzyl butyl phthalate, di-i-butyl phthalate, dibutyl phthalate (DBP), diethylhexyl phthalate (DEHP), and di-n-octhyl phthalate, using an ultra high performance liquid chromatograph equipped with a photodiode array detector. This method is quick, with minimal contamination, and was applied to the analysis of aromatic and deodorant aerosol products. Phthalates were detected in 15 of 52 samples purchased from 1999 to 2012 in Yokohama. Three types of phthalate (DEP, DBP, DEHP) were detected, and their concentrations ranged from 0.0085-0.23% DEP in nine samples, 0.012-0.045% DBP in four samples, and 0.012-0.033% DEHP in four samples. No other phthalate esters were detected. Furthermore, we estimated phthalate exposure via breathing in commonly used aromatic and deodorant aerosol products, then evaluated the associated risk. The estimated levels of phthalate exposure were lower than the tolerated daily limit, but the results indicated that aromatic and deodorant aerosol products could be a significant source of phthalate exposure.

Nanomaterial-based Microfluidic Chips for the Capture and Detection of Circulating Tumor Cells.

PubMed

Sun, Duanping; Chen, Zuanguang; Wu, Minhao; Zhang, Yuanqing

2017-01-01

Circulating tumor cells (CTCs), a type of cancer cells that spreads from primary or metastatic tumors into the bloodstream, can lead to a new fatal metastasis. As a new type of liquid biopsy, CTCs have become a hot pursuit and detection of CTCs offers the possibility for early diagnosis of cancers, earlier evaluation of chemotherapeutic efficacy and cancer recurrence, and choice of individual sensitive anti-cancer drugs. The fundamental challenges of capturing and characterizing CTCs are the extremely low number of CTCs in the blood and the intrinsic heterogeneity of CTCs. A series of microfluidic devices have been proposed for the analysis of CTCs with automation capability, precise flow behaviors, and significant advantages over the conventional larger scale systems. This review aims to provide in-depth insights into CTCs analysis, including various nanomaterial-based microfluidic chips for the capture and detection of CTCs based on the specific biochemical and physical properties of CTCs. The current developmental trends and promising research directions in the establishment of microfluidic chips for the capture and detection of CTCs are also discussed.

Identifying changing aviation threat environments within an adaptive Homeland Security Advisory System.

PubMed

Lee, Adrian J; Jacobson, Sheldon H

2012-02-01

A critical component of aviation security consists of screening passengers and baggage to protect airports and aircraft from terrorist threats. Advancements in screening device technology have increased the ability to detect these threats; however, specifying the operational configurations of these devices in response to changes in the threat environment can become difficult. This article proposes to use Fisher information as a statistical measure for detecting changes in the threat environment. The perceived risk of passengers, according to prescreening information and behavior analysis, is analyzed as the passengers sequentially enter the security checkpoint. The alarm responses from the devices used to detect threats are also analyzed to monitor significant changes in the frequency of threat items uncovered. The key results are that this information-based measure can be used within the Homeland Security Advisory System to indicate changes in threat conditions in real time, and provide the flexibility of security screening detection devices to responsively and automatically adapt operational configurations to these changing threat conditions. © 2012 Society for Risk Analysis. All rights reserved.

Audio-video feature correlation: faces and speech

NASA Astrophysics Data System (ADS)

Durand, Gwenael; Montacie, Claude; Caraty, Marie-Jose; Faudemay, Pascal

1999-08-01

This paper presents a study of the correlation of features automatically extracted from the audio stream and the video stream of audiovisual documents. In particular, we were interested in finding out whether speech analysis tools could be combined with face detection methods, and to what extend they should be combined. A generic audio signal partitioning algorithm as first used to detect Silence/Noise/Music/Speech segments in a full length movie. A generic object detection method was applied to the keyframes extracted from the movie in order to detect the presence or absence of faces. The correlation between the presence of a face in the keyframes and of the corresponding voice in the audio stream was studied. A third stream, which is the script of the movie, is warped on the speech channel in order to automatically label faces appearing in the keyframes with the name of the corresponding character. We naturally found that extracted audio and video features were related in many cases, and that significant benefits can be obtained from the joint use of audio and video analysis methods.

Highly sensitive and selective dynamic light-scattering assay for TNT detection using p-ATP attached gold nanoparticle.

PubMed

Dasary, Samuel S R; Senapati, Dulal; Singh, Anant Kumar; Anjaneyulu, Yerramilli; Yu, Hongtao; Ray, Paresh Chandra

2010-12-01

TNT is one of the most commonly used nitro aromatic explosives for landmines of military and terrorist activities. As a result, there is an urgent need for rapid and reliable methods for the detection of trace amount of TNT for screenings in airport, analysis of forensic samples, and environmental analysis. Driven by the need to detect trace amounts of TNT from environmental samples, this article demonstrates a label-free, highly selective, and ultrasensitive para-aminothiophenol (p-ATP) modified gold nanoparticle based dynamic light scattering (DLS) probe for TNT recognition in 100 pico molar (pM) level from ethanol:acetonitile mixture solution. Because of the formation of strong π-donor-acceptor interaction between TNT and p-ATP, para-aminothiophenol attached gold nanoparticles undergo aggregation in the presence of TNT, which changes the DLS intensity tremendously. A detailed mechanism for significant DLS intensity change has been discussed. Our experimental results show that TNT can be detected quickly and accurately without any dye tagging in 100 pM level with excellent discrimination against other nitro compounds.

Lineage divergence detected in the malaria vector Anopheles marajoara (Diptera: Culicidae) in Amazonian Brazil

PubMed Central

2010-01-01

Background Cryptic species complexes are common among anophelines. Previous phylogenetic analysis based on the complete mtDNA COI gene sequences detected paraphyly in the Neotropical malaria vector Anopheles marajoara. The "Folmer region" detects a single taxon using a 3% divergence threshold. Methods To test the paraphyletic hypothesis and examine the utility of the Folmer region, genealogical trees based on a concatenated (white + 3' COI sequences) dataset and pairwise differentiation of COI fragments were examined. The population structure and demographic history were based on partial COI sequences for 294 individuals from 14 localities in Amazonian Brazil. 109 individuals from 12 localities were sequenced for the nDNA white gene, and 57 individuals from 11 localities were sequenced for the ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2). Results Distinct A. marajoara lineages were detected by combined genealogical analysis and were also supported among COI haplotypes using a median joining network and AMOVA, with time since divergence during the Pleistocene (<100,000 ya). COI sequences at the 3' end were more variable, demonstrating significant pairwise differentiation (3.82%) compared to the more moderate 2.92% detected by the Folmer region. Lineage 1 was present in all localities, whereas lineage 2 was restricted mainly to the west. Mismatch distributions for both lineages were bimodal, likely due to multiple colonization events and spatial expansion (~798 - 81,045 ya). There appears to be gene flow within, not between lineages, and a partial barrier was detected near Rio Jari in Amapá state, separating western and eastern populations. In contrast, both nDNA data sets (white gene sequences with or without the retention of the 4th intron, and ITS2 sequences and length) detected a single A. marajoara lineage. Conclusions Strong support for combined data with significant differentiation detected in the COI and absent in the nDNA suggest that the divergence is recent, and detectable only by the faster evolving mtDNA. A within subgenus threshold of >2% may be more appropriate among sister taxa in cryptic anopheline complexes than the standard 3%. Differences in demographic history and climatic changes may have contributed to mtDNA lineage divergence in A. marajoara. PMID:20929572

Towards a global flood detection system using social media

NASA Astrophysics Data System (ADS)

de Bruijn, Jens; de Moel, Hans; Jongman, Brenden; Aerts, Jeroen

2017-04-01

It is widely recognized that an early warning is critical in improving international disaster response. Analysis of social media in real-time can provide valuable information about an event or help to detect unexpected events. For successful and reliable detection systems that work globally, it is important that sufficient data is available and that the algorithm works both in data-rich and data-poor environments. In this study, both a new geotagging system and multi-level event detection system for flood hazards was developed using Twitter data. Geotagging algorithms that regard one tweet as a single document are well-studied. However, no algorithms exist that combine several sequential tweets mentioning keywords regarding a specific event type. Within the time frame of an event, multiple users use event related keywords that refer to the same place name. This notion allows us to treat several sequential tweets posted in the last 24 hours as one document. For all these tweets, we collect a series of spatial indicators given in the tweet metadata and extract additional topological indicators from the text. Using these indicators, we can reduce ambiguity and thus better estimate what locations are tweeted about. Using these localized tweets, Bayesian change-point analysis is used to find significant increases of tweets mentioning countries, provinces or towns. In data-poor environments detection of events on a country level is possible, while in other, data-rich, environments detection on a city level is achieved. Additionally, on a city-level we analyse the spatial dependence of mentioned places. If multiple places within a limited spatial extent are mentioned, detection confidence increases. We run the algorithm using 2 years of Twitter data with flood related keywords in 13 major languages and validate against a flood event database. We find that the geotagging algorithm yields significantly more data than previously developed algorithms and successfully deals with ambiguous place names. In addition, we show that our detection system can both quickly and reliably detect floods, even in countries where data is scarce, while achieving high detail in countries where more data is available.

Care dependency of hospitalized children: testing the Care Dependency Scale for Paediatrics in a cross-cultural comparison.

PubMed

Tork, Hanan; Dassen, Theo; Lohrmann, Christa

2009-02-01

This paper is a report of a study to examine the psychometric properties of the Care Dependency Scale for Paediatrics in Germany and Egypt and to compare the care dependency of school-age children in both countries. Cross-cultural differences in care dependency of older adults have been documented in the literature, but little is known about the differences and similarities with regard to children's care dependency in different cultures. A convenience sample of 258 school-aged children from Germany and Egypt participated in the study in 2005. The reliability of the Care Dependency Scale for Paediatrics was assessed in terms of internal consistency and interrater reliability. Factor analysis (principal component analysis) was employed to verify the construct validity. A Visual Analogue Scale was used to investigate the criterion-related validity. Good internal consistency was detected both for the Arabic and German versions. Factor analysis revealed one factor for both versions. A Pearson's correlation between the Care Dependency Scale for Paediatrics and Visual Analogue Scale was statistically significant for both versions indicating criterion-related validity. Statistically significant differences between the participants were detected regarding the mean sum score on the Care Dependency Scale for Paediatrics. The Care Dependency Scale for Paediatrics is a reliable and valid tool for assessing the care dependency of children and is recommended for assessing the care dependency of children from different ethnic origins. Differences in care dependency between German and Egyptian children were detected, which might be due to cultural differences.

A New Method for the Fast Analysis of Trihalomethanes in Tap and Recycled Waters Using Headspace Gas Chromatography with Micro-Electron Capture Detection

PubMed Central

Alexandrou, Lydon D.; Meehan, Barry J.; Morrison, Paul D.; Jones, Oliver A. H.

2017-01-01

Chemical disinfection of water supplies brings significant public health benefits by reducing microbial contamination. The process can however, result in the formation of toxic compounds through interactions between disinfectants and organic material in the source water. These new compounds are termed disinfection by-products (DBPs). The most common are the trihalomethanes (THMs) such as trichloromethane (chloroform), dichlorobromomethane, chlorodibromomethane and tribromomethane (bromoform); these are commonly reported as a single value for total trihalomethanes (TTHMs). Analysis of DBPs is commonly performed via time- and solvent-intensive sample preparation techniques such as liquid–liquid and solid phase extraction. In this study, a method using headspace gas chromatography with micro-electron capture detection was developed and applied for the analysis of THMs in drinking and recycled waters from across Melbourne (Victoria, Australia). The method allowed almost complete removal of the sample preparation step whilst maintaining trace level detection limits (>1 ppb). All drinking water samples had TTHM concentrations below the Australian regulatory limit of 250 µg/L but some were above the U.S. EPA limit of 60 µg/L. The highest TTHM concentration was 67.2 µg/L and lowest 22.9 µg/L. For recycled water, samples taken directly from treatment plants held significantly higher concentrations (153.2 µg/L TTHM) compared to samples from final use locations (4.9–9.3 µg/L). PMID:28505068

Analysis of antimicrobial resistance genes detected in multidrug-resistant Salmonella enterica serovar Typhimurium isolated from food animals.

PubMed

Glenn, LaShanda M; Lindsey, Rebecca L; Frank, Joseph F; Meinersmann, Richard J; Englen, Mark D; Fedorka-Cray, Paula J; Frye, Jonathan G

2011-09-01

Multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium is the most prevalent penta-resistant serovar isolated from animals by the U.S. National Antimicrobial Resistance Monitoring System. Penta-resistant isolates are often resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline. To investigate MDR in Salmonella Typhimurium (including variant 5-), one isolate each from cattle, poultry, and swine with at least the ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline phenotype were selected for each year from 1997 to 2007 (n = 33) for microarray analysis of antimicrobial resistance, incompatibility IncA/C, and HI1 plasmid genes. Cluster analysis based on these data separated 31 of the isolates into two groups A and B (15 and 16 isolates, respectively). Isolates in group A were phage type DT104 or U302 and were mostly swine isolates (7/15). Genes detected included intI1, bla(PSE-1), floR, aadA, sulI, tet(G), and tetR, which are often found in Salmonella Genomic Island I. Isolates in group B had numerous IncA/C plasmid genes detected and were mostly cattle isolates (9/16). Genes detected included bla(CMY-2), floR, aac(3), aadA, aphA1, strA, strB, sulI, sulII, dfrA, dhf, tet(A)(B)(C)(D), and tetR, which are often found on MDR-AmpC IncA/C plasmids. The IncA/C replicon was also detected in all group B isolates. The two remaining isolates did not cluster with any others and both had many HI1 plasmid genes detected. Linkage disequilibrium analysis detected significant associations between plasmid replicon type, phage type, and animal source. These data suggest that MDR in Salmonella Typhimurium is associated with DT104/Salmonella Genomic Island I or IncA/C MDR-AmpC encoding plasmids and these genetic elements have persisted throughout the study period.

High-frequency oscillations in epilepsy and surgical outcome. A meta-analysis

PubMed Central

Höller, Yvonne; Kutil, Raoul; Klaffenböck, Lukas; Thomschewski, Aljoscha; Höller, Peter M.; Bathke, Arne C.; Jacobs, Julia; Taylor, Alexandra C.; Nardone, Raffaele; Trinka, Eugen

2015-01-01

High frequency oscillations (HFOs) are estimated as a potential marker for epileptogenicity. Current research strives for valid evidence that these HFOs could aid the delineation of the to-be resected area in patients with refractory epilepsy and improve surgical outcomes. In the present meta-analysis, we evaluated the relation between resection of regions from which HFOs can be detected and outcome after epilepsy surgery. We conducted a systematic review of all studies that related the resection of HFO-generating areas to postsurgical outcome. We related the outcome (seizure freedom) to resection ratio, that is, the ratio between the number of channels on which HFOs were detected and, among these, the number of channels that were inside the resected area. We compared the resection ratio between seizure free and not seizure free patients. In total, 11 studies were included. In 10 studies, ripples (80–200 Hz) were analyzed, and in 7 studies, fast ripples (>200 Hz) were studied. We found comparable differences (dif) and largely overlapping confidence intervals (CI) in resection ratios between outcome groups for ripples (dif = 0.18; CI: 0.10–0.27) and fast ripples (dif = 0.17; CI: 0.01–0.33). Subgroup analysis showed that automated detection (dif = 0.22; CI: 0.03–0.41) was comparable to visual detection (dif = 0.17; CI: 0.08–0.27). Considering frequency of HFOs (dif = 0.24; CI: 0.09–0.38) was related more strongly to outcome than considering each electrode that was showing HFOs (dif = 0.15; CI = 0.03–0.27). The effect sizes found in the meta-analysis are small but significant. Automated detection and application of a detection threshold in order to detect channels with a frequent occurrence of HFOs is important to yield a marker that could be useful in presurgical evaluation. In order to compare studies with different methodological approaches, detailed and standardized reporting is warranted. PMID:26539097

[Identification of an ideal noninvasive method to detect A3243G gene mutation in MELAS syndrome].

PubMed

Ma, Yi-nan; Fang, Fang; Yang, Yan-ling; Zhang, Ying; Wang, Song-tao; Xu, Yu-feng; Pei, Pei; Yuan, Yun; Bu, Ding-fang; Qi, Yu

2008-12-16

To identify a better non-invasive method to detect the carrier of mitochondrial A3243G mutation, a cause of mitochondrial encephalopathy-lactic acidosis-stroke like episode (MELAS) syndrome. DNA was extracted from the peripheral blood, urine, hair follicle, and saliva of 25 MELAS syndrome patients carrying A3243G mutation and their mothers and other maternal relatives, 33 persons in number, and the muscle tissues from 5 patients obtained by biopsy. A3243G mutation was detected by PCR-RFLP method, and the A3243G mutation ratio was identified by measuring the density of each band and calculation with the software AlphaEase 5.0. A3243G mutations were detected in all tissues of the 25 MELAS patients. The A3243G mutation ratio in urine was 62% +/- 9%, significantly higher than that in the blood [(36% +/- 10%), t = -11.13, P < 0.01]. A3243G mutations were detected in at least one tissue of the 28 maternal relatives. The A3243G mutation rates in their urine samples was 33.0% (5.0% - 70.4%), significantly higher than that in their blood samples [8.0% (0 - 33.3%), z = -4.197, P < 0.01]. There was no significant difference in A3243G mutation ratio among the samples of hair follicle, saliva, and blood. The A3243G mutation ratio in urine is significantly higher than those in blood samples of the patients and their maternal relatives. A noninvasive method, A3243G mutation ratio analysis of urine is superior to that in blood.

Clinical significance of hTERC gene amplification detection by FISH in the screening of cervical lesions.

PubMed

Zhang, Yuan; Wang, Xiaobei; Ma, Ling; Wang, Zehua; Hu, Lihua

2009-06-01

This study evaluated the clinical significance of hTERC gene amplification detection by fluorescence in situ hybridization (FISH) in the screening of cervical lesions. Cervical specimens of 50 high risk patients were detected by thin liquid-based cytology. The patients whose cytological results were classified as ASCUS or above were subjected to the subsequent colposcopic biopsies. Slides prepared from these 50 cervical specimens were analyzed for hTERC gene amplification using interphase FISH with the two-color hTERC probe. The results of the cytological analysis and those of subsequent biopsies, when available, were compared with the FISH-detected hTERC abnormalities. It was found that the positive rates of hTERC gene amplification in NILM, ASCUS, LSIL, HSIL, and SCC groups were 0.00, 28.57%, 57.14%, 100%, and 100%, respectively. The positive rates of hTERC gene amplification in HSIL and SCC groups were significantly higher than those in NILM, ASCUS and LSIL groups (all P<0.05). The mean percentages of cells with hTERC gene amplification in NILM, ASCUS, LSIL, HSIL, and SCC groups were 0.00, 10.50%, 36.00%, 79.00%, and 96.50%, respectively. Patients with HSIL or SCC cytological diagnoses had significantly higher mean percentages of cells with hTERC gene amplification than did patients with NILM, ASCUS or LSIL cytological diagnoses (all P<0.05). It was concluded that two-color interphase FISH could detect hTERC gene amplification to accurately distinguish HSIL and ISIL of cervical cells. It may be an adjunct to cytology screening, especially high-risk patients.

Evaluation of fluorescence in situ hybridization techniques to study long non-coding RNA expression in cultured cells

PubMed Central

Soares, Ricardo J; Maglieri, Giulia; Gutschner, Tony; Lund, Anders H; Nielsen, Boye S

2018-01-01

Abstract Deciphering the functions of long non-coding RNAs (lncRNAs) is facilitated by visualization of their subcellular localization using in situ hybridization (ISH) techniques. We evaluated four different ISH methods for detection of MALAT1 and CYTOR in cultured cells: a multiple probe detection approach with or without enzymatic signal amplification, a branched-DNA (bDNA) probe and an LNA-modified probe with enzymatic signal amplification. All four methods adequately stained MALAT1 in the nucleus in all of three cell lines investigated, HeLa, NHDF and T47D, and three of the methods detected the less expressed CYTOR. The sensitivity of the four ISH methods was evaluated by image analysis. In all three cell lines, the two methods involving enzymatic amplification gave the most intense MALAT1 signal, but the signal-to-background ratios were not different. CYTOR was best detected using the bDNA method. All four ISH methods showed significantly reduced MALAT1 signal in knock-out cells, and siRNA-induced knock-down of CYTOR resulted in significantly reduced CYTOR ISH signal, indicating good specificity of the probe designs and detection systems. Our data suggest that the ISH methods allow detection of both abundant and less abundantly expressed lncRNAs, although the latter required the use of the most specific and sensitive probe detection system. PMID:29059327

Further analysis of clinical feasibility of OCT-based glaucoma diagnosis with Pigment epithelium central limit- Inner limit of the retina Minimal Distance (PIMD)

NASA Astrophysics Data System (ADS)

Söderberg, Per G.; Malmberg, Filip; Sandberg-Melin, Camilla

2017-02-01

The present study aimed to elucidate if comparison of angular segments of Pigment epithelium central limit- Inner limit of the retina Minimal Distance, measured over 2π radians in the frontal plane (PIMD-2π) between visits of a patient, renders sufficient precision for detection of loss of nerve fibers in the optic nerve head. An optic nerve head raster scanned cube was captured with a TOPCON 3D OCT 2000 (Topcon, Japan) device in one early to moderate stage glaucoma eye of each of 13 patients. All eyes were recorded at two visits less than 1 month apart. At each visit, 3 volumes were captured. Each volume was extracted from the OCT device for analysis. Then, angular PIMD was segmented three times over 2π radians in the frontal plane, resolved with a semi-automatic algorithm in 500 equally separated steps, PIMD-2π. It was found that individual segmentations within volumes, within visits, within subjects can be phase adjusted to each other in the frontal plane using cross-correlation. Cross correlation was also used to phase adjust volumes within visits within subjects and visits to each other within subjects. Then, PIMD-2π for each subject was split into 250 bundles of 2 adjacent PIMDs. Finally, the sources of variation for estimates of segments of PIMD-2π were derived with analysis of variance assuming a mixed model. The variation among adjacent PIMDS was found very small in relation to the variation among segmentations. The variation among visits was found insignificant in relation to the variation among volumes and the variance for segmentations was found to be on the order of 20 % of that for volumes. The estimated variances imply that, if 3 segmentations are averaged within a volume and at least 10 volumes are averaged within a visit, it is possible to estimate around a 10 % reduction of a PIMD-2π segment from baseline to a subsequent visit as significant. Considering a loss rate for a PIMD-2π segment of 23 μm/yr., 4 visits per year, and averaging 3 segmentations per volume and 3 volumes per visit, a significant reduction from baseline can be detected with a power of 80 % in about 18 months. At higher loss rate for a PIMD-2π segment, a significant difference from baseline can be detected earlier. Averaging over more volumes per visit considerably decreases the time for detection of a significant reduction of a segment of PIMD-2π. Increasing the number of segmentations averaged per visit only slightly reduces the time for detection of a significant reduction. It is concluded that phase adjustment in the frontal plane with cross correlation allows high precision estimates of a segment of PIMD-2π that imply substantially shorter followup time for detection of a significant change than mean deviation (MD) in a visual field estimated with the Humphrey perimeter or neural rim area (NRA) estimated with the Heidelberg retinal tomograph.

Whole body vibration versus magnetic therapy on bone mineral density in elderly osteoporotic individuals.

PubMed

Shanb, Alsayed Abdelhameed; Youssef, Enas Fawzy; Muaidi, Qassim Ibrahim; Alothman, Abdullah Ahmed

2017-08-03

Osteoporosis usually develops gradually and progresses without significant signs and symptoms. It is one of the most common musculoskeletal conditions associated with aging. To evaluate the effects of whole body vibration (WBV) or magnetic therapy in addition to standard pharmacological treatment on bone mineral density (BMD) in elderly individuals being treated for osteoporosis. Eighty-five participants, 60-75 years of age, were randomly divided into three groups. All three groups received the same standard pharmacological treatment comprised of vitamin D, calcium, and alendronate sodium. In Group I, thirty participants were also exposed to WBV for 25 minutes in each session with two sessions per week for 4 months. In Group II, thirty participants were exposed to magnetic therapy for 50 minutes in each session with two sessions per week for 4 months. In Group III, twenty-five participants received only pharmacological treatment. Dual-energy X-ray absorptiometry was used to measure BMD of the lumbar spine and femoral heads before and after interventions. Venus blood sample was drawn for analysis of calcium and vitamin D. An ANOVA test detected significant (p< 0.05) differences in BMD after treatment among the three groups with no significant difference was detected between patients receiving WBV and magnetic therapy. Statistical t-tests detected significant (p< 0.05) increases in BMD after application of WBV or magnetic therapy in combination with pharmacological treatment, but no significant increase after pharmacological treatment alone. Addition of either WBV or magnetic therapy to standard pharmacological treatment for osteoporosis significantly increased BMD in elderly subjects. No significant difference in effectiveness was detected between these two alternative therapy modalities. Consequently, either WBV or magnetic therapy could be effectively applied in conjunction with pharmacological treatment to increase BMD in elderly osteoporotic patients.

High Prevalence of Anal Canal High-Risk Human Papillomavirus Infection in Patients With Crohn's Disease.

PubMed

Vuitton, Lucine; Jacquin, Elise; Parmentier, Anne-Laure; Crochet, Elise; Fein, Francine; Dupont-Gossart, Anne-Claire; Plastaras, Laurianne; Bretagne, Charles-Henri; Mauny, Frédéric; Koch, Stéphane; Prétet, Jean-Luc; Mougin, Christiane; Valmary-Degano, Séverine

2018-03-15

The increasing incidence of anal canal carcinomas requires better knowledge on anal human papillomavirus (HPV) infection. We aimed to assess anal canal HPV infection prevalence and risk factors among patients seen at a gastroenterology department in France. We analyzed anal tissue samples collected from 469 consecutive patients (median age 54 years, 52% women), including 112 who received immunosuppressant therapies and 101 with inflammatory bowel disease (70 with Crohn's disease), who underwent colonoscopy examinations from April 1, 2012 to April 30, 2015. HPV was detected and genotyped using the INNO-LiPA assay, and we collected medical and demographic data from all subjects. Risk factors for any HPV, high-risk HPV (HR-HPV) and HPV16 infection were assessed by bivariate and multivariate analysis. The primary outcomes association of HR-HPV or HPV16 with medical and demographic features. We detected HPV DNA in anal tissues from 34% of the subjects and HR-HPV in 18%. HPV16 was the most prevalent genotype (detected in 7%), followed by HPV51, HPV52, and HPV39. HR-HPV was detected in a significantly higher proportion of samples from women (23.1%) than men (12.8%) (P = .0035); HR-HPV and HPV16 were detected in a significantly higher proportion of patients with Crohn's disease (30.0%) than without (18.1%) (P = .005). Female sex, history of sexually transmitted disease, lifetime and past year-number of sexual partners, active smoking, and immunosuppressive therapies were independent risk factors for anal HR-HPV infection in multivariate analysis. One third of patients who underwent colonoscopy at a gastroenterology department were found to have anal canal HPV infection. We detected HR-HPV infection in almost 20% of patients and in a significantly higher proportion of patients with Crohn's disease than without. Increasing our knowledge of HPV infection of anal tissues could help physicians identify populations at risk and promote prophylaxis with vaccination and adequate screening. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

The effect of length and starting year on trend analyses of temperatures in Spanish mainland (1951-2010). Seasonal analysis: Winter (II)

NASA Astrophysics Data System (ADS)

Salinas Solé, Celia; Peña Angulo, Dhais; Gonzalez Hidalgo, Jose Carlos; Brunetti, Michele

2017-04-01

In this poster we applied the moving window approach (see Poster I of this collection) to analyze trends of winter and its corresponding months (December, January, February) temperature mean values of maximum (Tmax) and minimum (Tmin) in Spanish mainland to detect the effects of length period and starting year. Monthly series belong to Monthly Temperature dataset of Spanish mainland (MOTEDAS). Database contains in its grid format of 5236 pixels of monthly series (10x10 km). The threshold used in spatial analyses considers 20% of land under significant trend (p<0.05). The most striking results are as follow: • Seasonal trend analyses of Tmax shows that global trend 1951-2010 was positive and significant mostly in central-western areas; from 1970 to 2010 there is less than 20% of land with significant trend. In the case of Tmin no relevant significant period is detected. • Monthly Tmax analyses show that December significant trend changed from positive (>20%) in between 1955-2010 until 1962-2010, to negative from 1976-2010. Meanwhile January does not show relevant period with significant trend; finally Tmax in February shows different periods with positive significant trend (>20% of land) 1951-2010 to 1954-2010 and 1962-2010 to 1968-2010. No significant trend is detected after this data. • Monthly Tmin trend analyses show that except exceptional period, no months present any significant trend. As conclusions, we have detected that for winter and winter-months, Tmax trends are not significant from 1970 across Spanish mainland. In the case of Tmin we conclude that no significant trend have been occurred in any temporal windows analyzed. Results differ from what traditionally has been assumed that the increase of the average annual temperature was due to the increase of trends in the winter season. And these analyses also show that seasonal trend values could hide monthly behavior. So extreme caution should be taken into account when seasonal values are offered.

Staging of neuroendocrine tumours: comparison of [68Ga]DOTATOC multiphase PET/CT and whole-body MRI

PubMed Central

Schwenzer, N. F.; Sperling, O.; Aschoff, P.; Lichy, M. P.; Müller, M.; Brendle, C.; Werner, M. K.; Claussen, C. D.; Pfannenberg, C.

2013-01-01

Abstract Purpose: In patients with a neuroendocrine tumour (NET), the extent of disease strongly influences the outcome and multidisciplinary therapeutic management. Thus, systematic analysis of the diagnostic performance of the existing staging modalities is necessary. The aim of this study was to compare the diagnostic performance of 2 whole-body imaging modalities, [68Ga]DOTATOC positron emission tomography (PET)/computed tomography (CT) and magnetic resonance imaging (MRI) in patients with NET with regard to possible impact on treatment decisions. Materials and methods: [68Ga]DOTATOC-PET/CT and whole-body magnetic resonance imaging (wbMRI) were performed on 51 patients (25 females, 26 males, mean age 57 years) with histologically proven NET and suspicion of metastatic spread within a mean interval of 2.4 days (range 0–28 days). PET/CT was performed after intravenous administration of 150 MBq [68Ga]DOTATOC. The CT protocol comprised multiphase contrast-enhanced imaging. The MRI protocol consisted of standard sequences before and after intravenous contrast administration at 1.5 T. Each modality (PET, CT, PET/CT, wbMRI) was evaluated independently by 2 experienced readers. Consensus decision based on correlation of all imaging data, histologic and surgical findings and clinical follow-up was established as the standard of reference. Lesion-based and patient-based analysis was performed. Detection rates and accuracy were compared using the McNemar test. P values <0.05 were considered significant. The impact of whole-body imaging on the treatment decision was evaluated by the interdisciplinary tumour board of our institution. Results: 593 metastatic lesions were detected in 41 of 51 (80%) patients with NET (lung 54, liver 266, bone 131, lymph node 99, other 43). One hundred and twenty PET-negative lesions were detected by CT or MRI. Of all 593 lesions detected, PET identified 381 (64%) true-positive lesions, CT 482 (81%), PET/CT 545 (92%) and wbMRI 540 (91%). Comparison of lesion-based detection rates between PET/CT and wbMRI revealed significantly higher sensitivity of PET/CT for metastatic lymph nodes (100% vs 73%; P < 0.0001) and pulmonary lesions (100% vs 87%; P = 0.0233), whereas wbMRI had significantly higher detection rates for liver (99% vs 92%; P < 0.0001) and bone lesions (96% vs 82%; P < 0.0001). Of all 593 lesions, 22 were found only in PET, 11 only in CT and 47 only in wbMRI. The patient-based overall assessment of the metastatic status of the patient showed comparable sensitivity of PET/CT and MRI with slightly higher accuracy of PET/CT. Patient-based analysis of metastatic organ involvement revealed significantly higher accuracy of PET/CT for bone and lymph node metastases (100% vs 88%; P = 0.0412 and 98% vs 78%; P = 0.0044) and for the overall comparison (99% vs 89%; P < 0.0001). The imaging results influenced the treatment decision in 30 patients (59%) with comparable information from PET/CT and wbMRI in 30 patients, additional relevant information from PET/CT in 16 patients and from wbMRI in 7 patients. Conclusion: PET/CT and wbMRI showed comparable overall lesion-based detection rates for metastatic involvement in NET but significantly differed in organ-based detection rates with superiority of PET/CT for lymph node and pulmonary lesions and of wbMRI for liver and bone metastases. Patient-based analysis revealed superiority of PET/CT for NET staging. Individual treatment strategies benefit from complementary information from PET/CT and MRI. PMID:23466785

On the performance of energy detection-based CR with SC diversity over IG channel

NASA Astrophysics Data System (ADS)

Verma, Pappu Kumar; Soni, Sanjay Kumar; Jain, Priyanka

2017-12-01

Cognitive radio (CR) is a viable 5G technology to address the scarcity of the spectrum. Energy detection-based sensing is known to be the simplest method as far as hardware complexity is concerned. In this paper, the performance of spectrum sensing-based energy detection technique in CR networks over inverse Gaussian channel for selection combining diversity technique is analysed. More specifically, accurate analytical expressions for the average detection probability under different detection scenarios such as single channel (no diversity) and with diversity reception are derived and evaluated. Further, the detection threshold parameter is optimised by minimising the probability of error over several diversity branches. The results clearly show the significant improvement in the probability of detection when optimised threshold parameter is applied. The impact of shadowing parameters on the performance of energy detector is studied in terms of complimentary receiver operating characteristic curve. To verify the correctness of our analysis, the derived analytical expressions are corroborated via exact result and Monte Carlo simulations.

A novel coefficient for detecting and quantifying asymmetry of California electricity market based on asymmetric detrended cross-correlation analysis.

PubMed

Wang, Fang

2016-06-01

In order to detect and quantify asymmetry of two time series, a novel cross-correlation coefficient is proposed based on recent asymmetric detrended cross-correlation analysis (A-DXA), which we called A-DXA coefficient. The A-DXA coefficient, as an important extension of DXA coefficient ρDXA, contains two directional asymmetric cross-correlated indexes, describing upwards and downwards asymmetric cross-correlations, respectively. By using the information of directional covariance function of two time series and directional variance function of each series itself instead of power-law between the covariance function and time scale, the proposed A-DXA coefficient can well detect asymmetry between the two series no matter whether the cross-correlation is significant or not. By means of the proposed A-DXA coefficient conducted over the asymmetry for California electricity market, we found that the asymmetry between the prices and loads is not significant for daily average data in 1999 yr market (before electricity crisis) but extremely significant for those in 2000 yr market (during the crisis). To further uncover the difference of asymmetry between the years 1999 and 2000, a modified H statistic (MH) and ΔMH statistic are proposed. One of the present contributions is that the high MH values calculated for hourly data exist in majority months in 2000 market. Another important conclusion is that the cross-correlation with downwards dominates over the whole 1999 yr in contrast to the cross-correlation with upwards dominates over the 2000 yr.

Association between micronucleus frequency and cervical intraepithelial neoplasia grade in Thinprep cytological test and its significance.

PubMed

Shi, Yong-Hua; Wang, Bo-Wei; Tuokan, Talaf; Li, Qiao-Zhi; Zhang, Ya-Jing

2015-01-01

A micronucleus is an additional small nucleus formed due to chromosomes or chromosomal fragments fail to be incorporated into the nucleus during cell division. In this study, we assessed the utility of micronucleus counting as a screening tool in cervical precancerous lesions in Thinprep cytological test smears under oil immersion. High risk HPV was also detected by hybrid capture-2 in Thinprep cytological test smears. Our results showed that micronucleus counting was significantly higher in high-grade squamous intraepithelial lesion (HSIL) and invasive carcinoma cases compared to low-grade squamous intraepithelial lesion (LSIL) and non-neoplastic cases. Receiver operating characteristic (ROC) curve analysis revealed that micronucleus counting possessed a high degree of sensitivity and specificity for identifying HSIL and invasive carcinoma. Cut-off of 7.5 for MN counting gave a sensitivity of 89.6% and a specificity of 66.7% (P = 0.024 and AUC = 0.892) for detecting HSIL and invasive carcinoma lesions. Multiple linear regression analysis showed that only HSIL and invasive cancer lesions not age, duration of marital life and number of pregnancy are significantly associated with MN counting. The positive rate of high risk HPV was distinctly higher in LSIL, HSIL and invasive cancer than that in non-neoplstic categories. In conclusions, MN evaluation may be viewed as an effective biomarker for cervical cancer screening. The combination of MN count with HPV DNA detection and TCT may serve as an effective means to screen precancerous cervical lesions in most developing nations.

Streak Imaging Flow Cytometer for Rare Cell Analysis.

PubMed

Balsam, Joshua; Bruck, Hugh Alan; Ossandon, Miguel; Prickril, Ben; Rasooly, Avraham

2017-01-01

There is a need for simple and affordable techniques for cytology for clinical applications, especially for point-of-care (POC) medical diagnostics in resource-poor settings. However, this often requires adapting expensive and complex laboratory-based techniques that often require significant power and are too massive to transport easily. One such technique is flow cytometry, which has great potential for modification due to the simplicity of the principle of optical tracking of cells. However, it is limited in that regard due to the flow focusing technique used to isolate cells for optical detection. This technique inherently reduces the flow rate and is therefore unsuitable for rapid detection of rare cells which require large volume for analysis.To address these limitations, we developed a low-cost, mobile flow cytometer based on streak imaging. In our new configuration we utilize a simple webcam for optical detection over a large area associated with a wide-field flow cell. The new flow cell is capable of larger volume and higher throughput fluorescence detection of rare cells than the flow cells with hydrodynamic focusing used in conventional flow cytometry. The webcam is an inexpensive, commercially available system, and for fluorescence analysis we use a 1 W 450 nm blue laser to excite Syto-9 stained cells with emission at 535 nm. We were able to detect low concentrations of stained cells at high flow rates of 10 mL/min, which is suitable for rapidly analyzing larger specimen volumes to detect rare cells at appropriate concentration levels. The new rapid detection capabilities, combined with the simplicity and low cost of this device, suggest a potential for clinical POC flow cytometry in resource-poor settings associated with global health.

Histogram Analysis of Apparent Diffusion Coefficients for Occult Tonsil Cancer in Patients with Cervical Nodal Metastasis from an Unknown Primary Site at Presentation.

PubMed

Choi, Young Jun; Lee, Jeong Hyun; Kim, Hye Ok; Kim, Dae Yoon; Yoon, Ra Gyoung; Cho, So Hyun; Koh, Myeong Ju; Kim, Namkug; Kim, Sang Yoon; Baek, Jung Hwan

2016-01-01

To explore the added value of histogram analysis of apparent diffusion coefficient (ADC) values over magnetic resonance (MR) imaging and fluorine 18 ((18)F) fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT) for the detection of occult palatine tonsil squamous cell carcinoma (SCC) in patients with cervical nodal metastasis from a cancer of an unknown primary site. The institutional review board approved this retrospective study, and the requirement for informed consent was waived. Differences in the bimodal histogram parameters of the ADC values were assessed among occult palatine tonsil SCC (n = 19), overt palatine tonsil SCC (n = 20), and normal palatine tonsils (n = 20). One-way analysis of variance was used to analyze differences among the three groups. Receiver operating characteristic curve analysis was used to determine the best differentiating parameters. The increased sensitivity of histogram analysis over MR imaging and (18)F-FDG PET/CT for the detection of occult palatine tonsil SCC was evaluated as added value. Histogram analysis showed statistically significant differences in the mean, standard deviation, and 50th and 90th percentile ADC values among the three groups (P < .0045). Occult palatine tonsil SCC had a significantly higher standard deviation for the overall curves, mean and standard deviation of the higher curves, and 90th percentile ADC value, compared with normal palatine tonsils (P < .0167). Receiver operating characteristic curve analysis showed that the standard deviation of the overall curve best delineated occult palatine tonsil SCC from normal palatine tonsils, with a sensitivity of 78.9% (15 of 19 patients) and a specificity of 60% (12 of 20 patients). The added value of ADC histogram analysis was 52.6% over MR imaging alone and 15.8% over combined conventional MR imaging and (18)F-FDG PET/CT. Adding ADC histogram analysis to conventional MR imaging can improve the detection sensitivity for occult palatine tonsil SCC in patients with a cervical nodal metastasis originating from a cancer of an unknown primary site. © RSNA, 2015.

Magnetic resonance imaging in prostate cancer detection and management: a systematic review.

PubMed

Monni, Fabio; Fontanella, Paolo; Grasso, Angelica; Wiklund, Peter; Ou, Yen-Chuan; Randazzo, Marco; Rocco, Bernardo; Montanari, Emanuele; Bianchi, Giampaolo

2017-12-01

The aim of our work was to evaluate the role of multi-parametric magnetic resonance imaging (mpMRI) in detection and management of prostate cancer (PC); specifically investigating the efficacy of mpMRI-based biopsy techniques in terms of diagnostic yield of significant prostate neoplasm and the improved management of patients who choose conservative treatments or active surveillance. A systematic and critical analysis through Medline, Embase, Scopus and Web of Science databases was carried out in March 2016, following the PRISMA ("Preferred Reporting Items for Systematic Reviews and Meta-Analyses") statement. The search was conducted using the following key words: "MRI/TRUS-fusion biopsy," "PIRADS," "prostate cancer," "magnetic resonance imaging (MRI)," "multiparametric MRI (mpMRI)," "systematic prostate biopsy (SB)," "targeted prostate biopsy (TPB)." English language articles were reviewed for inclusion ability. Sixty-six studies were selected in order to evaluate the characteristics and limitations of traditional sample biopsy, the role of mpMRI in detection of PC, specifically the increased degree of diagnostic accuracy of targeted prostate biopsy compared to systematic biopsy (12 cores), and to transperineal saturation biopsies with trans-rectal ultrasound (TRUS) only. MpMRI can detect index lesions in approximately 90% of cases when compared to prostatectomy specimen. The diagnostic performance of biparametric MRI (T2w + DWI) is not inferior to mpMRI, offering valid options to diminish cost- and time-consumption. Since approximately 10% of significant lesions are still MRI-invisible, systematic cores biopsy seem to still be necessary. The analysis of the different techniques shows that in-bore MRI-guided biopsy and MRI/TRUS-fusion-guided biopsy are superior in detection of significant PC compared to visual estimation alone. MpMRI proved to be very effective in active surveillance, as it prevents underdetection of significant PC and it assesses low-risk disease accurately. In higher-risk disease, presurgical MRI may change the clinically-based surgical plan in up to a third of cases. Targeted prostate biopsy, guided by mpMRI, is able to improve diagnostic accuracy and to reduce the detection of insignificant PC. Since the negative predictive value (NPV) of mpMRI is still imperfect, systematic cores biopsy should not be omitted for optimal staging of disease. A process of a progressive and periodic evolution in the detection and radiological classification of prostate lesions (such as PIRADS), is still needed in patients in active surveillance and in radical prostatectomy planning.

99m Tc-MIP-1404-SPECT/CT for the detection of PSMA-positive lesions in 225 patients with biochemical recurrence of prostate cancer.

PubMed

Schmidkonz, Christian; Hollweg, Claudia; Beck, Michael; Reinfelder, Julia; Goetz, Theresa I; Sanders, James C; Schmidt, Daniela; Prante, Olaf; Bäuerle, Tobias; Cavallaro, Alexander; Uder, Michael; Wullich, Bernd; Goebell, Peter; Kuwert, Torsten; Ritt, Philipp

2018-01-01

99m Tc-MIP-1404 (Progenics Pharmaceuticals, Inc., New York, NY) is a novel, SPECT-compatible 99m Tc-labeled PSMA inhibitor for the detection of prostate cancer. We present results of its clinical use in a cohort of 225 men with histologically confirmed prostate cancer referred for workup of biochemical relapse. From April 2013 to April 2017, 99m Tc-MIP1404-scintigraphy was performed in 225 patients for workup of PSA biochemical relapse of prostate cancer. Whole-body planar and SPECT/CT images of the lower abdomen and thorax were obtained 3-4 h p.i. of 710 ± 64 MBq 99m Tc-MIP-1404. Images were visually analyzed for presence and location of abnormal uptake. In addition, quantitative analysis of the SPECT/CT data was carried out on a subset of 125 patients. Follow-up reports of subsequent therapeutic interventions were available for 59% (139) of all patients. Tracer-positive lesions were detected in 77% (174/225) of all patients. Detections occurred at the area of local recurrence in the prostate in 25% of patients (or a total of 56), with metastases in lymph nodes in 47% (105), bone in 27% (60), lung in 5% (12), and other locations in 2% (4) of patients. Detection rates were 90% at PSA levels ≥2 ng/mL and 54% below that threshold. Lesional SUVmax values were, on average, 32.2 ± 29.6 (0.8-142.2), and tumor-to-normal ratios 146.6 ± 160.5 (1.9-1482.4). The PSA level correlated significantly with total uptake of MIP-1404 in tumors (P < 0.001). Furthermore, total tumor uptake was significantly higher in patients with Gleason scores ≥8 compared to those with Gleason scores ≤7 (P < 0.05). In patients with androgen deprivation therapy, the detection rate was significantly higher compared to patients without androgen deprivation therapy (86% vs 71%, P < 0.001). Based on 99m Tc-MIP-1404-imaging and other information, an interdisciplinary tumor board review recommended changes to treatment plans in 74% (104/139) of those patients for whom the necessary documentation was available. SPECT/CT with 99m Tc-labeled MIP-1404 has a high probability in detecting PSMA-positive lesions in patients with elevated PSA. Statistical analysis disclosed significant relationship between quantitative 99m Tc-MIP-1404 uptake, PSA level, and Gleason score. © 2017 Wiley Periodicals, Inc.

Traumatic Brain Injury Detection Using Electrophysiological Methods

PubMed Central

Rapp, Paul E.; Keyser, David O.; Albano, Alfonso; Hernandez, Rene; Gibson, Douglas B.; Zambon, Robert A.; Hairston, W. David; Hughes, John D.; Krystal, Andrew; Nichols, Andrew S.

2015-01-01

Measuring neuronal activity with electrophysiological methods may be useful in detecting neurological dysfunctions, such as mild traumatic brain injury (mTBI). This approach may be particularly valuable for rapid detection in at-risk populations including military service members and athletes. Electrophysiological methods, such as quantitative electroencephalography (qEEG) and recording event-related potentials (ERPs) may be promising; however, the field is nascent and significant controversy exists on the efficacy and accuracy of the approaches as diagnostic tools. For example, the specific measures derived from an electroencephalogram (EEG) that are most suitable as markers of dysfunction have not been clearly established. A study was conducted to summarize and evaluate the statistical rigor of evidence on the overall utility of qEEG as an mTBI detection tool. The analysis evaluated qEEG measures/parameters that may be most suitable as fieldable diagnostic tools, identified other types of EEG measures and analysis methods of promise, recommended specific measures and analysis methods for further development as mTBI detection tools, identified research gaps in the field, and recommended future research and development thrust areas. The qEEG study group formed the following conclusions: (1) Individual qEEG measures provide limited diagnostic utility for mTBI. However, many measures can be important features of qEEG discriminant functions, which do show significant promise as mTBI detection tools. (2) ERPs offer utility in mTBI detection. In fact, evidence indicates that ERPs can identify abnormalities in cases where EEGs alone are non-disclosing. (3) The standard mathematical procedures used in the characterization of mTBI EEGs should be expanded to incorporate newer methods of analysis including non-linear dynamical analysis, complexity measures, analysis of causal interactions, graph theory, and information dynamics. (4) Reports of high specificity in qEEG evaluations of TBI must be interpreted with care. High specificities have been reported in carefully constructed clinical studies in which healthy controls were compared against a carefully selected TBI population. The published literature indicates, however, that similar abnormalities in qEEG measures are observed in other neuropsychiatric disorders. While it may be possible to distinguish a clinical patient from a healthy control participant with this technology, these measures are unlikely to discriminate between, for example, major depressive disorder, bipolar disorder, or TBI. The specificities observed in these clinical studies may well be lost in real world clinical practice. (5) The absence of specificity does not preclude clinical utility. The possibility of use as a longitudinal measure of treatment response remains. However, efficacy as a longitudinal clinical measure does require acceptable test–retest reliability. To date, very few test–retest reliability studies have been published with qEEG data obtained from TBI patients or from healthy controls. This is a particular concern because high variability is a known characteristic of the injured central nervous system. PMID:25698950

Traumatic brain injury detection using electrophysiological methods.

PubMed

Rapp, Paul E; Keyser, David O; Albano, Alfonso; Hernandez, Rene; Gibson, Douglas B; Zambon, Robert A; Hairston, W David; Hughes, John D; Krystal, Andrew; Nichols, Andrew S

2015-01-01

Measuring neuronal activity with electrophysiological methods may be useful in detecting neurological dysfunctions, such as mild traumatic brain injury (mTBI). This approach may be particularly valuable for rapid detection in at-risk populations including military service members and athletes. Electrophysiological methods, such as quantitative electroencephalography (qEEG) and recording event-related potentials (ERPs) may be promising; however, the field is nascent and significant controversy exists on the efficacy and accuracy of the approaches as diagnostic tools. For example, the specific measures derived from an electroencephalogram (EEG) that are most suitable as markers of dysfunction have not been clearly established. A study was conducted to summarize and evaluate the statistical rigor of evidence on the overall utility of qEEG as an mTBI detection tool. The analysis evaluated qEEG measures/parameters that may be most suitable as fieldable diagnostic tools, identified other types of EEG measures and analysis methods of promise, recommended specific measures and analysis methods for further development as mTBI detection tools, identified research gaps in the field, and recommended future research and development thrust areas. The qEEG study group formed the following conclusions: (1) Individual qEEG measures provide limited diagnostic utility for mTBI. However, many measures can be important features of qEEG discriminant functions, which do show significant promise as mTBI detection tools. (2) ERPs offer utility in mTBI detection. In fact, evidence indicates that ERPs can identify abnormalities in cases where EEGs alone are non-disclosing. (3) The standard mathematical procedures used in the characterization of mTBI EEGs should be expanded to incorporate newer methods of analysis including non-linear dynamical analysis, complexity measures, analysis of causal interactions, graph theory, and information dynamics. (4) Reports of high specificity in qEEG evaluations of TBI must be interpreted with care. High specificities have been reported in carefully constructed clinical studies in which healthy controls were compared against a carefully selected TBI population. The published literature indicates, however, that similar abnormalities in qEEG measures are observed in other neuropsychiatric disorders. While it may be possible to distinguish a clinical patient from a healthy control participant with this technology, these measures are unlikely to discriminate between, for example, major depressive disorder, bipolar disorder, or TBI. The specificities observed in these clinical studies may well be lost in real world clinical practice. (5) The absence of specificity does not preclude clinical utility. The possibility of use as a longitudinal measure of treatment response remains. However, efficacy as a longitudinal clinical measure does require acceptable test-retest reliability. To date, very few test-retest reliability studies have been published with qEEG data obtained from TBI patients or from healthy controls. This is a particular concern because high variability is a known characteristic of the injured central nervous system.

An Improved Multiplex Real-Time SYBR Green PCR Assay for Analysis of 24 Target Genes from 16 Bacterial Species in Fecal DNA Samples from Patients with Foodborne Illnesses.

PubMed

Kawase, Jun; Etoh, Yoshiki; Ikeda, Tetsuya; Yamaguchi, Keiji; Watahiki, Masanori; Shima, Tomoko; Kameyama, Mitsuhiro; Horikawa, Kazumi; Fukushima, Hiroshi; Goto, Ryoichi; Shirabe, Komei

2016-05-20

Here, we developed a new version of our original screening system (Rapid Foodborne Bacterial Screening 24; RFBS24), which can simultaneously detect 24 genes of foodborne pathogens in fecal DNA samples. This new version (RFBS24 ver. 5) detected all known stx2 subtypes, enterotoxigenic Escherichia coli (STh genotype), and Vibrio parahaemolyticus (trh2), which were not detected by the original RFBS24 assay. The detection limits of RFBS24 ver. 5 were approximately 5.6 × 10(-2)-5.6 × 10(-5) (ng DNA)/reaction, significantly lower (10- to 100-fold) than those of the original RFBS24 for the 22 target genes analyzed here. We also tested the new assay on fecal DNA samples from patients infected with Salmonella, Campylobacter, or enterohemorrhagic E. coli. The number of bacterial target genes detected by RFBS24 ver. 5 was greater than that detected by RFBS24. RFBS24 ver. 5 combined with an Ultra Clean Fecal DNA Isolation Kit showed adequate performance (sensitivity and specificity 89% and 100%, respectively, for Salmonella spp. and 100% and 83%, respectively, for Campylobacter jejuni) in terms of rapid detection of a causative pathogen during foodborne-illness outbreaks. Thus, RFBS24 ver. 5 is more useful than the previous assay system for detection of foodborne pathogens and offers quick simultaneous analysis of many targets and thus facilitates rapid dissemination of information to public health officials.

Comparative Evaluation of Veriflow®Listeria Species to USDA Culture-Based Method for the Detection of Listeria spp. in Food and Environmental Samples.

PubMed

Joelsson, Adam C; Terkhorn, Shawn P; Brown, Ashley S; Puri, Amrita; Pascal, Benjamin J; Gaudioso, Zara E; Siciliano, Nicholas A

2017-09-01

Veriflow® Listeria species (Veriflow LS) is a molecular-based assay for the presumptive detection of Listeria spp. from environmental surfaces (stainless steel, sealed concrete, plastic, and ceramic tile) and ready-to-eat (RTE) food matrixes (hot dogs and deli meat). The assay utilizes a PCR detection method coupled with a rapid, visual, flow-based assay that develops in 3 min post-PCR amplification and requires only a 24 h enrichment for maximum sensitivity. The Veriflow LS system eliminates the need for sample purification, gel electrophoresis, or fluorophore-based detection of target amplification and does not require complex data analysis. This Performance Tested MethodSM validation study demonstrated the ability of the Veriflow LS assay to detect low levels of artificially inoculated Listeria spp. in six distinct environmental and food matrixes. In each unpaired reference comparison study, probability of detection analysis indicated that there was no significant difference between the Veriflow LS method and the U.S. Department of Agriculture Food Safety and Inspection Service Microbiology Laboratory Guide Chapter 8.08 reference method. Fifty-one strains of various Listeria spp. were detected in the inclusivity study, and 35 nonspecific organisms went undetected in the exclusivity study. The study results show that the Veriflow LS is a sensitive, selective, and robust assay for the presumptive detection of Listeria spp. sampled from environmental surfaces (stainless steel, sealed concrete, plastic, and ceramic tile) and RTE food matrixes (hot dogs and deli meat).

Multi-resolution Gabor wavelet feature extraction for needle detection in 3D ultrasound

NASA Astrophysics Data System (ADS)

Pourtaherian, Arash; Zinger, Svitlana; Mihajlovic, Nenad; de With, Peter H. N.; Huang, Jinfeng; Ng, Gary C.; Korsten, Hendrikus H. M.

2015-12-01

Ultrasound imaging is employed for needle guidance in various minimally invasive procedures such as biopsy guidance, regional anesthesia and brachytherapy. Unfortunately, a needle guidance using 2D ultrasound is very challenging, due to a poor needle visibility and a limited field of view. Nowadays, 3D ultrasound systems are available and more widely used. Consequently, with an appropriate 3D image-based needle detection technique, needle guidance and interventions may significantly be improved and simplified. In this paper, we present a multi-resolution Gabor transformation for an automated and reliable extraction of the needle-like structures in a 3D ultrasound volume. We study and identify the best combination of the Gabor wavelet frequencies. High precision in detecting the needle voxels leads to a robust and accurate localization of the needle for the intervention support. Evaluation in several ex-vivo cases shows that the multi-resolution analysis significantly improves the precision of the needle voxel detection from 0.23 to 0.32 at a high recall rate of 0.75 (gain 40%), where a better robustness and confidence were confirmed in the practical experiments.

Giant Gold Nanowire Vesicle-Based Colorimetric and SERS Dual-Mode Immunosensor for Ultrasensitive Detection of Vibrio parahemolyticus.

PubMed

Guo, Zhiyong; Jia, Yaru; Song, Xinxin; Lu, Jing; Lu, Xuefei; Liu, Baoqing; Han, Jiaojiao; Huang, Youju; Zhang, Jiawei; Chen, Tao

2018-05-15

Conventional methods for the detection of Vibrio parahemolyticus (VP) usually need tedious, labor-intensive processes, and have low sensitivity, which further limits their practical applications. Herein, we developed a simple and efficient colorimetry and surface-enhanced Raman scattering (SERS) dual-mode immunosensor for sensitive detection of VP, by employing giant Au vesicles with anchored tiny gold nanowires (AuNW) as a smart probe. Due to the larger specific surface and special hollow structure of giant Au vesicles, silver staining would easily lead to vivid color change for colorimetric analysis and further amplify SERS signals. The t-test was further used to determine if two sets of data from colorimetry and SERS were significantly different from each other. The result shows that there was no significant difference between data from the two methods. Two sets of data can mutually validate each other and avoid false positive and negative detection. The designed colorimetry-SERS dual-mode sensor would be very promising in various applications such as food safety inspection, personal healthcare, and on-site environmental monitoring.

Testing for the Presence of Correlation Changes in a Multivariate Time Series: A Permutation Based Approach.

PubMed

Cabrieto, Jedelyn; Tuerlinckx, Francis; Kuppens, Peter; Hunyadi, Borbála; Ceulemans, Eva

2018-01-15

Detecting abrupt correlation changes in multivariate time series is crucial in many application fields such as signal processing, functional neuroimaging, climate studies, and financial analysis. To detect such changes, several promising correlation change tests exist, but they may suffer from severe loss of power when there is actually more than one change point underlying the data. To deal with this drawback, we propose a permutation based significance test for Kernel Change Point (KCP) detection on the running correlations. Given a requested number of change points K, KCP divides the time series into K + 1 phases by minimizing the within-phase variance. The new permutation test looks at how the average within-phase variance decreases when K increases and compares this to the results for permuted data. The results of an extensive simulation study and applications to several real data sets show that, depending on the setting, the new test performs either at par or better than the state-of-the art significance tests for detecting the presence of correlation changes, implying that its use can be generally recommended.

Driver fatigue detection through multiple entropy fusion analysis in an EEG-based system.

PubMed

Min, Jianliang; Wang, Ping; Hu, Jianfeng

2017-01-01

Driver fatigue is an important contributor to road accidents, and fatigue detection has major implications for transportation safety. The aim of this research is to analyze the multiple entropy fusion method and evaluate several channel regions to effectively detect a driver's fatigue state based on electroencephalogram (EEG) records. First, we fused multiple entropies, i.e., spectral entropy, approximate entropy, sample entropy and fuzzy entropy, as features compared with autoregressive (AR) modeling by four classifiers. Second, we captured four significant channel regions according to weight-based electrodes via a simplified channel selection method. Finally, the evaluation model for detecting driver fatigue was established with four classifiers based on the EEG data from four channel regions. Twelve healthy subjects performed continuous simulated driving for 1-2 hours with EEG monitoring on a static simulator. The leave-one-out cross-validation approach obtained an accuracy of 98.3%, a sensitivity of 98.3% and a specificity of 98.2%. The experimental results verified the effectiveness of the proposed method, indicating that the multiple entropy fusion features are significant factors for inferring the fatigue state of a driver.

Joint genome-wide association study for milk fatty acid traits in Chinese and Danish Holstein populations.

PubMed

Li, X; Buitenhuis, A J; Lund, M S; Li, C; Sun, D; Zhang, Q; Poulsen, N A; Su, G

2015-11-01

The identification of causal genes or genomic regions associated with fatty acids (FA) will enhance our understanding of the pathways underlying FA synthesis and provide opportunities for changing milk fat composition through a genetic approach. The linkage disequilibrium between adjacent markers is highly consistent between the Chinese and Danish Holstein populations, such that a joint genome-wide association study (GWAS) can be performed. In this study, a joint GWAS was performed for 16 milk FA traits based on data of 784 Chinese and 371 Danish Holstein cows genotyped by a high-density bovine single nucleotide polymorphism (SNP) array. A total of 486,464 SNP markers on 29 bovine autosomes were used. Bonferroni corrections were applied to adjust the significance thresholds for multiple testing at the genome- and chromosome-wide levels. According to the analysis of either the Chinese or Danish data individually, the total numbers of overlapping SNP that were significant at the chromosome level were 94 for C14:1, 208 for the C14 index, and 1 for C18:0. Joint analysis using the combined data of the 2 populations detected greater numbers of significant SNP compared with either of the individual populations alone for 7 and 10 traits at the genome- and chromosome-wide significance levels, respectively. Greater numbers of significant SNP were detected for C18:0 and the C18 index in the Chinese population compared with the joint analysis. Sixty-five significant SNP across all traits had significantly different effects in the 2 populations. Ten FA were influenced by a quantitative trait loci (QTL) region including DGAT1. Both C14:1 and the C14 index were influenced by a QTL region including SCD1 in the combined population. Other QTL regions also showed significant associations with the studied FA. A large region (14.9-24.9 Mbp) in BTA26 significantly influenced C14:1 and the C14 index in both populations, mostly likely due to the SNP in SCD1. A QTL region (69.97-73.69 Mbp) on BTA9 showed a significantly different effect on C18:0 between the 2 populations. Detection of these important SNP and the corresponding QTL regions will be helpful for follow-up studies to identify causal mutations and their interaction with environments for milk FA in dairy cattle. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Biomarker evidence of tobacco smoke exposure in children participating in lead screening.

PubMed

Joseph, Anne; Spector, Logan; Wickham, Katherine; Janis, Gregory; Winickoff, Jonathan; Lindgren, Bruce; Murphy, Sharon

2013-12-01

We assessed tobacco smoke exposure (TSE), defined according to detection of cotinine, in dried blood spots collected from children for lead screening. Dried blood spots collected from a national sample of 1541 Black and White children and submitted to a commercial laboratory for lead analysis were analyzed for cotinine. We used an anonymous administrative data set including information on children's characteristics to conduct univariate and multivariate analyses. Cotinine was detected in 61% of dried blood spots; 17% of samples had cotinine levels above 3 nanograms per gram. Median cotinine levels were significantly higher among Black than White children (0.66 ng/g vs 0.30 ng/g) and among Medicaid recipients (0.94 ng/g vs < 0.3 ng/g). In multivariate analyses, significant increases in cotinine levels were associated with Black (vs White) race, older age, Medicaid coverage, higher state smoking rate, and higher average winter temperature. Detectable cotinine levels were significantly associated with higher lead levels. TSE is highly prevalent among children undergoing lead screening, and exposure levels are greater among Black children and children on Medicaid. TSE may contribute to lead exposure. Concurrent lead screening and biological screening for TSE may be a feasible approach to increasing childhood TSE detection.

Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children.

PubMed

Finegold, Sydney M; Summanen, Paula H; Downes, Julia; Corbett, Karen; Komoriya, Tomoe

2017-06-01

We studied stool specimens from 33 autistic children aged 2-9 years with gastrointestinal (GI) abnormalities and 13 control children without autism and without GI symptoms. We performed quantitative comparison of all Clostridium species and Clostridium perfringens strains from the fecal microbiota by conventional, selective anaerobic culture methods. We isolated C. perfringens strains and performed PCR analysis for the main C. perfringens toxin genes, alpha, beta, beta2, epsilon, iota and C. perfringens enterotoxin gene. Our results indicate that autistic subjects with gastrointestinal disease harbor statistically significantly (p = 0.031) higher counts of C. perfringens in their gut compared to control children. Autistic subjects also harbor statistically significantly (p = 0.015) higher counts of beta2-toxin gene-producing C. perfringens in their gut compared to control children, and the incidence of beta2-toxin gene-producing C. perfringens is significantly higher in autistic subjects compared to control children (p = 0.014). Alpha toxin gene was detected in all C. perfringens strains studied. C. perfringens enterotoxin gene was detected from three autistic and one control subject. Beta, epsilon, and iota toxin genes were not detected from autistic or control subjects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Abnormal Superior Temporal Connectivity During Fear Perception in Schizophrenia

PubMed Central

Leitman, David I.; Loughead, James; Wolf, Daniel H.; Ruparel, Kosha; Kohler, Christian G.; Elliott, Mark A.; Bilker, Warren B.; Gur, Raquel E.; Gur, Ruben C.

2008-01-01

Patients with schizophrenia have difficulty in decoding facial affect. A study using event–related functional neuroimaging indicated that errors in fear detection in schizophrenia are associated with paradoxically higher activation in the amygdala and an associated network implicated in threat detection. Furthermore, this exaggerated activation to fearful faces correlated with severity of flat affect. These findings suggest that abnormal threat detection processing may reflect disruptions between nodes that comprise the affective appraisal circuit. Here we examined connectivity within this network by determining the pattern of intercorrelations among brain regions (regions of interest) significantly activated during fear identification in both healthy controls and patients using a novel procedure CORANOVA. This analysis tests differences in the interregional correlation strength between schizophrenia and healthy controls. Healthy subjects' task activation was principally characterized by robust correlations between medial structures like thalamus (THA) and amygdala (AMY) and middle frontal (MF), inferior frontal (IF), and prefrontal cortical (PFC) regions. In contrast, schizophrenia patients displayed no significant correlations between the medial regions and either MF or IF. Further, patients had significantly higher correlations between occipital lingual gyrus and superior temporal gyrus than healthy subjects. These between-group connectivity differences suggest that schizophrenia threat detection impairment may stem from abnormal stimulus integration. Such abnormal integration may disrupt the evaluation of threat within fronto-cortical regions. PMID:18550592

Detection of growth hormone doping by gene expression profiling of peripheral blood.

PubMed

Mitchell, Christopher J; Nelson, Anne E; Cowley, Mark J; Kaplan, Warren; Stone, Glenn; Sutton, Selina K; Lau, Amie; Lee, Carol M Y; Ho, Ken K Y

2009-12-01

GH abuse is a significant problem in many sports, and there is currently no robust test that allows detection of doping beyond a short window after administration. Our objective was to evaluate gene expression profiling in peripheral blood leukocytes in-vivo as a test for GH doping in humans. Seven men and thirteen women were administered GH, 2 mg/d sc for 8 wk. Blood was collected at baseline and at 8 wk. RNA was extracted from the white cell fraction. Microarray analysis was undertaken using Agilent 44K G4112F arrays using a two-color design. Quantitative RT-PCR using TaqMan gene expression assays was performed for validation of selected differentially expressed genes. GH induced an approximately 2-fold increase in circulating IGF-I that was maintained throughout the 8 wk of the study. GH induced significant changes in gene expression with 353 in women and 41 in men detected with a false discovery rate of less than 5%. None of the differentially expressed genes were common between men and women. The maximal changes were a doubling for up-regulated or halving for down-regulated genes, similar in magnitude to the variation between individuals. Quantitative RT-PCR for seven target genes showed good concordance between microarray and quantitative PCR data in women but not in men. Gene expression analysis of peripheral blood leukocytes is unlikely to be a viable approach for the detection of GH doping.

Detection of Human Papillomavirus 16-Specific IgG and IgM Antibodies in Patient Sera: A Potential Indicator of Oral Squamous Cell Carcinoma Risk Factor.

PubMed

Kerishnan, Jesinda P; Gopinath, Subash C B; Kai, Sia Bik; Tang, Thean-Hock; Ng, Helen Lee-Ching; Rahman, Zainal Ariff Abdul; Hashim, Uda; Chen, Yeng

2016-01-01

The association between human papillomavirus type 16 (HPV16) and oral cancer has been widely reported. However, detecting anti-HPV antibodies in patient sera to determine risk for oral squamous cell carcinoma (OSCC) has not been well studied. In the present investigation, a total of 206 OSCC serum samples from the Malaysian Oral Cancer Database & Tissue Bank System, with 134 control serum samples, were analyzed by enzyme-linked immunosorbant assay (ELISA) to detect HPV16-specific IgG and IgM antibodies. In addition, nested PCR analysis using comprehensive consensus primers (PGMY09/11 and GP5(+)/6(+)) was used to confirm the presence of HPV. Furthermore, we have evaluated the association of various additional causal factors (e.g., smoking, alcohol consumption, and betel quid chewing) in HPV-infected OSCC patients. Statistical analysis of the Malaysian population indicated that OSCC was more prevalent in female Indian patients that practices betel quid chewing. ELISA revealed that HPV16 IgG, which demonstrates past exposure, could be detected in 197 (95.6%) OSCC patients and HPV16-specific IgM was found in a total of 42 (20.4%) OSCC patients, indicating current exposure. Taken together, our study suggest that HPV infection may play a significant role in OSCC (OR: 13.6; 95% CI: 3.89-47.51) and HPV16-specific IgG and IgM antibodies could represent a significant indicator of risk factors in OSCC patients.

Metabolomic and Transcriptomic Comparison of Solid-State and Submerged Fermentation of Penicillium expansum KACC 40815

PubMed Central

Park, Hye Min; Singh, Digar; Lee, Choong Hwan

2016-01-01

Penicillium spp. are known to harbor a wide array of secondary metabolites with cryptic bioactivities. However, the metabolomics of these species is not well-understood in terms of different fermentation models and conditions. The present study involved metabolomics profiling and transcriptomic analysis of Penicillium expansum 40815 under solid-state fermentation (SSF) and submerged fermentation (SmF). Metabolite profiling was carried out using ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry with multivariate analysis, followed by transcriptomic analyses of differentially expressed genes. In principal component analysis, the metabolite profiling data was studied under different experimental sets, including SSF and SmF. The significantly different metabolites such as polyketide metabolites (agonodepside B, rotiorin, verrucosidin, and ochrephilone) and corresponding gene transcripts (polyketide synthase, aromatic prenyltransferase, and terpenoid synthase) were primarily detected under SmF conditions. In contrast, the meroterpenoid compounds (andrastin A and C) and their genes transcripts were exclusively detected under SSF conditions. We demonstrated that the metabolite production and its corresponding gene expression levels in P. expansum 40815 were significantly influenced by the varying growth parameters and the immediate environment. This study further provides a foundation to produce specific metabolites by regulating fermentation conditions. PMID:26863302

Analysis of degree of nonlinearity and stochastic nature of HRV signal during meditation using delay vector variance method.

PubMed

Reddy, L Ram Gopal; Kuntamalla, Srinivas

2011-01-01

Heart rate variability analysis is fast gaining acceptance as a potential non-invasive means of autonomic nervous system assessment in research as well as clinical domains. In this study, a new nonlinear analysis method is used to detect the degree of nonlinearity and stochastic nature of heart rate variability signals during two forms of meditation (Chi and Kundalini). The data obtained from an online and widely used public database (i.e., MIT/BIH physionet database), is used in this study. The method used is the delay vector variance (DVV) method, which is a unified method for detecting the presence of determinism and nonlinearity in a time series and is based upon the examination of local predictability of a signal. From the results it is clear that there is a significant change in the nonlinearity and stochastic nature of the signal before and during the meditation (p value > 0.01). During Chi meditation there is a increase in stochastic nature and decrease in nonlinear nature of the signal. There is a significant decrease in the degree of nonlinearity and stochastic nature during Kundalini meditation.

Tracing the biotransformation of polychlorinated biphenyls (PCBs) in common carp (Cryprinus carpio): Enantiomeric fraction and compound-specific stable carbon isotope analyses.

PubMed

Tang, Bin; Luo, Xiao-Jun; Zeng, Yan-Hong; Sun, Run-Xia; Chen, Hua-Shan; Li, Zong-Rui; Mai, Bi-Xian

2016-09-01

Metabolites of polychlorinated biphenyls (PCBs) in fish are difficult to detect in vivo due to the complexity of biometabolism. In the present study, atropisomeric fraction analysis of chiral PCB congeners and compound-specific isotopic analysis (CSIA) were applied to trace the biotransformation of PCBs in fish by exposure of common carp (Cryprinus carpio) to the commercial PCB mixture Aroclor 1242. Stereoselective elimination of the chiral PCB congeners 91, 95, and 136 was observed, indicating a stereoselective biotransformation process. The δ(13)C values of PCBs 5/8, 18, and 20/33 in fish were increased compared with those in the spiked food, while PCBs 47/48 and 49 showed significant heavy isotope depletion. These results suggested a significant biotransformation of the corresponding individual PCB congeners although the potential PCB metabolites, hydroxylated PCBs (OH-PCBs) and methylsulfone PCBs (MeSO2-PCBs), were not detected in the fish tissue samples throughout this experiment. The results of the present study demonstrated that a combination of chiral analysis and CSIA is a promising new approach for investigating the biotransformation of PCBs in biota. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metabolomic and Transcriptomic Comparison of Solid-State and Submerged Fermentation of Penicillium expansum KACC 40815.

PubMed

Kim, Hyang Yeon; Heo, Do Yeon; Park, Hye Min; Singh, Digar; Lee, Choong Hwan

2016-01-01

Penicillium spp. are known to harbor a wide array of secondary metabolites with cryptic bioactivities. However, the metabolomics of these species is not well-understood in terms of different fermentation models and conditions. The present study involved metabolomics profiling and transcriptomic analysis of Penicillium expansum 40815 under solid-state fermentation (SSF) and submerged fermentation (SmF). Metabolite profiling was carried out using ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry with multivariate analysis, followed by transcriptomic analyses of differentially expressed genes. In principal component analysis, the metabolite profiling data was studied under different experimental sets, including SSF and SmF. The significantly different metabolites such as polyketide metabolites (agonodepside B, rotiorin, verrucosidin, and ochrephilone) and corresponding gene transcripts (polyketide synthase, aromatic prenyltransferase, and terpenoid synthase) were primarily detected under SmF conditions. In contrast, the meroterpenoid compounds (andrastin A and C) and their genes transcripts were exclusively detected under SSF conditions. We demonstrated that the metabolite production and its corresponding gene expression levels in P. expansum 40815 were significantly influenced by the varying growth parameters and the immediate environment. This study further provides a foundation to produce specific metabolites by regulating fermentation conditions.

Kernel-Phase Interferometry for Super-Resolution Detection of Faint Companions

NASA Astrophysics Data System (ADS)

Factor, Samuel M.; Kraus, Adam L.

2017-01-01

Direct detection of close in companions (exoplanets or binary systems) is notoriously difficult. While coronagraphs and point spread function (PSF) subtraction can be used to reduce contrast and dig out signals of companions under the PSF, there are still significant limitations in separation and contrast. Non-redundant aperture masking (NRM) interferometry can be used to detect companions well inside the PSF of a diffraction limited image, though the mask discards ˜95% of the light gathered by the telescope and thus the technique is severely flux limited. Kernel-phase analysis applies interferometric techniques similar to NRM to a diffraction limited image utilizing the full aperture. Instead of non-redundant closure-phases, kernel-phases are constructed from a grid of points on the full aperture, simulating a redundant interferometer. I have developed my own faint companion detection pipeline which utilizes an Bayesian analysis of kernel-phases. I have used this pipeline to search for new companions in archival images from HST/NICMOS in order to constrain planet and binary formation models at separations inaccessible to previous techniques. Using this method, it is possible to detect a companion well within the classical λ/D Rayleigh diffraction limit using a fraction of the telescope time as NRM. This technique can easily be applied to archival data as no mask is needed and will thus make the detection of close in companions cheap and simple as no additional observations are needed. Since the James Webb Space Telescope (JWST) will be able to perform NRM observations, further development and characterization of kernel-phase analysis will allow efficient use of highly competitive JWST telescope time.

Kernel-Phase Interferometry for Super-Resolution Detection of Faint Companions

NASA Astrophysics Data System (ADS)

Factor, Samuel

2016-10-01

Direct detection of close in companions (binary systems or exoplanets) is notoriously difficult. While chronagraphs and point spread function (PSF) subtraction can be used to reduce contrast and dig out signals of companions under the PSF, there are still significant limitations in separation and contrast. While non-redundant aperture masking (NRM) interferometry can be used to detect companions well inside the PSF of a diffraction limited image, the mask discards 95% of the light gathered by the telescope and thus the technique is severely flux limited. Kernel-phase analysis applies interferometric techniques similar to NRM though utilizing the full aperture. Instead of closure-phases, kernel-phases are constructed from a grid of points on the full aperture, simulating a redundant interferometer. I propose to develop my own faint companion detection pipeline which utilizes an MCMC analysis of kernel-phases. I will search for new companions in archival images from NIC1 and ACS/HRC in order to constrain binary and planet formation models at separations inaccessible to previous techniques. Using this method, it is possible to detect a companion well within the classical l/D Rayleigh diffraction limit using a fraction of the telescope time as NRM. This technique can easily be applied to archival data as no mask is needed and will thus make the detection of close in companions cheap and simple as no additional observations are needed. Since the James Webb Space Telescope (JWST) will be able to perform NRM observations, further development and characterization of kernel-phase analysis will allow efficient use of highly competitive JWST telescope time.

The antimicrobial susceptibility, biofilm formation and genotypic profiles of Staphylococcus haemolyticus from bloodstream infections

PubMed Central

Silva, Patricia Vollú; Cruz, Raquel Souza; Keim, Luiz Sérgio; de Paula, Geraldo Renato; Carvalho, Bernadete Teixeira Ferreira; Coelho, Leonardo Rocchetto; Carvalho, Maria Cícera da Silva; da Rosa, Joel Mauricio Corrêa; Figueiredo, Agnes Marie Sá; Teixeira, Lenise Arneiro

2013-01-01

We analysed the antimicrobial susceptibility, biofilm formation and genotypic profiles of 27 isolates of Staphylococcus haemolyticus obtained from the blood of 19 patients admitted to a hospital in Rio de Janeiro, Brazil. Our analysis revealed a clinical significance of 36.8% and a multi-resistance rate of 92.6% among these isolates. All but one isolate carried the mecA gene. The staphylococcal cassette chromosome mec type I was the most prevalent mec element detected (67%). Nevertheless, the isolates showed clonal diversity based on pulsed-field gel electrophoresis analysis. The ability to form biofilms was detected in 66% of the isolates studied. Surprisingly, no icaAD genes were found among the biofilm-producing isolates. PMID:24037208

The antimicrobial susceptibility, biofilm formation and genotypic profiles of Staphylococcus haemolyticus from bloodstream infections.

PubMed

Silva, Patricia Vollú; Cruz, Raquel Souza; Keim, Luiz Sérgio; Paula, Geraldo Renato de; Carvalho, Bernadete Teixeira Ferreira; Coelho, Leonardo Rocchetto; Carvalho, Maria Cícera da Silva; Rosa, Joel Mauricio Corrêa da; Figueiredo, Agnes Marie Sá; Teixeira, Lenise Arneiro

2013-09-01

We analysed the antimicrobial susceptibility, biofilm formation and genotypic profiles of 27 isolates of Staphylococcus haemolyticus obtained from the blood of 19 patients admitted to a hospital in Rio de Janeiro, Brazil. Our analysis revealed a clinical significance of 36.8% and a multi-resistance rate of 92.6% among these isolates. All but one isolate carried the mecA gene. The staphylococcal cassette chromosome mec type I was the most prevalent mec element detected (67%). Nevertheless, the isolates showed clonal diversity based on pulsed-field gel electrophoresis analysis. The ability to form biofilms was detected in 66% of the isolates studied. Surprisingly, no icaAD genes were found among the biofilm-producing isolates.

Detection of chaos: New approach to atmospheric pollen time-series analysis

NASA Astrophysics Data System (ADS)

Bianchi, M. M.; Arizmendi, C. M.; Sanchez, J. R.

1992-09-01

Pollen and spores are biological particles that are ubiquitous to the atmosphere and are pathologically significant, causing plant diseases and inhalant allergies. One of the main objectives of aerobiological surveys is forecasting. Prediction models are required in order to apply aerobiological knowledge to medical or agricultural practice; a necessary condition of these models is not to be chaotic. The existence of chaos is detected through the analysis of a time series. The time series comprises hourly counts of atmospheric pollen grains obtained using a Burkard spore trap from 1987 to 1989 at Mar del Plata. Abraham's method to obtain the correlation dimension was applied. A low and fractal dimension shows chaotic dynamics. The predictability of models for atomspheric pollen forecasting is discussed.

Whole-genome CNV analysis: advances in computational approaches.

PubMed

Pirooznia, Mehdi; Goes, Fernando S; Zandi, Peter P

2015-01-01

Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development.

Computed tomography angiography reveals the crime instrument – case report

PubMed Central

Banaszek, Anna; Guziński, Maciej; Sąsiadek, Marek

2010-01-01

Summary Background: The development of multislice CT technology enabled imaging of post-traumatic brain lesions with isotropic resolution, which led to unexpected results in the presented case Case Report: An unconscious, 49-year-old male with a suspected trauma underwent a routine CT examination of the head, which revealed an unusual intracerebral bleeding and therefore was followed by CT angiography (CTA). The thorough analysis of CTA source scans led to the detection of the bleeding cause. Conclusions: The presented case showed that a careful analysis of a CT scan allows not only to define the extent of pathological lesions in the intracranial space but it also helps to detect the crime instrument, which is of medico-legal significance. PMID:22802784

Through Wall Radar Classification of Human Micro-Doppler Using Singular Value Decomposition Analysis

PubMed Central

Ritchie, Matthew; Ash, Matthew; Chen, Qingchao; Chetty, Kevin

2016-01-01

The ability to detect the presence as well as classify the activities of individuals behind visually obscuring structures is of significant benefit to police, security and emergency services in many situations. This paper presents the analysis from a series of experimental results generated using a through-the-wall (TTW) Frequency Modulated Continuous Wave (FMCW) C-Band radar system named Soprano. The objective of this analysis was to classify whether an individual was carrying an item in both hands or not using micro-Doppler information from a FMCW sensor. The radar was deployed at a standoff distance, of approximately 0.5 m, outside a residential building and used to detect multiple people walking within a room. Through the application of digital filtering, it was shown that significant suppression of the primary wall reflection is possible, significantly enhancing the target signal to clutter ratio. Singular Value Decomposition (SVD) signal processing techniques were then applied to the micro-Doppler signatures from different individuals. Features from the SVD information have been used to classify whether the person was carrying an item or walking free handed. Excellent performance of the classifier was achieved in this challenging scenario with accuracies up to 94%, suggesting that future through wall radar sensors may have the ability to reliably recognize many different types of activities in TTW scenarios using these techniques. PMID:27589760

Through Wall Radar Classification of Human Micro-Doppler Using Singular Value Decomposition Analysis.

PubMed

Ritchie, Matthew; Ash, Matthew; Chen, Qingchao; Chetty, Kevin

2016-08-31

The ability to detect the presence as well as classify the activities of individuals behind visually obscuring structures is of significant benefit to police, security and emergency services in many situations. This paper presents the analysis from a series of experimental results generated using a through-the-wall (TTW) Frequency Modulated Continuous Wave (FMCW) C-Band radar system named Soprano. The objective of this analysis was to classify whether an individual was carrying an item in both hands or not using micro-Doppler information from a FMCW sensor. The radar was deployed at a standoff distance, of approximately 0.5 m, outside a residential building and used to detect multiple people walking within a room. Through the application of digital filtering, it was shown that significant suppression of the primary wall reflection is possible, significantly enhancing the target signal to clutter ratio. Singular Value Decomposition (SVD) signal processing techniques were then applied to the micro-Doppler signatures from different individuals. Features from the SVD information have been used to classify whether the person was carrying an item or walking free handed. Excellent performance of the classifier was achieved in this challenging scenario with accuracies up to 94%, suggesting that future through wall radar sensors may have the ability to reliably recognize many different types of activities in TTW scenarios using these techniques.

Carbapenemase-producing Enterobacteriaceae: Risk factors for infection and impact of resistance on outcomes

PubMed Central

Mariappan, Shanthi; Sekar, Uma; Kamalanathan, Arunagiri

2017-01-01

Background: Carbapenemase-producing Enterobacteriaceae (CPE) have increased in recent years leading to limitations of treatment options. The present study was undertaken to detect CPE, risk factors for acquiring them and their impact on clinical outcomes. Methods: This retrospective observational study included 111 clinically significant Enterobacteriaceae resistant to cephalosporins subclass III and exhibiting a positive modified Hodge test. Screening for carbapenemase production was done by phenotypic methods, and polymerase chain reaction was performed to detect genes encoding them. Retrospectively, the medical records of the patients were perused to assess risk factors for infections with CPE and their impact. The data collected were duration of hospital stay, Intensive Care Unit (ICU) stay, use of invasive devices, mechanical ventilation, the presence of comorbidities, and antimicrobial therapy. The outcome was followed up. Univariate and multivariate analysis of the data were performed using SPSS software. Results: Carbapenemase-encoding genes were detected in 67 isolates. The genes detected were New Delhi metallo-β-lactamase, Verona integron-encoded metallo-β-lactamase, and oxacillinase-181.Although univariate analysis identified risk factors associated with acquiring CPE infections as ICU stay (P = 0.021), mechanical ventilation (P = 0.013), indwelling device (P = 0.011), diabetes mellitus (P = 0.036), usage of multiple antimicrobial agents (P = 0.007), administration of carbapenems (P = 0.042), presence of focal infection or sepsis (P = 0.013), and surgical interventions (P = 0.016), multivariate analysis revealed that all these factors were insignificant. Mortality rate was 56.7% in patients with CPE infections. By both univariate and multivariate analysis of impact of the variables on mortality in these patients, the significant factors were mechanical ventilation (odds ratio [OR]: 0.141, 95% confidence interval [CI]: 0.024–0.812) and presence of indwelling invasive device (OR: 8.034; 95% CI: 2.060–31.335). Conclusion: In this study, no specific factor was identified as an independent risk for acquisition of CPE infection. However, as it is evident by multivariate analysis, there is an increased risk of mortality in patients with CPE infections when they are ventilated and are supported by indwelling devices. PMID:28251105

A non-radioisotopic quantitative competitive polymerase chain reaction method: application in measurement of human herpesvirus 7 load.

PubMed

Kidd, I M; Clark, D A; Emery, V C

2000-06-01

Quantitative-competitive polymerase chain reaction (QCPCR) is a well-optimised and objective methodology for the determination of viral load in clinical specimens. A major advantage of QCPCR is the ability to control for the differential modulation of the PCR process in the presence of potentially inhibitory material. QCPCR protocols were developed previously for CMV, HHV-6, HHV-7 and HHV-8 and relied upon radioactively labelled primers, followed by autoradiography of the separated and digested PCR products to quantify viral load. Whilst this approach offers high accuracy and dynamic range, non-radioactive approaches would be attractive. Here, an alternative detection system is reported, based on simple ethidium bromide staining and computer analysis of the separated reaction products, which enables its adoption in the analysis of a large number of samples. In calibration experiments using cloned HHV-7 DNA, the ethidium bromide detection method showed an improved correlation with known copy number over that obtained with the isotopic method. In addition, 67 HHV-7 PCR positive blood samples, derived from immunocompromised patients, were quantified using both detection techniques. The results showed a highly significant correlation with no significant difference between the two methods. The applicability of the computerised densitometry method in the routine laboratory is discussed.

Noninvasive detection of lung cancer using exhaled breath

PubMed Central

Fu, Xiao-An; Li, Mingxiao; Knipp, Ralph J; Nantz, Michael H; Bousamra, Michael

2014-01-01

Early detection of lung cancer is a key factor for increasing the survival rates of lung cancer patients. The analysis of exhaled breath is promising as a noninvasive diagnostic tool for diagnosis of lung cancer. We demonstrate the quantitative analysis of carbonyl volatile organic compounds (VOCs) and identification of lung cancer VOC markers in exhaled breath using unique silicon microreactor technology. The microreactor consists of thousands of micropillars coated with an ammonium aminooxy salt for capture of carbonyl VOCs in exhaled breath by means of oximation reactions. Captured aminooxy-VOC adducts are analyzed by nanoelectrospray Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry (MS). The concentrations of 2-butanone, 2-hydroxyacetaldehyde, 3-hydroxy-2-butanone, and 4-hydroxyhexenal (4-HHE) in the exhaled breath of lung cancer patients (n = 97) were significantly higher than in the exhaled breath of healthy smoker and nonsmoker controls (n = 88) and patients with benign pulmonary nodules (n = 32). The concentration of 2-butanone in exhaled breath of patients (n = 51) with stages II though IV non–small cell lung cancer (NSCLC) was significantly higher than in exhaled breath of patients with stage I (n = 34). The carbonyl VOC profile in exhaled breath determined using this new silicon microreactor technology provides for the noninvasive detection of lung cancer. PMID:24402867

Novel ionic liquid matrices for qualitative and quantitative detection of carbohydrates by matrix assisted laser desorption/ionization mass spectrometry.

PubMed

Zhao, Xiaoyong; Shen, Shanshan; Wu, Datong; Cai, Pengfei; Pan, Yuanjiang

2017-09-08

Analysis of carbohydrates based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still challenging and researchers have been devoting themselves to efficient matrices discovery. In the present study, the design, synthesis, qualitative and quantitative performance of non-derivative ionic liquid matrices (ILMs) were reported. DHB/N-methylaniline (N-MA) and DHB/N-ethylaniline (N-EA), performing best for carbohydrate detection, have been screened out. The limit of detection for oligosaccharide provided by DHB/N-MA and DHB/N-EA were as low as 10 fmol. DHB/N-MA and DHB/N-EA showed significantly higher ion generation efficiency than DHB. The comparison of capacity to probe polysaccharide between these two ILMs and DHB also revealed their powerful potential. Their outstanding performance were probably due to lower proton affinities and stronger UV absorption at λ = 355 nm. What is more, taking DHB/N-MA as an example, quantitative analysis of fructo-oligosaccharide mixtures extracted and identified from rice noodles has been accomplished sensitively using an internal standard method. Overall, DHB/N-MA and DHB/N-EA exhibited excellent performance and might be significant sources as the carbohydrate matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

Vaccination of alpacas against Rift Valley fever virus: Safety, immunogenicity and pathogenicity of MP-12 vaccine.

PubMed

Rissmann, M; Ulrich, R; Schröder, C; Hammerschmidt, B; Hanke, D; Mroz, C; Groschup, M H; Eiden, M

2017-01-23

Rift Valley fever (RVF) is an emerging zoonosis of major public health concern in Africa and Arabia. Previous outbreaks attributed camelids a significant role in the epidemiology of Rift Valley fever virus (RVFV), making them an important target species for vaccination. Using three alpacas as model-organisms for dromedary camels, the safety, immunogenicity and pathogenicity of the MP-12 vaccine were evaluated in this study. To compare both acute and subacute effects, animals were euthanized at 3 and 31days post infection (dpi). Clinical monitoring, analysis of liver enzymes and hematological parameters demonstrated the tolerability of the vaccine, as no significant adverse effects were observed. Comprehensive analysis of serological parameters illustrated the immunogenicity of the vaccine, eliciting high neutralizing antibody titers and antibodies targeting different viral antigens. RVFV was detected in serum and liver of the alpaca euthanized 3dpi, whereas no virus was detectable at 31dpi. Viral replication was confirmed by detection of various RVFV-antigens in hepatocytes by immunohistochemistry and the presence of mild multifocal necrotizing hepatitis. In conclusion, results indicate that MP-12 is a promising vaccine candidate but still has a residual pathogenicity, which requires further investigation. Copyright © 2016 Elsevier Ltd. All rights reserved.