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  1. Theory and Application of DNA Histogram Analysis.

    Science.gov (United States)

    Bagwell, Charles Bruce

    The underlying principles and assumptions associated with DNA histograms are discussed along with the characteristics of fluorescent probes. Information theory was described and used to calculate the information content of a DNA histogram. Two major types of DNA histogram analyses are proposed: parametric and nonparametric analysis. Three levels…

  2. The equivalent Histograms in clinical practice

    International Nuclear Information System (INIS)

    Pizarro Trigo, F.; Teijeira Garcia, M.; Zaballos Carrera, S.

    2013-01-01

    Is frequently abused of The tolerances established for organ at risk [1] in diagrams of standard fractionation (2Gy/session, 5 sessions per week) when applied to Dose-Volume histograms non-standard schema. The purpose of this work is to establish when this abuse may be more important and realize a transformation of fractionation non-standard of histograms dosis-volumen. Is exposed a case that can be useful to make clinical decisions. (Author)

  3. Clinical Utility of Blood Cell Histogram Interpretation.

    Science.gov (United States)

    Thomas, E T Arun; Bhagya, S; Majeed, Abdul

    2017-09-01

    An automated haematology analyser provides blood cell histograms by plotting the sizes of different blood cells on X-axis and their relative number on Y-axis. Histogram interpretation needs careful analysis of Red Blood Cell (RBC), White Blood Cell (WBC) and platelet distribution curves. Histogram analysis is often a neglected part of the automated haemogram which if interpreted well, has significant potential to provide diagnostically relevant information even before higher level investigations are ordered.

  4. DNA IMAGE CYTOMETRY IN PROGNOSTICATION OF COLORECTAL CANCER: PRACTICAL CONSIDERATIONS OF THE TECHNIQUE AND INTERPRETATION OF THE HISTOGRAMS

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    Abdelbaset Buhmeida

    2011-05-01

    Full Text Available The role of DNA content as a prognostic factor in colorectal cancer (CRC is highly controversial. Some of these controversies are due to purely technical reasons, e.g. variable practices in interpreting the DNA histograms, which is problematic particularly in advanced cases. In this report, we give a detailed account on various options how these histograms could be optimally interpreted, with the idea of establishing the potential value of DNA image cytometry in prognosis and in selection of proper treatment. Material consists of nuclei isolated from 50 ƒĘm paraffin sections from 160 patients with stage II, III or IV CRC diagnosed, treated and followed-up in our clinic. The nuclei were stained with the Feulgen stain. Nuclear DNA was measured using computer-assisted image cytometry. We applied 4 different approaches to analyse the DNA histograms: 1 appearance of the histogram (ABCDE approach, 2 range of DNA values, 3 peak evaluation, and 4 events present at high DNA values. Intra-observer reproducibility of these four histogram interpretation was 89%, 95%, 96%, and 100%, respectively. We depicted selected histograms to illustrate the four analytical approaches in cases with different stages of CRC, with variable disease outcome. In our analysis, the range of DNA values was the best prognosticator, i.e., the tumours with the widest histograms had the most ominous prognosis. These data implicate that DNA cytometry based on isolated nuclei is valuable in predicting the prognosis of CRC. Different interpretation techniques differed in their reproducibility, but the method showing the best prognostic value also had high reproducibility in our analysis.

  5. Automatic analysis of flow cytometric DNA histograms from irradiated mouse male germ cells

    International Nuclear Information System (INIS)

    Lampariello, F.; Mauro, F.; Uccelli, R.; Spano, M.

    1989-01-01

    An automatic procedure for recovering the DNA content distribution of mouse irradiated testis cells from flow cytometric histograms is presented. First, a suitable mathematical model is developed, to represent the pattern of DNA content and fluorescence distribution in the sample. Then a parameter estimation procedure, based on the maximum likelihood approach, is constructed by means of an optimization technique. This procedure has been applied to a set of DNA histograms relative to different doses of 0.4-MeV neutrons and to different time intervals after irradiation. In each case, a good agreement between the measured histograms and the corresponding fits has been obtained. The results indicate that the proposed method for the quantitative analysis of germ cell DNA histograms can be usefully applied to the study of the cytotoxic and mutagenic action of agents of toxicological interest such as ionizing radiations.18 references

  6. Quick cytogenetic screening of breeding bulls using flow cytometric sperm DNA histogram analysis.

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    Nagy, Szabolcs; Polgár, Péter J; Andersson, Magnus; Kovács, András

    2016-09-01

    The aim of the present study was to test the FXCycle PI/RNase kit for routine DNA analyses in order to detect breeding bulls and/or insemination doses carrying cytogenetic aberrations. In a series of experiments we first established basic DNA histogram parameters of cytogenetically healthy breeding bulls by measuring the intraspecific genome size variation of three animals, then we compared the histogram profiles of bulls carrying cytogenetic defects to the baseline values. With the exception of one case the test was able to identify bulls with cytogenetic defects. Therefore, we conclude that the assay could be incorporated into the laboratory routine where flow cytometry is applied for semen quality control.

  7. Histogram analysis of diffusion measures in clinically isolated syndromes and relapsing-remitting multiple sclerosis

    International Nuclear Information System (INIS)

    Yu Chunshui; Lin Fuchun; Liu Yaou; Duan Yunyun; Lei Hao; Li Kuncheng

    2008-01-01

    Objective: The purposes of our study were to employ diffusion tensor imaging (DTI)-based histogram analysis to determine the presence of occult damage in clinically isolated syndrome (CIS), to compare its severity with relapsing-remitting multiple sclerosis (RRMS), and to determine correlations between DTI histogram measures and clinical and MRI indices in these two diseases. Materials and methods: DTI scans were performed in 19 CIS and 19 RRMS patients and 19 matched healthy volunteers. Histogram analyses of mean diffusivity and fractional anisotropy were performed in normal-appearing brain tissue (NABT), normal-appearing white matter (NAWM) and gray matter (NAGM). Correlations were analyzed between these measures and expanded disability status scale (EDSS) scores, T 2 WI lesion volumes (LV) and normalized brain tissue volumes (NBTV) in CIS and RRMS patients. Results: Significant differences were found among CIS, RRMS and control groups in the NBTV and most of the DTI histogram measures of the NABT, NAWM and NAGM. In CIS patients, some DTI histogram measures showed significant correlations with LV and NBTV, but none of them with EDSS. In RRMS patients, however, some DTI histogram measures were significantly correlated with LV, NBTV and EDSS. Conclusion: Occult damage occurs in both NAGM and NAWM in CIS, but the severity is milder than that in RRMS. In CIS and RRMS, the occult damage might be related to both T2 lesion load and brain tissue atrophy. Some DTI histogram measures might be useful for assessing the disease progression in RRMS patients

  8. The equivalent Histograms in clinical practice; Los histogramas equivalentes en la practica clinica

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    Pizarro Trigo, F.; Teijeira Garcia, M.; Zaballos Carrera, S.

    2013-07-01

    Is frequently abused of The tolerances established for organ at risk [1] in diagrams of standard fractionation (2Gy/session, 5 sessions per week) when applied to Dose-Volume histograms non-standard schema. The purpose of this work is to establish when this abuse may be more important and realize a transformation of fractionation non-standard of histograms dosis-volumen. Is exposed a case that can be useful to make clinical decisions. (Author)

  9. Influence of Sampling Practices on the Appearance of DNA Image Histograms of Prostate Cells in FNAB Samples

    Directory of Open Access Journals (Sweden)

    Abdelbaset Buhmeida

    1999-01-01

    Full Text Available Twenty‐one fine needle aspiration biopsies (FNAB of the prostate, diagnostically classified as definitely malignant, were studied. The Papanicolaou or H&E stained samples were destained and then stained for DNA with the Feulgen reaction. DNA cytometry was applied after different sampling rules. The histograms varied according to the sampling rule applied. Because free cells between cell groups were easier to measure than cells in the cell groups, two sampling rules were tested in all samples: (i cells in the cell groups were measured, and (ii free cells between cell groups were measured. Abnormal histograms were more common after the sampling rule based on free cells, suggesting that abnormal patterns are best revealed through the free cells in these samples. The conclusions were independent of the applied histogram interpretation method.

  10. [Clinical application of MRI histogram in evaluation of muscle fatty infiltration].

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    Zheng, Y M; Du, J; Li, W Z; Wang, Z X; Zhang, W; Xiao, J X; Yuan, Y

    2016-10-18

    To describe a method based on analysis of the histogram of intensity values produced from the magnetic resonance imaging (MRI) for quantifying the degree of fatty infiltration. The study included 25 patients with dystrophinopathy. All the subjects underwent muscle MRI test at thigh level. The histogram M values of 250 muscles adjusted for subcutaneous fat, representing the degree of fatty infiltration, were compared with the expert visual reading using the modified Mercuri scale. There was a significant positive correlation between the histogram M values and the scores of visual reading (r=0.854, Phistogram M values was similar to that of visual reading and results in literature. The histogram M values had stronger correlations with the clinical data than the scores of visual reading as follows: the correlations with age (r=0.730, Phistogram M values analysis had better repeatability than visual reading with the interclass correlation coefficient was 0.998 (95% CI: 0.997-0.998, PHistogram M values analysis of MRI with the advantages of repeatability and objectivity can be used to evaluate the degree of muscle fatty infiltration.

  11. Histogram analysis of diffusion kurtosis imaging of nasopharyngeal carcinoma: Correlation between quantitative parameters and clinical stage.

    Science.gov (United States)

    Xu, Xiao-Quan; Ma, Gao; Wang, Yan-Jun; Hu, Hao; Su, Guo-Yi; Shi, Hai-Bin; Wu, Fei-Yun

    2017-07-18

    To evaluate the correlation between histogram parameters derived from diffusion-kurtosis (DK) imaging and the clinical stage of nasopharyngeal carcinoma (NPC). High T-stage (T3/4) NPC showed significantly higher Kapp-mean (P = 0.018), Kapp-median (P = 0.029) and Kapp-90th (P = 0.003) than low T-stage (T1/2) NPC. High N-stage NPC (N2/3) showed significantly lower Dapp-mean (P = 0.002), Dapp-median (P = 0.002) and Dapp-10th (P Histogram parameters, including mean, median, 10th, 90th percentiles, skewness and kurtosis of Dapp and Kapp were calculated. Patients were divided into low and high T, N and clinical stage based on American Joint Committee on Cancer (AJCC) staging system. Differences of histogram parameters between low and high T, N and AJCC stages were compared using t test. Multiple receiver operating characteristic (ROC) curves were used to determine and compare the value of significant parameters in predicting high T, N and AJCC stage, respectively. DK imaging-derived parameters correlated well with clinical stage of NPC, therefore could serve as an adjunctive imaging technique for evaluating NPC.

  12. BED-Volume histograms calculation for routine clinical dosimetry in brachytherapy

    International Nuclear Information System (INIS)

    Galelli, M.; Feroldi, P.

    1995-01-01

    The consideration of volumes is essential in Brachytherapy clinical dosimetry (I.C.R.U). Indeed, several indices, all based on dose-volume histograms (DVHs), have been designed in order to evaluate: before the therapy the volumetric quality of different possible implant geometries; during the therapy the consistency of the real and the previsional implants. Radiobiological evaluations, considering the dose deposition temporal pattern of treatment, can be usefully added to dosimetric calculations, to compare different treatment schedules. The Linear-Quadratic model is the most used: radiobiological modelisation and Biologically Effective Dose (BED) is principal related dosimetric quantity. Therefore, the consideration of BED-volume histogram (BED-VHs) is a straightforward extension of DVHs. In practice, BED-VHs can help relative comparisons and optimisations in treatment planning when combined to dose-volume histograms. Since 1994 the dosimetric calculations for all the gynecological brachytherapy treatments are performed considering also DVHs and BED-VHs. In this presentation we show the methods of BEDVHs calculation, together with some typical results

  13. Characterization of Diffusion Metric Map Similarity in Data From a Clinical Data Repository Using Histogram Distances

    Science.gov (United States)

    Warner, Graham C.; Helmer, Karl G.

    2018-01-01

    As the sharing of data is mandated by funding agencies and journals, reuse of data has become more prevalent. It becomes imperative, therefore, to develop methods to characterize the similarity of data. While users can group data based on the acquisition parameters stored in the file headers, these gives no indication whether a file can be combined with other data without increasing the variance in the data set. Methods have been implemented that characterize the signal-to-noise ratio or identify signal drop-outs in the raw image files, but potential users of data often have access to calculated metric maps and these are more difficult to characterize and compare. Here we describe a histogram-distance-based method applied to diffusion metric maps of fractional anisotropy and mean diffusivity that were generated using data extracted from a repository of clinically-acquired MRI data. We describe the generation of the data set, the pitfalls specific to diffusion MRI data, and the results of the histogram distance analysis. We find that, in general, data from GE scanners are less similar than are data from Siemens scanners. We also find that the distribution of distance metric values is not Gaussian at any selection of the acquisition parameters considered here (field strength, number of gradient directions, b-value, and vendor). PMID:29568257

  14. Identification of column edges of DNA fragments by using K-means clustering and mean algorithm on lane histograms of DNA agarose gel electrophoresis images

    Science.gov (United States)

    Turan, Muhammed K.; Sehirli, Eftal; Elen, Abdullah; Karas, Ismail R.

    2015-07-01

    Gel electrophoresis (GE) is one of the most used method to separate DNA, RNA, protein molecules according to size, weight and quantity parameters in many areas such as genetics, molecular biology, biochemistry, microbiology. The main way to separate each molecule is to find borders of each molecule fragment. This paper presents a software application that show columns edges of DNA fragments in 3 steps. In the first step the application obtains lane histograms of agarose gel electrophoresis images by doing projection based on x-axis. In the second step, it utilizes k-means clustering algorithm to classify point values of lane histogram such as left side values, right side values and undesired values. In the third step, column edges of DNA fragments is shown by using mean algorithm and mathematical processes to separate DNA fragments from the background in a fully automated way. In addition to this, the application presents locations of DNA fragments and how many DNA fragments exist on images captured by a scientific camera.

  15. Inverse optimization of objective function weights for treatment planning using clinical dose-volume histograms

    Science.gov (United States)

    Babier, Aaron; Boutilier, Justin J.; Sharpe, Michael B.; McNiven, Andrea L.; Chan, Timothy C. Y.

    2018-05-01

    We developed and evaluated a novel inverse optimization (IO) model to estimate objective function weights from clinical dose-volume histograms (DVHs). These weights were used to solve a treatment planning problem to generate ‘inverse plans’ that had similar DVHs to the original clinical DVHs. Our methodology was applied to 217 clinical head and neck cancer treatment plans that were previously delivered at Princess Margaret Cancer Centre in Canada. Inverse plan DVHs were compared to the clinical DVHs using objective function values, dose-volume differences, and frequency of clinical planning criteria satisfaction. Median differences between the clinical and inverse DVHs were within 1.1 Gy. For most structures, the difference in clinical planning criteria satisfaction between the clinical and inverse plans was at most 1.4%. For structures where the two plans differed by more than 1.4% in planning criteria satisfaction, the difference in average criterion violation was less than 0.5 Gy. Overall, the inverse plans were very similar to the clinical plans. Compared with a previous inverse optimization method from the literature, our new inverse plans typically satisfied the same or more clinical criteria, and had consistently lower fluence heterogeneity. Overall, this paper demonstrates that DVHs, which are essentially summary statistics, provide sufficient information to estimate objective function weights that result in high quality treatment plans. However, as with any summary statistic that compresses three-dimensional dose information, care must be taken to avoid generating plans with undesirable features such as hotspots; our computational results suggest that such undesirable spatial features were uncommon. Our IO-based approach can be integrated into the current clinical planning paradigm to better initialize the planning process and improve planning efficiency. It could also be embedded in a knowledge-based planning or adaptive radiation therapy framework to

  16. Histogram analysis of apparent diffusion coefficient maps for assessing thymic epithelial tumours: correlation with world health organization classification and clinical staging.

    Science.gov (United States)

    Kong, Ling-Yan; Zhang, Wei; Zhou, Yue; Xu, Hai; Shi, Hai-Bin; Feng, Qing; Xu, Xiao-Quan; Yu, Tong-Fu

    2018-04-01

    To investigate the value of apparent diffusion coefficients (ADCs) histogram analysis for assessing World Health Organization (WHO) pathological classification and Masaoka clinical stages of thymic epithelial tumours. 37 patients with histologically confirmed thymic epithelial tumours were enrolled. ADC measurements were performed using hot-spot ROI (ADC HS-ROI ) and histogram-based approach. ADC histogram parameters included mean ADC (ADC mean ), median ADC (ADC median ), 10 and 90 percentile of ADC (ADC 10 and ADC 90 ), kurtosis and skewness. One-way ANOVA, independent-sample t-test, and receiver operating characteristic were used for statistical analyses. There were significant differences in ADC mean , ADC median , ADC 10 , ADC 90 and ADC HS-ROI among low-risk thymoma (type A, AB, B1; n = 14), high-risk thymoma (type B2, B3; n = 9) and thymic carcinoma (type C, n = 14) groups (all p-values histogram analysis may assist in assessing the WHO pathological classification and Masaoka clinical stages of thymic epithelial tumours. Advances in knowledge: 1. ADC histogram analysis could help to assess WHO pathological classification of thymic epithelial tumours. 2. ADC histogram analysis could help to evaluate Masaoka clinical stages of thymic epithelial tumours. 3. ADC 10 might be a promising imaging biomarker for assessing and characterizing thymic epithelial tumours.

  17. Clinical implementation of dose-volume histogram predictions for organs-at-risk in IMRT planning

    International Nuclear Information System (INIS)

    Moore, K L; Appenzoller, L M; Tan, J; Michalski, J M; Thorstad, W L; Mutic, S

    2014-01-01

    True quality control (QC) of the planning process requires quantitative assessments of treatment plan quality itself, and QC in IMRT has been stymied by intra-patient anatomical variability and inherently complex three-dimensional dose distributions. In this work we describe the development of an automated system to reduce clinical IMRT planning variability and improve plan quality using mathematical models that predict achievable OAR DVHs based on individual patient anatomy. These models rely on the correlation of expected dose to the minimum distance from a voxel to the PTV surface, whereby a three-parameter probability distribution function (PDF) was used to model iso-distance OAR subvolume dose distributions. DVH models were obtained by fitting the evolution of the PDF with distance. Initial validation on clinical cohorts of 40 prostate and 24 head-and-neck plans demonstrated highly accurate model-based predictions for achievable DVHs in rectum, bladder, and parotid glands. By quantifying the integrated difference between candidate DVHs and predicted DVHs, the models correctly identified plans with under-spared OARs, validated by replanning all cases and correlating any realized improvements against the predicted gains. Clinical implementation of these predictive models was demonstrated in the PINNACLE treatment planning system by use of existing margin expansion utilities and the scripting functionality inherent to the system. To maintain independence from specific planning software, a system was developed in MATLAB to directly process DICOM-RT data. Both model training and patient-specific analyses were demonstrated with significant computational accelerations from parallelization.

  18. Diagnostic accuracy of ultrasonic histogram features to evaluate radiation toxicity of the parotid glands: a clinical study of xerostomia following head-and-neck cancer radiotherapy.

    Science.gov (United States)

    Yang, Xiaofeng; Tridandapani, Srini; Beitler, Jonathan J; Yu, David S; Chen, Zhengjia; Kim, Sungjin; Bruner, Deborah W; Curran, Walter J; Liu, Tian

    2014-10-01

    To investigate the diagnostic accuracy of ultrasound histogram features in the quantitative assessment of radiation-induced parotid gland injury and to identify potential imaging biomarkers for radiation-induced xerostomia (dry mouth)-the most common and debilitating side effect after head-and-neck radiotherapy (RT). Thirty-four patients, who have developed xerostomia after RT for head-and-neck cancer, were enrolled. Radiation-induced xerostomia was defined by the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer morbidity scale. Ultrasound scans were performed on each patient's parotids bilaterally. The 34 patients were stratified into the acute-toxicity groups (16 patients, ≤ 3 months after treatment) and the late-toxicity group (18 patients, > 3 months after treatment). A separate control group of 13 healthy volunteers underwent similar ultrasound scans of their parotid glands. Six sonographic features were derived from the echo-intensity histograms to assess acute and late toxicity of the parotid glands. The quantitative assessments were compared to a radiologist's clinical evaluations. The diagnostic accuracy of these ultrasonic histogram features was evaluated with the receiver operating characteristic (ROC) curve. With an area under the ROC curve greater than 0.90, several histogram features demonstrated excellent diagnostic accuracy for evaluation of acute and late toxicity of parotid glands. Significant differences (P xerostomia monitoring and assessment. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  19. Whole-tumour diffusion kurtosis MR imaging histogram analysis of rectal adenocarcinoma: Correlation with clinical pathologic prognostic factors.

    Science.gov (United States)

    Cui, Yanfen; Yang, Xiaotang; Du, Xiaosong; Zhuo, Zhizheng; Xin, Lei; Cheng, Xintao

    2018-04-01

    To investigate potential relationships between diffusion kurtosis imaging (DKI)-derived parameters using whole-tumour volume histogram analysis and clinicopathological prognostic factors in patients with rectal adenocarcinoma. 79 consecutive patients who underwent MRI examination with rectal adenocarcinoma were retrospectively evaluated. Parameters D, K and conventional ADC were measured using whole-tumour volume histogram analysis. Student's t-test or Mann-Whitney U-test, receiver operating characteristic curves and Spearman's correlation were used for statistical analysis. Almost all the percentile metrics of K were correlated positively with nodal involvement, higher histological grades, the presence of lymphangiovascular invasion (LVI) and circumferential margin (CRM) (phistogram analysis, especially K parameters, were associated with important prognostic factors of rectal cancer. • K correlated positively with some important prognostic factors of rectal cancer. • K mean showed higher AUC and specificity for differentiation of nodal involvement. • DKI metrics with whole-tumour volume histogram analysis depicted tumour heterogeneity.

  20. Dose-Volume Histogram Parameters and Clinical Factors Associated With Pleural Effusion After Chemoradiotherapy in Esophageal Cancer Patients

    International Nuclear Information System (INIS)

    Shirai, Katsuyuki; Tamaki, Yoshio; Kitamoto, Yoshizumi; Murata, Kazutoshi; Satoh, Yumi; Higuchi, Keiko; Nonaka, Tetsuo; Ishikawa, Hitoshi; Katoh, Hiroyuki; Takahashi, Takeo; Nakano, Takashi

    2011-01-01

    Purpose: To investigate the dose-volume histogram parameters and clinical factors as predictors of pleural effusion in esophageal cancer patients treated with concurrent chemoradiotherapy (CRT). Methods and Materials: Forty-three esophageal cancer patients treated with definitive CRT from January 2001 to March 2007 were reviewed retrospectively on the basis of the following criteria: pathologically confirmed esophageal cancer, available computed tomography scan for treatment planning, 6-month follow-up after CRT, and radiation dose ≥50 Gy. Exclusion criteria were lung metastasis, malignant pleural effusion, and surgery. Mean heart dose, mean total lung dose, and percentages of heart or total lung volume receiving ≥10-60 Gy (Heart-V 10 to V 60 and Lung-V 10 to V 60 , respectively) were analyzed in relation to pleural effusion. Results: The median follow-up time was 26.9 months (range, 6.7-70.2) after CRT. Of the 43 patients, 15 (35%) developed pleural effusion. By univariate analysis, mean heart dose, Heart-V 10 to V 60 , and Lung-V 50 to V 60 were significantly associated with pleural effusion. Poor performance status, primary tumor of the distal esophagus, and age ≥65 years were significantly related with pleural effusion. Multivariate analysis identified Heart-V 50 as the strongest predictive factor for pleural effusion (p = 0.01). Patients with Heart-V 50 50 50 ≥40% had 6%, 44%, and 64% of pleural effusion, respectively (p 50 is a useful parameter for assessing the risk of pleural effusion and should be reduced to avoid pleural effusion.

  1. The Amazing Histogram.

    Science.gov (United States)

    Vandermeulen, H.; DeWreede, R. E.

    1983-01-01

    Presents a histogram drawing program which sorts real numbers in up to 30 categories. Entered data are sorted and saved in a text file which is then used to generate the histogram. Complete Applesoft program listings are included. (JN)

  2. Information granules in image histogram analysis.

    Science.gov (United States)

    Wieclawek, Wojciech

    2018-04-01

    A concept of granular computing employed in intensity-based image enhancement is discussed. First, a weighted granular computing idea is introduced. Then, the implementation of this term in the image processing area is presented. Finally, multidimensional granular histogram analysis is introduced. The proposed approach is dedicated to digital images, especially to medical images acquired by Computed Tomography (CT). As the histogram equalization approach, this method is based on image histogram analysis. Yet, unlike the histogram equalization technique, it works on a selected range of the pixel intensity and is controlled by two parameters. Performance is tested on anonymous clinical CT series. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Clinical strains of acinetobacter classified by DNA-DNA hybridization

    International Nuclear Information System (INIS)

    Tjernberg, I.; Ursing, J.

    1989-01-01

    A collection of Acinetobacter strains consisting of 168 consecutive clinical strains and 30 type and reference strains was studied by DNA-DNA hybridization and a few phenotypic tests. The field strains could be allotted to 13 DNA groups. By means of reference strains ten of these could be identified with groups described by Bouvet and Grimont (1986), while three groups were new; they were given the numbers 13-15. The type strain of A. radioresistens- recently described by Nishimura et al. (1988) - was shown to be a member of DNA group 12, which comprised 31 clinical isolates. Of the 19 strains of A. junii, eight showed hemolytic acitivity on sheep and human blood agar and an additional four strains on human blood agar only. Strains of this species have previously been regarded as non-hemolytic. Reciprocal DNA pairing data for the reference strains of the DNA gropus were treated by UPGMA clustering. The reference strains for A. calcoaceticus, A. baumannii and DNA groups 3 and 13 formed a cluster with about 70% relatedness within the cluster. Other DNA groups joined at levels below 60%. (author)

  4. Clinical strains of acinetobacter classified by DNA-DNA hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Tjernberg, I; Ursing, J [Department of Medical Microbiology, University of Lund, Malmoe General Hospital, Malmoe (Sweden)

    1989-01-01

    A collection of Acinetobacter strains consisting of 168 consecutive clinical strains and 30 type and reference strains was studied by DNA-DNA hybridization and a few phenotypic tests. The field strains could be allotted to 13 DNA groups. By means of reference strains ten of these could be identified with groups described by Bouvet and Grimont (1986), while three groups were new; they were given the numbers 13-15. The type strain of A. radioresistens- recently described by Nishimura et al. (1988) - was shown to be a member of DNA group 12, which comprised 31 clinical isolates. Of the 19 strains of A. junii, eight showed hemolytic acitivity on sheep and human blood agar and an additional four strains on human blood agar only. Strains of this species have previously been regarded as non-hemolytic. Reciprocal DNA pairing data for the reference strains of the DNA gropus were treated by UPGMA clustering. The reference strains for A. calcoaceticus, A. baumannii and DNA groups 3 and 13 formed a cluster with about 70% relatedness within the cluster. Other DNA groups joined at levels below 60%. (author).

  5. Histogram score contributes for reliability of DNA content estimatives in Brachiaria spp Notas do histograma contribuem para a confiabilidade das estimativas do conteúdo de DNA de Brachiaria spp

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    Ana Luiza de Oliveira Timbó

    2012-12-01

    Full Text Available Flow cytometry allows to estimate the DNA content of a large number of plants quickly. However, inadequate protocols can compromise the reliability of these estimates leading to variations in the values of DNA content the same species. The objective of this study was to propose an efficient protocol to estimate the DNA content of Brachiaria spp. genotypes with different ploidy levels using flow cytometry. We evaluated four genotypes (B. ruziziensis diploid and artificially tetraploidized; a tetraploid B. brizantha and a natural triploid hybrid, three buffer solutions (MgSO4, Galbraith and Tris-HCl and three species as internal reference standards (Raphanus sativus, Solanum lycopersicum e Pisum sativum. The variables measured were: histogram score (1-5, coefficient of variation and estimation of DNA content. The best combination for the analysis of Brachiaria spp. DNA content was the use of MgSO4 buffer with R. sativus as a internal reference standard. Genome sizes expressed in picograms of DNA are presented for all genotypes and the importance of the histogram score on the results reliability of DNA content analyses were discussed.A citometria de fluxo permite estimar o conteúdo de DNA de um grande número de plantas rapidamente. No entanto, protocolos inadequados podem comprometer a confiabilidade dessas estimativas, levando a variações nos valores de conteúdo de DNA para uma mesma espécie. Neste trabalho, objetivou-se propor um protocolo eficiente para a estimativa do conteúdo de DNA de genótipos de Brachiaria spp. com diferentes níveis de ploidia, utilizando a citometria de fluxo. Foram avaliados quatro genótipos (B. ruziziensis, diploide e tetraploidizada artificialmente; B. brizantha tetraploide e um híbrido natural triploide, 3 soluções tampões (MgSO4, Galbraith e Tris-HCl e três espécies como padrões de referência interno (Raphanus sativus, Solanum lycopersicum e Pisum sativum. As variáveis mensuradas foram: nota do

  6. The histogramming tool hparse

    International Nuclear Information System (INIS)

    Nikulin, V.; Shabratova, G.

    2005-01-01

    A general-purpose package aimed to simplify the histogramming in the data analysis is described. The proposed dedicated language for writing the histogramming scripts provides an effective and flexible tool for definition of a complicated histogram set. The script is more transparent and much easier to maintain than corresponding C++ code. In the TTree analysis it could be a good complement to the TTreeViewer class: the TTreeViewer is used for choice of the required histogram/cut set, while the hparse enables one to generate a code for systematic analysis

  7. Clinical case of Mitochondrial DNA Depletion

    Directory of Open Access Journals (Sweden)

    A. V. Degtyareva

    2017-01-01

    Full Text Available The article reports clinical case of early neonatal manifestation of a rare genetic disease – mitochondrial DNA depletion syndrome, confirmed in laboratory in Russia. Mutations of FBXL4, which encodes an orphan mitochondrial F-box protein, involved in the maintenance of mitochondrial DNA (mtDNA, ultimately leading to disruption of mtDNA replication and decreased activity of mitochondrial respiratory chain complexes. It’s a reason of abnormalities in clinically affected tissues, most of all the muscular system and the brain. In our case hydronephrosis on the right, subependimal cysts of the brain, partial intestinal obstruction accompanied by polyhydramnios were diagnosed antenatal. Baby’s condition at birth was satisfactory and worsened dramatically towards the end of the first day of life. Clinical presentation includes sepsis-like symptom complex, neonatal depression, muscular hypotonia, persistent decompensated lactic acidosis, increase in the concentration of mitochondrial markers in blood plasma and urine, and changes in the basal ganglia of the brain. Imaging of the brain by magnetic resonance imaging (MRI demonstrated global volume loss particularly the subcortical and periventricular white matter with significant abnormal signal in bilateral basal ganglia and brainstem with associated delayed myelination. Differential diagnosis was carried out with hereditary diseases that occur as a «sepsis-like» symptom complex, accompanied by lactic acidosis: a group of metabolic disorders of amino acids, organic acids, β-oxidation defects of fatty acids, respiratory mitochondrial chain disorders and glycogen storage disease. The diagnosis was confirmed after sequencing analysis of 62 mytochondrial genes by NGS (Next Generation Sequencing. Reported disease has an unfavorable prognosis, however, accurate diagnosis is very important for genetic counseling and helps prevent the re-birth of a sick child in the family.

  8. Machine assisted histogram classification

    Science.gov (United States)

    Benyó, B.; Gaspar, C.; Somogyi, P.

    2010-04-01

    LHCb is one of the four major experiments under completion at the Large Hadron Collider (LHC). Monitoring the quality of the acquired data is important, because it allows the verification of the detector performance. Anomalies, such as missing values or unexpected distributions can be indicators of a malfunctioning detector, resulting in poor data quality. Spotting faulty or ageing components can be either done visually using instruments, such as the LHCb Histogram Presenter, or with the help of automated tools. In order to assist detector experts in handling the vast monitoring information resulting from the sheer size of the detector, we propose a graph based clustering tool combined with machine learning algorithm and demonstrate its use by processing histograms representing 2D hitmaps events. We prove the concept by detecting ion feedback events in the LHCb experiment's RICH subdetector.

  9. Machine assisted histogram classification

    Energy Technology Data Exchange (ETDEWEB)

    Benyo, B; Somogyi, P [BME-IIT, H-1117 Budapest, Magyar tudosok koerutja 2. (Hungary); Gaspar, C, E-mail: Peter.Somogyi@cern.c [CERN-PH, CH-1211 Geneve 23 (Switzerland)

    2010-04-01

    LHCb is one of the four major experiments under completion at the Large Hadron Collider (LHC). Monitoring the quality of the acquired data is important, because it allows the verification of the detector performance. Anomalies, such as missing values or unexpected distributions can be indicators of a malfunctioning detector, resulting in poor data quality. Spotting faulty or ageing components can be either done visually using instruments, such as the LHCb Histogram Presenter, or with the help of automated tools. In order to assist detector experts in handling the vast monitoring information resulting from the sheer size of the detector, we propose a graph based clustering tool combined with machine learning algorithm and demonstrate its use by processing histograms representing 2D hitmaps events. We prove the concept by detecting ion feedback events in the LHCb experiment's RICH subdetector.

  10. Histogram Estimators of Bivariate Densities

    National Research Council Canada - National Science Library

    Husemann, Joyce A

    1986-01-01

    One-dimensional fixed-interval histogram estimators of univariate probability density functions are less efficient than the analogous variable-interval estimators which are constructed from intervals...

  11. COLOUR IMAGE ENHANCEMENT BASED ON HISTOGRAM EQUALIZATION

    OpenAIRE

    Kanika Kapoor and Shaveta Arora

    2015-01-01

    Histogram equalization is a nonlinear technique for adjusting the contrast of an image using its histogram. It increases the brightness of a gray scale image which is different from the mean brightness of the original image. There are various types of Histogram equalization techniques like Histogram Equalization, Contrast Limited Adaptive Histogram Equalization, Brightness Preserving Bi Histogram Equalization, Dualistic Sub Image Histogram Equalization, Minimum Mean Brightness Error Bi Histog...

  12. Investigating Student Understanding of Histograms

    Science.gov (United States)

    Kaplan, Jennifer J.; Gabrosek, John G.; Curtiss, Phyllis; Malone, Chris

    2014-01-01

    Histograms are adept at revealing the distribution of data values, especially the shape of the distribution and any outlier values. They are included in introductory statistics texts, research methods texts, and in the popular press, yet students often have difficulty interpreting the information conveyed by a histogram. This research identifies…

  13. The Histogram-Area Connection

    Science.gov (United States)

    Gratzer, William; Carpenter, James E.

    2008-01-01

    This article demonstrates an alternative approach to the construction of histograms--one based on the notion of using area to represent relative density in intervals of unequal length. The resulting histograms illustrate the connection between the area of the rectangles associated with particular outcomes and the relative frequency (probability)…

  14. Reproducibility of brain ADC histograms

    International Nuclear Information System (INIS)

    Steens, S.C.A.; Buchem, M.A. van; Admiraal-Behloul, F.; Schaap, J.A.; Hoogenraad, F.G.C.; Wheeler-Kingshott, C.A.M.; Tofts, P.S.; Cessie, S. le

    2004-01-01

    The aim of this study was to assess the effect of differences in acquisition technique on whole-brain apparent diffusion coefficient (ADC) histogram parameters, as well as to assess scan-rescan reproducibility. Diffusion-weighted imaging (DWI) was performed in 7 healthy subjects with b-values 0-800, 0-1000, and 0-1500 s/mm 2 and fluid-attenuated inversion recovery (FLAIR) DWI with b-values 0-1000 s/mm 2 . All sequences were repeated with and without repositioning. The peak location, peak height, and mean ADC of the ADC histograms and mean ADC of a region of interest (ROI) in the white matter were compared using paired-sample t tests. Scan-rescan reproducibility was assessed using paired-sample t tests, and repeatability coefficients were reported. With increasing maximum b-values, ADC histograms shifted to lower values, with an increase in peak height (p<0.01). With FLAIR DWI, the ADC histogram shifted to lower values with a significantly higher, narrower peak (p<0.01), although the ROI mean ADC showed no significant differences. For scan-rescan reproducibility, no significant differences were observed. Different DWI pulse sequences give rise to different ADC histograms. With a given pulse sequence, however, ADC histogram analysis is a robust and reproducible technique. Using FLAIR DWI, the partial-voluming effect of cerebrospinal fluid, and thus its confounding effect on histogram analyses, can be reduced

  15. DNA-abzymes in autoimmune diseases in clinic and experiment

    Directory of Open Access Journals (Sweden)

    T E Naumova

    2003-01-01

    Full Text Available DNA-abzymes enzymes in autoimmune diseases in clinic and experiment T.E. Naumova, O.M. Durova, A.G. Gabibov, Z.S. Alekberova, S. V. Suchkov DNA-hydrolyzing autoantibodies (AAB or DNA-abzymes can be found in autoimmune diseases in clinic and experiment. Technology of serum express screening for presence of DNA abzymes is described. Comparative study of DNA-hydrolising activity in patients with different forms of systemic and organ-specific autoimmune diseases was performed. Blood of clinically healthy donors was usually free of IgG DNA-abzymes. DNA-abzymes were most often revealed in patients with systemic lupus erythematosus (SLE and rheumatoid arthritis (RA less often in patients with organ-specific forms of autoimmune disturbances. The results of the study confirm the hypothesis of autoimmune origin of IgG DNA abzymes and demonstrate the possibility to use them in clinical practice for monitoring to disease activity in SLE and RA.

  16. Preclinical and clinical safety studies on DNA vaccines.

    NARCIS (Netherlands)

    Schalk, Johanna A C; Mooi, Frits R; Berbers, Guy A M; Aerts, Leon A G J M van; Ovelgönne, Hans; Kimman, Tjeerd G

    2007-01-01

    DNA vaccines are based on the transfer of genetic material, encoding an antigen, to the cells of the vaccine recipient. Despite high expectations of DNA vaccines as a result of promising preclinical data their clinical utility remains unproven. However, much data is gathered in preclinical and

  17. Complexity of possibly gapped histogram and analysis of histogram

    Science.gov (United States)

    Fushing, Hsieh; Roy, Tania

    2018-02-01

    We demonstrate that gaps and distributional patterns embedded within real-valued measurements are inseparable biological and mechanistic information contents of the system. Such patterns are discovered through data-driven possibly gapped histogram, which further leads to the geometry-based analysis of histogram (ANOHT). Constructing a possibly gapped histogram is a complex problem of statistical mechanics due to the ensemble of candidate histograms being captured by a two-layer Ising model. This construction is also a distinctive problem of Information Theory from the perspective of data compression via uniformity. By defining a Hamiltonian (or energy) as a sum of total coding lengths of boundaries and total decoding errors within bins, this issue of computing the minimum energy macroscopic states is surprisingly resolved by applying the hierarchical clustering algorithm. Thus, a possibly gapped histogram corresponds to a macro-state. And then the first phase of ANOHT is developed for simultaneous comparison of multiple treatments, while the second phase of ANOHT is developed based on classical empirical process theory for a tree-geometry that can check the authenticity of branches of the treatment tree. The well-known Iris data are used to illustrate our technical developments. Also, a large baseball pitching dataset and a heavily right-censored divorce data are analysed to showcase the existential gaps and utilities of ANOHT.

  18. Complexity of possibly gapped histogram and analysis of histogram.

    Science.gov (United States)

    Fushing, Hsieh; Roy, Tania

    2018-02-01

    We demonstrate that gaps and distributional patterns embedded within real-valued measurements are inseparable biological and mechanistic information contents of the system. Such patterns are discovered through data-driven possibly gapped histogram, which further leads to the geometry-based analysis of histogram (ANOHT). Constructing a possibly gapped histogram is a complex problem of statistical mechanics due to the ensemble of candidate histograms being captured by a two-layer Ising model. This construction is also a distinctive problem of Information Theory from the perspective of data compression via uniformity. By defining a Hamiltonian (or energy) as a sum of total coding lengths of boundaries and total decoding errors within bins, this issue of computing the minimum energy macroscopic states is surprisingly resolved by applying the hierarchical clustering algorithm. Thus, a possibly gapped histogram corresponds to a macro-state. And then the first phase of ANOHT is developed for simultaneous comparison of multiple treatments, while the second phase of ANOHT is developed based on classical empirical process theory for a tree-geometry that can check the authenticity of branches of the treatment tree. The well-known Iris data are used to illustrate our technical developments. Also, a large baseball pitching dataset and a heavily right-censored divorce data are analysed to showcase the existential gaps and utilities of ANOHT.

  19. MRI histogram analysis enables objective and continuous classification of intervertebral disc degeneration.

    Science.gov (United States)

    Waldenberg, Christian; Hebelka, Hanna; Brisby, Helena; Lagerstrand, Kerstin Magdalena

    2018-05-01

    Magnetic resonance imaging (MRI) is the best diagnostic imaging method for low back pain. However, the technique is currently not utilized in its full capacity, often failing to depict painful intervertebral discs (IVDs), potentially due to the rough degeneration classification system used clinically today. MR image histograms, which reflect the IVD heterogeneity, may offer sensitive imaging biomarkers for IVD degeneration classification. This study investigates the feasibility of using histogram analysis as means of objective and continuous grading of IVD degeneration. Forty-nine IVDs in ten low back pain patients (six males, 25-69 years) were examined with MRI (T2-weighted images and T2-maps). Each IVD was semi-automatically segmented on three mid-sagittal slices. Histogram features of the IVD were extracted from the defined regions of interest and correlated to Pfirrmann grade. Both T2-weighted images and T2-maps displayed similar histogram features. Histograms of well-hydrated IVDs displayed two separate peaks, representing annulus fibrosus and nucleus pulposus. Degenerated IVDs displayed decreased peak separation, where the separation was shown to correlate strongly with Pfirrmann grade (P histogram appearances. Histogram features correlated well with IVD degeneration, suggesting that IVD histogram analysis is a suitable tool for objective and continuous IVD degeneration classification. As histogram analysis revealed IVD heterogeneity, it may be a clinical tool for characterization of regional IVD degeneration effects. To elucidate the usefulness of histogram analysis in patient management, IVD histogram features between asymptomatic and symptomatic individuals needs to be compared.

  20. CHIL - a comprehensive histogramming language

    International Nuclear Information System (INIS)

    Milner, W.T.; Biggerstaff, J.A.

    1984-01-01

    A high level language, CHIL, has been developed for use in processing event-by-event experimental data at the Holifield Heavy Ion Research Facility (HHIRF) using PERKIN-ELMER 3230 computers. CHIL has been fully integrated into all software which supports on-line and off-line histogramming and off-line preprocessing. CHIL supports simple gates, free-form-gates (2-D regions of arbitrary shape), condition test and branch statements, bit-tests, loops, calls to up to three user supplied subroutines and histogram generating statements. Any combination of 1, 2, 3 or 4-D histograms (32 megachannels max) may be recorded at 16 or 32 bits/channel. User routines may intercept the data being processed and modify it as desired. The CPU-intensive part of the processing utilizes microcoded routines which enhance performance by about a factor of two

  1. CHILA A comprehensive histogramming language

    International Nuclear Information System (INIS)

    Milner, W.T.; Biggerstaff, J.A.

    1985-01-01

    A high level language, CHIL, has been developed for use in processing event-by-event experimental data at the Holifield Heavy Ion Research Facility (HHIRF) using PERKIN-ELMER 3230 computers. CHIL has been fully integrated into all software which supports on-line and off-line histogramming and off-line preprocessing. CHIL supports simple gates, free-form-gates (2-D regions of arbitrary shape), condition test and branch statements, bit-tests, loops, calls to up to three user supplied subroutines and histogram generating statements. Any combination of 1, 2, 3 or 4-D histograms (32 megachannels max) may be recorded at 16 or 32 bits/channel. User routines may intercept the data being processed and modify it as desired. The CPU-intensive part of the processing utilizes microcoded routines which enhance performance by about a factor of two

  2. Multispectral histogram normalization contrast enhancement

    Science.gov (United States)

    Soha, J. M.; Schwartz, A. A.

    1979-01-01

    A multispectral histogram normalization or decorrelation enhancement which achieves effective color composites by removing interband correlation is described. The enhancement procedure employs either linear or nonlinear transformations to equalize principal component variances. An additional rotation to any set of orthogonal coordinates is thus possible, while full histogram utilization is maintained by avoiding the reintroduction of correlation. For the three-dimensional case, the enhancement procedure may be implemented with a lookup table. An application of the enhancement to Landsat multispectral scanning imagery is presented.

  3. Live histograms in moving windows

    International Nuclear Information System (INIS)

    Zhil'tsov, V.E.

    1989-01-01

    Application of computer graphics for specific hardware testing is discussed. The hardware is position sensitive detector (multiwire proportional chamber) which is used in high energy physics experiments, and real-out electronics for it. Testing program is described (XPERT), which utilises multi-window user interface. Data are represented as histograms in windows. The windows on the screen may be moved, reordered, their sizes may be changed. Histograms may be put to any window, and hardcopy may be made. Some program internals are discussed. The computer environment is quite simple: MS-DOS IBM PC/XT, 256 KB RAM, CGA, 5.25'' FD, Epson MX. 4 refs.; 7 figs

  4. HBV DNA Integration: Molecular Mechanisms and Clinical Implications

    Science.gov (United States)

    Tu, Thomas; Budzinska, Magdalena A.; Shackel, Nicholas A.; Urban, Stephan

    2017-01-01

    Chronic infection with the Hepatitis B Virus (HBV) is a major cause of liver-related morbidity and mortality. One peculiar observation in cells infected with HBV (or with closely‑related animal hepadnaviruses) is the presence of viral DNA integration in the host cell genome, despite this form being a replicative dead-end for the virus. The frequent finding of somatic integration of viral DNA suggests an evolutionary benefit for the virus; however, the mechanism of integration, its functions, and the clinical implications remain unknown. Here we review the current body of knowledge of HBV DNA integration, with particular focus on the molecular mechanisms and its clinical implications (including the possible consequences of replication-independent antigen expression and its possible role in hepatocellular carcinoma). HBV DNA integration is likely to influence HBV replication, persistence, and pathogenesis, and so deserves greater attention in future studies. PMID:28394272

  5. Histogram deconvolution - An aid to automated classifiers

    Science.gov (United States)

    Lorre, J. J.

    1983-01-01

    It is shown that N-dimensional histograms are convolved by the addition of noise in the picture domain. Three methods are described which provide the ability to deconvolve such noise-affected histograms. The purpose of the deconvolution is to provide automated classifiers with a higher quality N-dimensional histogram from which to obtain classification statistics.

  6. LHCb: Machine assisted histogram classification

    CERN Multimedia

    Somogyi, P; Gaspar, C

    2009-01-01

    LHCb is one of the four major experiments under completion at the Large Hadron Collider (LHC). Monitoring the quality of the acquired data is important, because it allows the verification of the detector performance. Anomalies, such as missing values or unexpected distributions can be indicators of a malfunctioning detector, resulting in poor data quality. Spotting faulty components can be either done visually using instruments such as the LHCb Histogram Presenter, or by automated tools. In order to assist detector experts in handling the vast monitoring information resulting from the sheer size of the detector, a graph-theoretic based clustering tool, combined with machine learning algorithms is proposed and demonstrated by processing histograms representing 2D event hitmaps. The concept is proven by detecting ion feedback events in the LHCb RICH subdetector.

  7. Visualizing Contour Trees within Histograms

    DEFF Research Database (Denmark)

    Kraus, Martin

    2010-01-01

    Many of the topological features of the isosurfaces of a scalar volume field can be compactly represented by its contour tree. Unfortunately, the contour trees of most real-world volume data sets are too complex to be visualized by dot-and-line diagrams. Therefore, we propose a new visualization...... that is suitable for large contour trees and efficiently conveys the topological structure of the most important isosurface components. This visualization is integrated into a histogram of the volume data; thus, it offers strictly more information than a traditional histogram. We present algorithms...... to automatically compute the graph layout and to calculate appropriate approximations of the contour tree and the surface area of the relevant isosurface components. The benefits of this new visualization are demonstrated with the help of several publicly available volume data sets....

  8. Discrimination of paediatric brain tumours using apparent diffusion coefficient histograms

    International Nuclear Information System (INIS)

    Bull, Jonathan G.; Clark, Christopher A.; Saunders, Dawn E.

    2012-01-01

    To determine if histograms of apparent diffusion coefficients (ADC) can be used to differentiate paediatric brain tumours. Imaging of histologically confirmed tumours with pre-operative ADC maps were reviewed (54 cases, 32 male, mean age 6.1 years; range 0.1-15.8 years) comprising 6 groups. Whole tumour ADC histograms were calculated; normalised for volume. Stepwise logistic regression analysis was used to differentiate tumour types using histogram metrics, initially for all groups and then for specific subsets. All 6 groups (5 dysembryoplastic neuroectodermal tumours, 22 primitive neuroectodermal tumours (PNET), 5 ependymomas, 7 choroid plexus papillomas, 4 atypical teratoid rhabdoid tumours (ATRT) and 9 juvenile pilocytic astrocytomas (JPA)) were compared. 74% (40/54) were correctly classified using logistic regression of ADC histogram parameters. In the analysis of posterior fossa tumours, 80% of ependymomas, 100% of astrocytomas and 94% of PNET-medulloblastoma were classified correctly. All PNETs were discriminated from ATRTs (22 PNET and 4 supratentorial ATRTs) (100%). ADC histograms are useful in differentiating paediatric brain tumours, in particular, the common posterior fossa tumours of childhood. PNETs were differentiated from supratentorial ATRTs, in all cases, which has important implications in terms of clinical management. (orig.)

  9. Decomposition analysis of differential dose volume histograms

    International Nuclear Information System (INIS)

    Heuvel, Frank van den

    2006-01-01

    Dose volume histograms are a common tool to assess the value of a treatment plan for various forms of radiation therapy treatment. The purpose of this work is to introduce, validate, and apply a set of tools to analyze differential dose volume histograms by decomposing them into physically and clinically meaningful normal distributions. A weighted sum of the decomposed normal distributions (e.g., weighted dose) is proposed as a new measure of target dose, rather than the more unstable point dose. The method and its theory are presented and validated using simulated distributions. Additional validation is performed by analyzing simple four field box techniques encompassing a predefined target, using different treatment energies inside a water phantom. Furthermore, two clinical situations are analyzed using this methodology to illustrate practical usefulness. A comparison of a treatment plan for a breast patient using a tangential field setup with wedges is compared to a comparable geometry using dose compensators. Finally, a normal tissue complication probability (NTCP) calculation is refined using this decomposition. The NTCP calculation is performed on a liver as organ at risk in a treatment of a mesothelioma patient with involvement of the right lung. The comparison of the wedged breast treatment versus the compensator technique yields comparable classical dose parameters (e.g., conformity index ≅1 and equal dose at the ICRU dose point). The methodology proposed here shows a 4% difference in weighted dose outlining the difference in treatment using a single parameter instead of at least two in a classical analysis (e.g., mean dose, and maximal dose, or total dose variance). NTCP-calculations for the mesothelioma case are generated automatically and show a 3% decrease with respect to the classical calculation. The decrease is slightly dependant on the fractionation and on the α/β-value utilized. In conclusion, this method is able to distinguish clinically

  10. System for histogram entry, retrieval, and plotting

    International Nuclear Information System (INIS)

    Kellogg, M.; Gallup, J.M.; Shlaer, S.; Spencer, N.

    1977-10-01

    This manual describes the systems for producing histograms and dot plots that were designed for use in connection with the Q general-purpose data-acquisition system. These systems allow for the creation of histograms; the entry, retrieval, and plotting of data in the form of histograms; and the dynamic display of scatter plots as data are acquired. Although the systems are designed for use with Q, they can also be used as a part of other applications. 3 figures

  11. Clinical trial participant characteristics and saliva and DNA metrics

    Directory of Open Access Journals (Sweden)

    Richards Julie

    2009-10-01

    Full Text Available Abstract Background Clinical trial and epidemiological studies need high quality biospecimens from a representative sample of participants to investigate genetic influences on treatment response and disease. Obtaining blood biospecimens presents logistical and financial challenges. As a result, saliva biospecimen collection is becoming more frequent because of the ease of collection and lower cost. This article describes an assessment of saliva biospecimen samples collected through the mail, trial participant demographic and behavioral characteristics, and their association with saliva and DNA quantity and quality. Methods Saliva biospecimens were collected using the Oragene® DNA Self-Collection Kits from participants in a National Cancer Institute funded smoking cessation trial. Saliva biospecimens from 565 individuals were visually inspected for clarity prior to and after DNA extraction. DNA samples were then quantified by UV absorbance, PicoGreen®, and qPCR. Genotyping was performed on 11 SNPs using TaqMan® SNP assays and two VNTR assays. Univariate, correlation, and analysis of variance analyses were conducted to observe the relationship between saliva sample and participant characteristics. Results The biospecimen kit return rate was 58.5% among those invited to participate (n = 967 and 47.1% among all possible COMPASS participants (n = 1202. Significant gender differences were observed with males providing larger saliva volume (4.7 vs. 4.5 ml, p = 0.019, samples that were more likely to be judged as cloudy (39.5% vs. 24.9%, p 0.21, P Conclusion Findings from this study show that demographic and behavioral characteristics of smoking cessation trial participants have significant associations with saliva and DNA metrics, but not with the performance of TaqMan® SNP or VNTR genotyping assays. Trial registration COMPASS; registered as NCT00301145 at clinicaltrials.gov.

  12. Algorithms for adaptive histogram equalization

    International Nuclear Information System (INIS)

    Pizer, S.M.; Austin, J.D.; Cromartie, R.; Geselowitz, A.; Ter Haar Romeny, B.; Zimmerman, J.B.; Zuiderveld, K.

    1986-01-01

    Adaptive histogram equalization (ahe) is a contrast enhancement method designed to be broadly applicable and having demonstrated effectiveness [Zimmerman, 1985]. However, slow speed and the overenhancement of noise it produces in relatively homogeneous regions are two problems. The authors summarize algorithms designed to overcome these and other concerns. These algorithms include interpolated ahe, to speed up the method on general purpose computers; a version of interpolated ahe designed to run in a few seconds on feedback processors; a version of full ahe designed to run in under one second on custom VLSI hardware; and clipped ahe, designed to overcome the problem of overenhancement of noise contrast. The authors conclude that clipped ahe should become a method of choice in medical imaging and probably also in other areas of digital imaging, and that clipped ahe can be made adequately fast to be routinely applied in the normal display sequence

  13. Systemic oxidatively generated DNA/RNA damage in clinical depression

    DEFF Research Database (Denmark)

    Jorgensen, Anders; Krogh, Jesper; Miskowiak, Kamilla

    2013-01-01

    oxidatively generated DNA and RNA damage, 8-oxo-7,8-dihydro-2-deoxyguanosine (8-oxodG) and 8-oxo-7,8-dihydroguanosine (8-oxoGuo), respectively, were determined in healthy controls (N=28), moderately depressed, non-medicated patients (N=26) and severely depressed patients eligible for electroconvulsive therapy...... for trend=0.004). The 8-oxoGuo excretion was further increased after clinically effective ECT compared with pre-ECT values (P=0.006). There were no differences in 8-oxodG excretion between the groups or pre- vs. post-ECT. LIMITATIONS: Small sample size and the inclusion of both unipolar and bipolar patients...

  14. WORKER, a program for histogram manipulation

    International Nuclear Information System (INIS)

    Bolger, J.E.; Ellinger, H.; Moore, C.F.

    1979-01-01

    A set of programs is provided which may link to any user-written program, permitting dynamic creation of histograms as well as display, manipulation and transfer of histogrammed data. With wide flexibility, constants within the user's code may be set or monitored at any time during execution. (Auth.)

  15. Interpreting Histograms. As Easy as It Seems?

    Science.gov (United States)

    Lem, Stephanie; Onghena, Patrick; Verschaffel, Lieven; Van Dooren, Wim

    2014-01-01

    Histograms are widely used, but recent studies have shown that they are not as easy to interpret as it might seem. In this article, we report on three studies on the interpretation of histograms in which we investigated, namely, (1) whether the misinterpretation by university students can be considered to be the result of heuristic reasoning, (2)…

  16. Spline smoothing of histograms by linear programming

    Science.gov (United States)

    Bennett, J. O.

    1972-01-01

    An algorithm for an approximating function to the frequency distribution is obtained from a sample of size n. To obtain the approximating function a histogram is made from the data. Next, Euclidean space approximations to the graph of the histogram using central B-splines as basis elements are obtained by linear programming. The approximating function has area one and is nonnegative.

  17. Bi-Histogram Equalization with Brightnes Preservation Using Contras Enhancement

    OpenAIRE

    A. Anitha Rani; Gowthami Rajagopal; A. Jagadeswaran

    2014-01-01

    Contrast enhancement is an important factor in the image preprocesing step. One of the widely acepted contrast enhancement method is the histogram equalization. Although histogram equalization achieves comparatively beter performance on almost al types of image, global histogram equalization sometimes produces excesive visual deterioration. A new extension of bi- histogram equalization caled Bi-Histogram Equalization with Neighborhod Metric (BHENM). First, large histogram bins that cause w...

  18. Pilot study in the treatment of endometrial carcinoma with 3D image-based high-dose-rate brachytherapy using modified Heyman packing: Clinical experience and dose-volume histogram analysis

    International Nuclear Information System (INIS)

    Weitmann, Hajo Dirk; Poetter, Richard; Waldhaeusl, Claudia; Nechvile, Elisabeth; Kirisits, Christian; Knocke, Tomas Hendrik

    2005-01-01

    Purpose: The aim of this study was to evaluate dose distribution within uterus (clinical target volume [CTV]) and tumor (gross tumor volume [GTV]) and the resulting clinical outcome based on systematic three-dimensional treatment planning with dose-volume adaptation. Dose-volume assessment and adaptation in organs at risk and its impact on side effects were investigated in parallel. Methods and Materials: Sixteen patients with either locally confined endometrial carcinoma (n = 15) or adenocarcinoma of uterus and ovaries after bilateral salpingo-oophorectomy (n = 1) were included. Heyman packing was performed with mean 11 Norman-Simon applicators (3-18). Three-dimensional treatment planning based on computed tomography (n = 29) or magnetic resonance imaging (n = 18) was done in all patients with contouring of CTV, GTV, and organs at risk. Dose-volume adaptation was achieved by dwell location and time variation (intensity modulation). Twelve patients treated with curative intent received five to seven fractions of high-dose-rate brachytherapy (7 Gy per fraction) corresponding to a total dose of 60 Gy (2 Gy per fraction and α/β of 10 Gy) to the CTV. Four patients had additional external beam radiotherapy (range, 10-40 Gy). One patient had salvage brachytherapy and 3 patients were treated with palliative intent. A dose-volume histogram analysis was performed in all patients. On average, 68% of the CTV and 92% of the GTV were encompassed by the 60 Gy reference volume. Median minimum dose to 90% of CTV and GTV (D90) was 35.3 Gy and 74 Gy, respectively. Results: All patients treated with curative intent had complete remission (12/12). After a median follow-up of 47 months, 5 patients are alive without tumor. Seven patients died without tumor from intercurrent disease after median 22 months. The patient with salvage treatment had a second local recurrence after 27 months and died of endometrial carcinoma after 57 months. In patients treated with palliative intent

  19. Regionally adaptive histogram equalization of the chest

    International Nuclear Information System (INIS)

    Sherrier, R.H.; Johnson, G.A.

    1986-01-01

    Advances in digital chest radiography have resulted in the acquisition of high-quality digital images of the human chest. With these advances, there arises a genuine need for image processing algorithms, specific to chest images. The author has implemented the technique of histogram equalization, noting the problems encountered when it is adapted to chest images. These problems have been successfully solved with a regionally adaptive histogram equalization method. Histograms are calculated locally and then modified according to both the mean pixel value of a given region and certain characteristics of the cumulative distribution function. The method allows certain regions of the chest radiograph to be enhanced differentially

  20. Color Histogram Diffusion for Image Enhancement

    Science.gov (United States)

    Kim, Taemin

    2011-01-01

    Various color histogram equalization (CHE) methods have been proposed to extend grayscale histogram equalization (GHE) for color images. In this paper a new method called histogram diffusion that extends the GHE method to arbitrary dimensions is proposed. Ranges in a histogram are specified as overlapping bars of uniform heights and variable widths which are proportional to their frequencies. This diagram is called the vistogram. As an alternative approach to GHE, the squared error of the vistogram from the uniform distribution is minimized. Each bar in the vistogram is approximated by a Gaussian function. Gaussian particles in the vistoram diffuse as a nonlinear autonomous system of ordinary differential equations. CHE results of color images showed that the approach is effective.

  1. Adaptive histogram equalization and its variations

    NARCIS (Netherlands)

    Pizer, S.M.; Amburn, E.P.; Austin, J.D.; Cromartie, R.; Geselowitz, A.; Greer, Trey; Haar Romenij, ter B.M.; Zimmerman, J.B.; Zuiderveld, K.J.

    1987-01-01

    Adaptive histogram equalization (ahe) is a contrast enhancement method designed to be broadly applicable and having demonstrated effectiveness. However, slow speed and the overenhancement of noise it produces in relatively homogeneous regions are two problems. We report algorithms designed to

  2. Subtracting and Fitting Histograms using Profile Likelihood

    CERN Document Server

    D'Almeida, F M L

    2008-01-01

    It is known that many interesting signals expected at LHC are of unknown shape and strongly contaminated by background events. These signals will be dif cult to detect during the rst years of LHC operation due to the initial low luminosity. In this work, one presents a method of subtracting histograms based on the pro le likelihood function when the background is previously estimated by Monte Carlo events and one has low statistics. Estimators for the signal in each bin of the histogram difference are calculated so as limits for the signals with 68.3% of Con dence Level in a low statistics case when one has a exponential background and a Gaussian signal. The method can also be used to t histograms when the signal shape is known. Our results show a good performance and avoid the problem of negative values when subtracting histograms.

  3. The Online Histogram Presenter for the ATLAS experiment: A modular system for histogram visualization

    International Nuclear Information System (INIS)

    Dotti, Andrea; Adragna, Paolo; Vitillo, Roberto A

    2010-01-01

    The Online Histogram Presenter (OHP) is the ATLAS tool to display histograms produced by the online monitoring system. In spite of the name, the Online Histogram Presenter is much more than just a histogram display. To cope with the large amount of data, the application has been designed to minimise the network traffic; sophisticated caching, hashing and filtering algorithms reduce memory and CPU usage. The system uses Qt and ROOT for histogram visualisation and manipulation. In addition, histogram visualisation can be extensively customised through configuration files. Finally, its very modular architecture features a lightweight plug-in system, allowing extensions to accommodate specific user needs. After an architectural overview of the application, the paper is going to present in detail the solutions adopted to increase the performance and a description of the plug-in system.

  4. The Online Histogram Presenter for the ATLAS experiment: A modular system for histogram visualization

    Energy Technology Data Exchange (ETDEWEB)

    Dotti, Andrea [CERN, CH-1211 Genve 23 Switzerland (Switzerland); Adragna, Paolo [Physics Department, Queen Mary, University of London Mile End Road London E1 4RP UK (United Kingdom); Vitillo, Roberto A, E-mail: andrea.dotti@cern.c [INFN Sezione di Pisa, Ed. C Largo Bruno Pontecorvo 3, 56127 Pisa (Italy)

    2010-04-01

    The Online Histogram Presenter (OHP) is the ATLAS tool to display histograms produced by the online monitoring system. In spite of the name, the Online Histogram Presenter is much more than just a histogram display. To cope with the large amount of data, the application has been designed to minimise the network traffic; sophisticated caching, hashing and filtering algorithms reduce memory and CPU usage. The system uses Qt and ROOT for histogram visualisation and manipulation. In addition, histogram visualisation can be extensively customised through configuration files. Finally, its very modular architecture features a lightweight plug-in system, allowing extensions to accommodate specific user needs. After an architectural overview of the application, the paper is going to present in detail the solutions adopted to increase the performance and a description of the plug-in system.

  5. Comments on 'Reconsidering the definition of a dose-volume histogram'-dose-mass histogram (DMH) versus dose-volume histogram (DVH) for predicting radiation-induced pneumonitis

    International Nuclear Information System (INIS)

    Mavroidis, Panayiotis; Plataniotis, Georgios A; Gorka, Magdalena Adamus; Lind, Bengt K

    2006-01-01

    In a recently published paper (Nioutsikou et al 2005 Phys. Med. Biol. 50 L17) the authors showed that the use of the dose-mass histogram (DMH) concept is a more accurate descriptor of the dose delivered to lung than the traditionally used dose-volume histogram (DVH) concept. Furthermore, they state that if a functional imaging modality could also be registered to the anatomical imaging modality providing a functional weighting across the organ (functional mass) then the more general and realistic concept of the dose-functioning mass histogram (D[F]MH) could be an even more appropriate descriptor. The comments of the present letter to the editor are in line with the basic arguments of that work since their general conclusions appear to be supported by the comparison of the DMH and DVH concepts using radiobiological measures. In this study, it is examined whether the dose-mass histogram (DMH) concept deviated significantly from the widely used dose-volume histogram (DVH) concept regarding the expected lung complications and if there are clinical indications supporting these results. The problem was investigated theoretically by applying two hypothetical dose distributions (Gaussian and semi-Gaussian shaped) on two lungs of uniform and varying densities. The influence of the deviation between DVHs and DMHs on the treatment outcome was estimated by using the relative seriality and LKB models using the Gagliardi et al (2000 Int. J. Radiat. Oncol. Biol. Phys. 46 373) and Seppenwoolde et al (2003 Int. J. Radiat. Oncol. Biol. Phys. 55 724) parameter sets for radiation pneumonitis, respectively. Furthermore, the biological equivalent of their difference was estimated by the biologically effective uniform dose (D-bar) and equivalent uniform dose (EUD) concepts, respectively. It is shown that the relation between the DVHs and DMHs varies depending on the underlying cell density distribution and the applied dose distribution. However, the range of their deviation in terms of

  6. The Research of Histogram Enhancement Technique Based on Matlab Software

    Directory of Open Access Journals (Sweden)

    Li Kai

    2014-08-01

    Full Text Available Histogram enhancement technique has been widely applied as a typical pattern in digital image processing. The paper is based on Matlab software, through the two ways of histogram equalization and histogram specification technologies to deal with the darker images, using two methods of partial equilibrium and mapping histogram to transform the original histograms, thereby enhanced the image information. The results show that these two kinds of techniques both can significantly improve the image quality and enhance the image feature.

  7. Sterile paper points as a bacterial DNA-contamination source in microbiome profiles of clinical samples

    NARCIS (Netherlands)

    van der Horst, J.; Buijs, M.J.; Laine, M.L.; Wismeijer, D.; Loos, B.G.; Crielaard, W.; Zaura, E.

    2013-01-01

    Objectives High throughput sequencing of bacterial DNA from clinical samples provides untargeted, open-ended information on the entire microbial community. The downside of this approach is the vulnerability to DNA contamination from other sources than the clinical sample. Here we describe

  8. Retrospective Reconstructions of Active Bone Marrow Dose-Volume Histograms

    International Nuclear Information System (INIS)

    Veres, Cristina; Allodji, Rodrigue S.; Llanas, Damien; Vu Bezin, Jérémi; Chavaudra, Jean; Mège, Jean Pierre; Lefkopoulos, Dimitri; Quiniou, Eric; Deutsh, Eric; Vathaire, Florent de; Diallo, Ibrahima

    2014-01-01

    Purpose: To present a method for calculating dose-volume histograms (DVH's) to the active bone marrow (ABM) of patients who had undergone radiation therapy (RT) and subsequently developed leukemia. Methods and Materials: The study focuses on 15 patients treated between 1961 and 1996. Whole-body RT planning computed tomographic (CT) data were not available. We therefore generated representative whole-body CTs similar to patient anatomy. In addition, we developed a method enabling us to obtain information on the density distribution of ABM all over the skeleton. Dose could then be calculated in a series of points distributed all over the skeleton in such a way that their local density reflected age-specific data for ABM distribution. Dose to particular regions and dose-volume histograms of the entire ABM were estimated for all patients. Results: Depending on patient age, the total number of dose calculation points generated ranged from 1,190,970 to 4,108,524. The average dose to ABM ranged from 0.3 to 16.4 Gy. Dose-volume histograms analysis showed that the median doses (D 50% ) ranged from 0.06 to 12.8 Gy. We also evaluated the inhomogeneity of individual patient ABM dose distribution according to clinical situation. It was evident that the coefficient of variation of the dose for the whole ABM ranged from 1.0 to 5.7, which means that the standard deviation could be more than 5 times higher than the mean. Conclusions: For patients with available long-term follow-up data, our method provides reconstruction of dose-volume data comparable to detailed dose calculations, which have become standard in modern CT-based 3-dimensional RT planning. Our strategy of using dose-volume histograms offers new perspectives to retrospective epidemiological studies

  9. Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring.

    Science.gov (United States)

    Chang, Yi; Tolani, Bhairavi; Nie, Xiuhong; Zhi, Xiuyi; Hu, Mu; He, Biao

    2017-01-01

    Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.

  10. ACTION RECOGNITION USING SALIENT NEIGHBORING HISTOGRAMS

    DEFF Research Database (Denmark)

    Ren, Huamin; Moeslund, Thomas B.

    2013-01-01

    Combining spatio-temporal interest points with Bag-of-Words models achieves state-of-the-art performance in action recognition. However, existing methods based on “bag-ofwords” models either are too local to capture the variance in space/time or fail to solve the ambiguity problem in spatial...... and temporal dimensions. Instead, we propose a salient vocabulary construction algorithm to select visual words from a global point of view, and form compact descriptors to represent discriminative histograms in the neighborhoods. Those salient neighboring histograms are then trained to model different actions...

  11. Oriented Shape Index Histograms for Cell Classification

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo; Dahl, Anders Bjorholm; Larsen, Rasmus

    2015-01-01

    We propose a novel extension to the shape index histogram feature descriptor where the orientation of the second-order curvature is included in the histograms. The orientation of the shape index is reminiscent but not equal to gradient orientation which is widely used for feature description. We...... evaluate our new feature descriptor using a public dataset consisting of HEp-2 cell images from indirect immunoflourescence lighting. Our results show that we can improve classification performance significantly when including the shape index orientation. Notably, we show that shape index orientation...

  12. A comparison of automatic histogram constructions

    NARCIS (Netherlands)

    Davies, P.L.; Gather, U.; Nordman, D.J.; Weinert, H.

    2009-01-01

    Even for a well-trained statistician the construction of a histogram for a given real-valued data set is a difficult problem. It is even more difficult to construct a fully automatic procedure which specifies the number and widths of the bins in a satisfactory manner for a wide range of data sets.

  13. Review: Clinical aspects of hereditary DNA Mismatch repair gene mutations

    NARCIS (Netherlands)

    Sijmons, Rolf H.; Hofstra, Robert M. W.

    Inherited mutations of the DNA Mismatch repair genes MLH1, MSH2, MSH6 and PMS2 can result in two hereditary tumor syndromes: the adult-onset autosomal dominant Lynch syndrome, previously referred to as Hereditary Non-Polyposis Colorectal Cancer (HNPCC) and the childhood-onset autosomal recessive

  14. Environmental pollution and DNA methylation: carcinogenesis, clinical significance, and practical applications.

    Science.gov (United States)

    Cao, Yi

    2015-09-01

    Environmental pollution is one of the main causes of human cancer. Exposures to environmental carcinogens result in genetic and epigenetic alterations which induce cell transformation. Epigenetic changes caused by environmental pollution play important roles in the development and progression of environmental pollution-related cancers. Studies on DNA methylation are among the earliest and most conducted epigenetic research linked to cancer. In this review, the roles of DNA methylation in carcinogenesis and their significance in clinical medicine were summarized, and the effects of environmental pollutants, particularly air pollutants, on DNA methylation were introduced. Furthermore, prospective applications of DNA methylation to environmental pollution detection and cancer prevention were discussed.

  15. Efficient contrast enhancement through log-power histogram modification

    NARCIS (Netherlands)

    Wu, T.; Toet, A.

    2014-01-01

    A simple power-logarithm histogram modification operator is proposed to enhance digital image contrast. First a logarithm operator reduces the effect of spikes and transforms the image histogram into a smoothed one that approximates a uniform histogram while retaining the relative size ordering of

  16. Detection of Adriamycin-DNA adducts by accelerator mass spectrometry at clinically relevant Adriamycin concentrations.

    Science.gov (United States)

    Coldwell, Kate E; Cutts, Suzanne M; Ognibene, Ted J; Henderson, Paul T; Phillips, Don R

    2008-09-01

    Limited sensitivity of existing assays has prevented investigation of whether Adriamycin-DNA adducts are involved in the anti-tumour potential of Adriamycin. Previous detection has achieved a sensitivity of a few Adriamycin-DNA adducts/10(4) bp DNA, but has required the use of supra-clinical drug concentrations. This work sought to measure Adriamycin-DNA adducts at sub-micromolar doses using accelerator mass spectrometry (AMS), a technique with origins in geochemistry for radiocarbon dating. We have used conditions previously validated (by less sensitive decay counting) to extract [(14)C]Adriamycin-DNA adducts from cells and adapted the methodology to AMS detection. Here we show the first direct evidence of Adriamycin-DNA adducts at clinically-relevant Adriamycin concentrations. [(14)C]Adriamycin treatment (25 nM) resulted in 4.4 +/- 1.0 adducts/10(7) bp ( approximately 1300 adducts/cell) in MCF-7 breast cancer cells, representing the best sensitivity and precision reported to date for the covalent binding of Adriamycin to DNA. The exceedingly sensitive nature of AMS has enabled over three orders of magnitude increased sensitivity of Adriamycin-DNA adduct detection and revealed adduct formation within an hour of drug treatment. This method has been shown to be highly reproducible for the measurement of Adriamycin-DNA adducts in tumour cells in culture and can now be applied to the detection of these adducts in human tissues.

  17. Gamma histograms for radiotherapy plan evaluation

    International Nuclear Information System (INIS)

    Spezi, Emiliano; Lewis, D. Geraint

    2006-01-01

    Background and purpose: The technique known as the 'γ evaluation method' incorporates pass-fail criteria for both distance-to-agreement and dose difference analysis of 3D dose distributions and provides a numerical index (γ) as a measure of the agreement between two datasets. As the γ evaluation index is being adopted in more centres as part of treatment plan verification procedures for 2D and 3D dose maps, the development of methods capable of encapsulating the information provided by this technique is recommended. Patients and methods: In this work the concept of γ index was extended to create gamma histograms (GH) in order to provide a measure of the agreement between two datasets in two or three dimensions. Gamma area histogram (GAH) and gamma volume histogram (GVH) graphs were produced using one or more 2D γ maps generated for each slice of the irradiated volume. GHs were calculated for IMRT plans, evaluating the 3D dose distribution from a commercial treatment planning system (TPS) compared to a Monte Carlo (MC) calculation used as reference dataset. Results: The extent of local anatomical inhomogenities in the plans under consideration was strongly correlated with the level of difference between reference and evaluated calculations. GHs provided an immediate visual representation of the proportion of the treated volume that fulfilled the γ criterion and offered a concise method for comparative numerical evaluation of dose distributions. Conclusions: We have introduced the concept of GHs and investigated its applications to the evaluation and verification of IMRT plans. The gamma histogram concept set out in this paper can provide a valuable technique for quantitative comparison of dose distributions and could be applied as a tool for the quality assurance of treatment planning systems

  18. Robust histogram-based image retrieval

    Czech Academy of Sciences Publication Activity Database

    Höschl, Cyril; Flusser, Jan

    2016-01-01

    Roč. 69, č. 1 (2016), s. 72-81 ISSN 0167-8655 R&D Projects: GA ČR GA15-16928S Institutional support: RVO:67985556 Keywords : Image retrieval * Noisy image * Histogram * Convolution * Moments * Invariants Subject RIV: JD - Computer Applications, Robotics Impact factor: 1.995, year: 2016 http://library.utia.cas.cz/separaty/2015/ZOI/hoschl-0452147.pdf

  19. Clinical Radiation Sensitivity With DNA Repair Disorders: An Overview

    International Nuclear Information System (INIS)

    Pollard, Julianne M.; Gatti, Richard A.

    2009-01-01

    Adverse reactions to radiotherapy represent a confounding phenomenon in radiation oncology. These reactions are rare, and many have been associated with individuals with DNA repair disorders such as ataxia-telangiectasia and Nijmegen Breakage syndrome. A paucity of published data is available detailing such circumstances. This overview describes four exemplary situations, a comprehensive list of 32 additional cases, and some insights gleaned from this overall experience. Fanconi anemia was associated with more than one-half of the reports. The lowest dose given to a patient that resulted in a reaction was 3 Gy, given to an ataxia-telangiectasia patient. Most patients died within months of exposure. It is clear that the patients discussed in this report had complicated illnesses, in addition to cancer, and the radiotherapy administered was most likely their best option. However, the underlying DNA repair defects make conventional radiation doses dangerous. Our findings support previous wisdom that radiotherapy should either be avoided or the doses should be selected with great care in the case of these radiosensitive genotypes, which must be recognized by their characteristic phenotypes, until more rapid, reliable, and functional assays of DNA repair become available.

  20. Unstable Periodic Orbit Analysis of Histograms of Chaotic Time Series

    International Nuclear Information System (INIS)

    Zoldi, S.M.

    1998-01-01

    Using the Lorenz equations, we have investigated whether unstable periodic orbits (UPOs) associated with a strange attractor may predict the occurrence of the robust sharp peaks in histograms of some experimental chaotic time series. Histograms with sharp peaks occur for the Lorenz parameter value r=60.0 but not for r=28.0 , and the sharp peaks for r=60.0 do not correspond to a histogram derived from any single UPO. However, we show that histograms derived from the time series of a non-Axiom-A chaotic system can be accurately predicted by an escape-time weighting of UPO histograms. copyright 1998 The American Physical Society

  1. Interpretation of erythrocyte histograms obtained from automated hematology analyzers in hematologic diseases

    Directory of Open Access Journals (Sweden)

    Ali Maleki

    2015-12-01

    Full Text Available Background: Presently, the graphical data of blood cells (histograms and cytograms or/ scattergrams that they are usually available in all modern automated hematology analyzers are an integral a part of automated complete blood count (CBC. To find incorrect results from automated hematology analyzer and establish the samples that require additional analysis, Laboratory employees will use those data for quality control of obtaining results, to assist identification of complex and troublesome cases. Methods: During this descriptive analytic study, in addition to erythrocyte graphs from variety of patients, referring from March 2013 to Feb 2014 to our clinical laboratory, Zagros Hospital, Kermanshah, Iran, are given, the papers published in relevant literature as well as available published manuals of automatic blood cell counters were used. articles related to the key words of erythrocyte graphs and relevant literature as well as available published manuals of automatic blood cell counters were searched from valid databases such as Springer Link, google scholar, Pubmed and Sciencedirect. Then, the articles related to erythrogram, erythrocyte histogram and hematology analyzer graphs are involved in diagnosis of hematological disorder were searched and selected for this study. Results: Histograms and different automated CBC parameter become abnormal in various pathologic conditions, and can present important clues for diagnosis and treatment of hematologic and non-hematologic disorders. In several instances, these histograms have characteristic appearances in an exceedingly wide range of pathological conditions. In some hematologic disorders like iron deficiency or megaloblastic anemia, a sequential histogram can clearly show the progressive treatment and management. Conclusion: These graphical data are often accompanied by other automated CBC parameter and microscopic examination of peripheral blood smears (PBS, and can help in monitoring and

  2. Opto-electronic DNA chip-based integrated card for clinical diagnostics.

    Science.gov (United States)

    Marchand, Gilles; Broyer, Patrick; Lanet, Véronique; Delattre, Cyril; Foucault, Frédéric; Menou, Lionel; Calvas, Bernard; Roller, Denis; Ginot, Frédéric; Campagnolo, Raymond; Mallard, Frédéric

    2008-02-01

    Clinical diagnostics is one of the most promising applications for microfluidic lab-on-a-chip or lab-on-card systems. DNA chips, which provide multiparametric data, are privileged tools for genomic analysis. However, automation of molecular biology protocol and use of these DNA chips in fully integrated systems remains a great challenge. Simplicity of chip and/or card/instrument interfaces is amongst the most critical issues to be addressed. Indeed, current detection systems for DNA chip reading are often complex, expensive, bulky and even limited in terms of sensitivity or accuracy. Furthermore, for liquid handling in the lab-on-cards, many devices use complex and bulky systems, either to directly manipulate fluids, or to ensure pneumatic or mechanical control of integrated valves. All these drawbacks prevent or limit the use of DNA-chip-based integrated systems, for point-of-care testing or as a routine diagnostics tool. We present here a DNA-chip-based protocol integration on a plastic card for clinical diagnostics applications including: (1) an opto-electronic DNA-chip, (2) fluid handling using electrically activated embedded pyrotechnic microvalves with closing/opening functions. We demonstrate both fluidic and electric packaging of the optoelectronic DNA chip without major alteration of its electronical and biological functionalities, and fluid control using novel electrically activable pyrotechnic microvalves. Finally, we suggest a complete design of a card dedicated to automation of a complex biological protocol with a fully electrical fluid handling and DNA chip reading.

  3. Chi-square tests for comparing weighted histograms

    International Nuclear Information System (INIS)

    Gagunashvili, N.D.

    2010-01-01

    Weighted histograms in Monte Carlo simulations are often used for the estimation of probability density functions. They are obtained as a result of random experiments with random events that have weights. In this paper, the bin contents of a weighted histogram are considered as a sum of random variables with a random number of terms. Generalizations of the classical chi-square test for comparing weighted histograms are proposed. Numerical examples illustrate an application of the tests for the histograms with different statistics of events and different weighted functions. The proposed tests can be used for the comparison of experimental data histograms with simulated data histograms as well as for the two simulated data histograms.

  4. Clinical utility of circulating cell-free DNA in advanced colorectal cancer.

    Directory of Open Access Journals (Sweden)

    Allan A Lima Pereira

    Full Text Available Circulating cell-free DNA (cfDNA isolated from the plasma of cancer patients (pts has been shown to reflect the genomic mutation profile of the tumor. However, physician and patient assessment of clinical utility of these assays in patients with metastatic colorectal cancer (mCRC has not been previously described.Patients were prospectively consented to a prospective genomic matching protocol (Assessment of Targeted Therapies Against Colorectal Cancer [ATTACC], with collection of blood for cfDNA extraction and sequencing of a 54-gene panel in a CLIA-certified lab. Formalin-fixed, paraffin-embedded (FFPE tissue from prior resections or biopsies underwent 50-gene sequencing. Results from both assays were returned to the treating physicians for patient care and clinical trial selection. Follow-up surveys of treating physicians and chart reviews assessed clinical utility.128 mCRC pts were enrolled between 6/2014 and 1/2015. Results were returned in median of 13 and 26 days for cfDNA and FFPE sequencing, respectively. With cfDNA sequencing, 78% (100/128 of samples had a detectable somatic genomic alteration. 50% of cfDNA cases had potentially actionable alterations, and 60% of these could be genomically matched to at least one clinical trial in our institution. 50% (15/30 of these pts enrolled onto an identified matched trial. Physicians reported that the cfDNA testing improved the quality of care they could provide in 73% of the cases, and that 89% of pts reported greater satisfaction with the efforts to personalize experimental therapeutic agents.cfDNA sequencing can provide timely information on potentially actionable mutations and amplifications, thereby facilitating clinical trial enrollment and improving the perceived quality of care.

  5. Detection of Cytomegalovirus DNA in Serum Correlates with Clinical Cytomegalovirus Retinitis in AIDS

    DEFF Research Database (Denmark)

    Hansen, K.K.; Ricksten, A.; Hofmann, B.

    1994-01-01

    The high sensitivity of nested polymerase chain reaction (PCR) offers the possibility of rapid detection of cytomegalovirus (CMV) DNA in serum. Five consecutive serum samples were examined from 52 human immunodeficiency virus (HIV)-seropositive patients (19 of whom had clinically presumed diagnosis...... became positive with the onset of clinical retinitis. In contrast, 29 of 33 HIV-seropositive subjects without clinical CMV chorioretinitis and matched with respect to age and CD4 T cell numbers were negative for CMV DNA in all 5 serum samples. Thus, the presence of CMV DNA in serum analyzed by PCR...... is a good predictive marker of CMV retinitis in HIV-seropositive subjects. A positive PCR results supports the clinical diagnosis and may be useful for monitoring response to antiviral treatment....

  6. Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

    OpenAIRE

    Hasan, Mohammad R.; Rawat, Arun; Tang, Patrick; Jithesh, Puthen V.; Thomas, Eva; Tan, Rusung; Tilley, Peter

    2016-01-01

    Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspi...

  7. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies

    DEFF Research Database (Denmark)

    von Stechow, Louise; Olsen, Jesper V

    2017-01-01

    Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways......) in the DDR. Finally, we provide an outlook on how proteomics studies of the DDR could aid clinical developments on multiple levels. This article is protected by copyright. All rights reserved....

  8. optBINS: Optimal Binning for histograms

    Science.gov (United States)

    Knuth, Kevin H.

    2018-03-01

    optBINS (optimal binning) determines the optimal number of bins in a uniform bin-width histogram by deriving the posterior probability for the number of bins in a piecewise-constant density model after assigning a multinomial likelihood and a non-informative prior. The maximum of the posterior probability occurs at a point where the prior probability and the the joint likelihood are balanced. The interplay between these opposing factors effectively implements Occam's razor by selecting the most simple model that best describes the data.

  9. Boundary condition histograms for modulated phases

    International Nuclear Information System (INIS)

    Benakli, M.; Gabay, M.; Saslow, W.M.

    1997-11-01

    Boundary conditions strongly affect the results of numerical computations for finite size inhomogeneous or incommensurate structures. We present a method which allows to deal with this problem, both for ground state and for critical properties: it combines fluctuating boundary conditions and specific histogram techniques. Our approach concerns classical as well as quantum systems. In particular, current-current correlation functions, which probe large scale coherence of the states, can be accurately evaluated. We illustrate our method on a frustrated two dimensional XY model. (author)

  10. Clinical differences in patients with mitochondriocytopathies due to nuclear versus mitochondrial DNA mutations.

    Science.gov (United States)

    Rubio-Gozalbo, M E; Dijkman, K P; van den Heuvel, L P; Sengers, R C; Wendel, U; Smeitink, J A

    2000-01-01

    Defects in oxidative phosphorylation (OXPHOS) are genetically unique because the different components involved in this process, respiratory chain enzyme complexes (I, III, and IV) and complex V, are encoded by nuclear and mitochondrial genome. The objective of the study was to assess whether there are clinical differences in patients suffering from OXPHOS defects caused by nuclear or mitochondrial DNA (mtDNA) mutations. We studied 16 families with > or = two siblings with a genetically established OXPHOS deficiency, four due to a nuclear gene mutation and 12 due to a mtDNA mutation. Siblings with a nuclear gene mutation showed very similar clinical pictures that became manifest in the first years (ranging from first months to early childhood). There was a severe progressive course. Seven of the eight children died in their first decade. Conversely, siblings with a mtDNA mutation had clinical pictures that varied from almost alike to very distinct. They became symptomatic at an older age (ranging from childhood to adulthood), with the exception of defects associated with Leigh or Leigh-like phenotype. The clinical course was more gradual and relatively less severe; four of the 26 patients died, one in his second year, another in her second decade and two in their sixth decade. There are differences in age at onset, severity of clinical course, outcome, and intrafamilial variability in patients affected of an OXPHOS defect due to nuclear or mtDNA mutations. Patients with nuclear mutations become symptomatic at a young age, and have a severe clinical course. Patients with mtDNA mutations show a wider clinical spectrum of age at onset and severity. These differences may be of importance regarding the choice of which genome to study in affected patients as well as with respect to genetic counseling. Copyright 2000 Wiley-Liss, Inc.

  11. Incremental Prognostic Value of Apparent Diffusion Coefficient Histogram Analysis in Head and Neck Squamous Cell Carcinoma.

    Science.gov (United States)

    Li, Xiaoxia; Yuan, Ying; Ren, Jiliang; Shi, Yiqian; Tao, Xiaofeng

    2018-03-26

    We aimed to investigate the incremental prognostic value of apparent diffusion coefficient (ADC) histogram analysis in patients with head and neck squamous cell carcinoma (HNSCC) and integrate it into a multivariate prognostic model. A retrospective review of magnetic resonance imaging findings was conducted in patients with pathologically confirmed HNSCC between June 2012 and December 2015. For each tumor, six histogram parameters were derived: the 10th, 50th, and 90th percentiles of ADC (ADC 10 , ADC 50 , and ADC 90 ); mean ADC values (ADC mean ); kurtosis; and skewness. The clinical variables included age, sex, smoking status, tumor volume, and tumor node metastasis stage. The association of these histogram and clinical variables with overall survival (OS) was determined. Further validation of the histogram parameters as independent biomarkers was performed using multivariate Cox proportional hazard models combined with clinical variables, which was compared to the clinical model. Models were assessed with C index and receiver operating characteristic curve analyses for the 12- and 36-month OS. Ninety-six patients were eligible for analysis. Median follow-up was 877 days (range, 54-1516 days). A total of 29 patients died during follow-up (30%). Patients with higher ADC values (ADC 10  > 0.958 × 10 -3 mm 2 /s, ADC 50  > 1.089 × 10 -3 mm 2 /s, ADC 90  > 1.152 × 10 -3 mm 2 /s, ADC mean  > 1.047 × 10 -3 mm 2 /s) and lower kurtosis (≤0.967) were significant predictors of poor OS (P histogram analysis has incremental prognostic value in patients with HNSCC and increases the performance of a multivariable prognostic model in addition to clinical variables. Copyright © 2018 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

  12. Design and implement of BESIII online histogramming software

    International Nuclear Information System (INIS)

    Li Fei; Wang Liang; Liu Yingjie; Chinese Academy of Sciences, Beijing; Zhu Kejun; Zhao Jingwei

    2007-01-01

    The online histogramming software is an important part of the BESIII DAQ (Data Acquisition) system. This article introduces the main requirements and design of the online histogramming software and presents how to produce, transmit and gather histograms in the distributed environment in the current software implement. The article also illustrate one smart, simple and easy to expand way of setup with xml configure database. (authors)

  13. A monitoring program of the histograms based on ROOT package

    International Nuclear Information System (INIS)

    Zhou Yongzhao; Liang Hao; Chen Yixin; Xue Jundong; Yang Tao; Gong Datao; Jin Ge; Yu Xiaoqi

    2002-01-01

    KHBOOK is a histogram monitor and browser based on ROOT package, which reads the histogram file in HBOOK format from Physmon, converts it into ROOT format, and browses the histograms in Repeat and Overlap modes to monitor and trace the quality of the data from DAQ. KHBOOK is a program of small memory, easy maintenance and fast running as well, using mono-behavior classes and a communication class of C ++

  14. Development of Piezoelectric DNA-Based Biosensor for Direct Detection of Mycobacterium Tuberculosis in Clinical Specimens

    Directory of Open Access Journals (Sweden)

    Thongchai KAEWPHINIT

    2010-02-01

    Full Text Available This study was focused on establishment of piezoelectric biosensor for direct detection of Mycobacterium tuberculosis (MTB in clinical specimens. The quartz crystal immobilized via 3-mercaptopropionic acid (MPA/avidin/DNA biotinylated probe on gold surface and hybridization of the DNA target to DNA biotinylated probe. The optimal concentration of MPA, avidin and 5’-biotinylated DNA probe for immobilization of specific DNA probe on gold surface were 15 mM, 0.1 mg/ml and 1.5 μM, respectively. The detection of genomic DNA digestion in the range from 0.5 to 30 μg/ml. The fabricated biosensor was evaluated through an examination of 200 samples. No cross hybridization were observed against M. avium complex (MAC and other microorganism. This target DNA preparation without amplification will reduce time consuming, costs, and the tedious step of amplification. This study can be extended to develop the new method which is high sensitivity, specificity, cheap, easy to use, and rapid for detection of MTB in many fields.

  15. Sequence homology at the breakpoint and clinical phenotype of mitochondrial DNA deletion syndromes.

    Science.gov (United States)

    Sadikovic, Bekim; Wang, Jing; El-Hattab, Ayman W; Landsverk, Megan; Douglas, Ganka; Brundage, Ellen K; Craigen, William J; Schmitt, Eric S; Wong, Lee-Jun C

    2010-12-20

    Mitochondrial DNA (mtDNA) deletions are a common cause of mitochondrial disorders. Large mtDNA deletions can lead to a broad spectrum of clinical features with different age of onset, ranging from mild mitochondrial myopathies (MM), progressive external ophthalmoplegia (PEO), and Kearns-Sayre syndrome (KSS), to severe Pearson syndrome. The aim of this study is to investigate the molecular signatures surrounding the deletion breakpoints and their association with the clinical phenotype and age at onset. MtDNA deletions in 67 patients were characterized using array comparative genomic hybridization (aCGH) followed by PCR-sequencing of the deletion junctions. Sequence homology including both perfect and imperfect short repeats flanking the deletion regions were analyzed and correlated with clinical features and patients' age group. In all age groups, there was a significant increase in sequence homology flanking the deletion compared to mtDNA background. The youngest patient group (deletion distribution in size and locations, with a significantly lower sequence homology flanking the deletion, and the highest percentage of deletion mutant heteroplasmy. The older age groups showed rather discrete pattern of deletions with 44% of all patients over 6 years old carrying the most common 5 kb mtDNA deletion, which was found mostly in muscle specimens (22/41). Only 15% (3/20) of the young patients (deletion, which is usually present in blood rather than muscle. This group of patients predominantly (16 out of 17) exhibit multisystem disorder and/or Pearson syndrome, while older patients had predominantly neuromuscular manifestations including KSS, PEO, and MM. In conclusion, sequence homology at the deletion flanking regions is a consistent feature of mtDNA deletions. Decreased levels of sequence homology and increased levels of deletion mutant heteroplasmy appear to correlate with earlier onset and more severe disease with multisystem involvement.

  16. Design of a Clinical Information Management System to Support DNA Analysis Laboratory Operation

    OpenAIRE

    Dubay, Christopher J.; Zimmerman, David; Popovich, Bradley

    1995-01-01

    The LabDirector system has been developed at the Oregon Health Sciences University to support the operation of our clinical DNA analysis laboratory. Through an iterative design process which has spanned two years, we have produced a system that is both highly tailored to a clinical genetics production laboratory and flexible in its implementation, to support the rapid growth and change of protocols and methodologies in use in the field. The administrative aspects of the system are integrated ...

  17. Calculation of complication probability of pion treatment at PSI using dose-volume histograms

    International Nuclear Information System (INIS)

    Nakagawa, Keiichi; Akanuma, Atsuo; Aoki, Yukimasa

    1991-01-01

    In the conformation technique a target volume is irradiated uniformly as in conventional radiations, whereas surrounding tissue and organs are nonuniformly irradiated. Clinical data on radiation injuries that accumulate with conventional radiation are not applicable without appropriate compensation. Recently a putative solution of this problem was proposed by Lyman using dose-volume histograms. This histogram reduction method reduces a given dose-volume histogram of an organ to a single step which corresponds to the equivalent complication probability by interpolation. As a result it converts nonuniform radiation into a unique dose to the whole organ which has the equivalent likelihood of radiation injury. This method is based on low LET radiation with conventional fractionation schedules. When it is applied to high LET radiation such as negative pion treatment, a high LET dose should be converted to an equivalent photon dose using an appropriate value of RBE. In the present study the histogram reduction method was applied to actual patients treated by the negative pion conformation technique at the Paul Scherrer Institute. Out of evaluable 90 cases of pelvic tumors, 16 developed grade III-IV bladder injury, and 7 developed grade III-IV rectal injury. The 90 cases were divided into roughly equal groups according to the equivalent doses to the entire bladder and rectum. Complication rates and equivalent doses to the full organs in these groups could be represented by a sigmoid dose-effect relation. When RBE from a pion dose to a photon dose is assumed to be 2.1 for bladder injury, the rates of bladder complications fit best to the theoretical complication curve. When the RBE value was 2.3, the rates of rectal injury fit the theoretical curve best. These values are close to the conversion factor of 2.0 that is used in clinical practice at PSI. This agreement suggests the clinical feasibility of the histogram reduction method in conformation radiotherapy. (author)

  18. Value-at-risk estimation with fuzzy histograms

    NARCIS (Netherlands)

    Almeida, R.J.; Kaymak, U.

    2008-01-01

    Value at risk (VaR) is a measure for senior management that summarises the financial risk a company faces into one single number. In this paper, we consider the use of fuzzy histograms for quantifying the value-at-risk of a portfolio. It is shown that the use of fuzzy histograms provides a good

  19. Multiple histogram method and static Monte Carlo sampling

    NARCIS (Netherlands)

    Inda, M.A.; Frenkel, D.

    2004-01-01

    We describe an approach to use multiple-histogram methods in combination with static, biased Monte Carlo simulations. To illustrate this, we computed the force-extension curve of an athermal polymer from multiple histograms constructed in a series of static Rosenbluth Monte Carlo simulations. From

  20. Calibration of 14C Histograms : A Comparison of Methods

    NARCIS (Netherlands)

    Stolk, Ad; Törnqvist, Torbjörn E.; Hekhuis, Kilian P.V.; Berendsen, Henk J.A.; Plicht, Johannes van der

    1994-01-01

    The interpretation of C-14 histograms is complicated by the non-linearity of the C-14 time scale in terms of Calendar years, which may result in clustering of C-14 ages in certain time intervals unrelated to the (geologic or archaeologic) phenomenon of interest. One can calibrate C-14 histograms for

  1. DNA decontamination methods for internal quality management in clinical PCR laboratories.

    Science.gov (United States)

    Wu, Yingping; Wu, Jianyong; Zhang, Zhihui; Cheng, Chen

    2018-03-01

    The polymerase chain reaction (PCR) technique, one of the most commonly applied methods in diagnostic and molecular biology, has a frustrating downside: the occurrence of false-positive signals due to contamination. In previous research, various DNA decontamination methods have been developed to overcome this limitation. Unfortunately, the use of random or poorly focused sampling methods for monitoring air and/or object surfaces leads to the incomplete elimination during decontamination procedures. We herein attempted to develop a novel DNA decontamination method (environmental surveillance, including surface and air sampling) and quality management program for clinical molecular diagnostic laboratories (or clinical PCR laboratories). Here, we performed a step-by-step evaluation of current DNA decontamination methods and developed an effective procedure for assessing the presence of decontaminating DNA via PCR analysis. Performing targeted environmental surveillance by sampling, which reached optimal performance over 2 weeks, and the decontamination process had been verified as reliable. Additionally, the process was validated to not affect PCR amplification efficiency based on a comparative study. In this study, effective guidelines for DNA decontamination were developed. The method employed ensured that surface DNA contamination could be effectively identified and eliminated. Furthermore, our study highlighted the importance of overall quality assurance and good clinical laboratory practices for preventing contamination, which are key factors for compliance with regulatory or accreditation requirements. Taken together, we provided the evidence that the presented scheme ranged from troubleshooting to the elimination of surface contamination, could serve as critical foundation for developing regular environmental surveillance guidelines for PCR laboratories. © 2017 Wiley Periodicals, Inc.

  2. DPAK and HPAK: a versatile display and histogramming package

    International Nuclear Information System (INIS)

    Logg, C.A.; Boyarski, A.M.; Cook, A.J.; Cottrell, R.L.A.; Sund, S.

    1979-07-01

    The features of a display and histogram package which requires a minimal number of subroutine calls in order to generate graphic output in many flavors on a variety of devices are described. Default options are preset to values that are generally most wanted, but the default values may be readily changed to the user's needs. The description falls naturally into two parts, namely, the set of routines (DPAK) for displaying data on some device, and the set of routines (HPAK) for generating histograms. HPAK provides a means of allocating memory for histograms, accumulating data into histograms, and subsequently displaying the hisotgrams via calls to the DPAK routines. Histograms and displays of either one or two independent variables can be made

  3. Absolute and relative dose-surface and dose-volume histograms of the bladder: which one is the most representative for the actual treatment?

    International Nuclear Information System (INIS)

    Hoogeman, Mischa S; Peeters, Stephanie T H; Bois, Josien de; Lebesque, Joos V

    2005-01-01

    The purpose of this study was to quantify to what extent relative and absolute bladder dose-volume and dose-surface histograms of the planning CT scan were representative for the actual treatment. We used data of 17 patients, who each received 11 repeat CT scans and a planning CT scan. The repeat CT scans were matched on the planning CT scan by the bony anatomy. Clinical treatment plans were used to evaluate the impact of bladder filling changes on the four histogram types. The impact was quantified by calculating for this patient group the correlation coefficient between the planning histogram and the treatment histogram. We found that the absolute dose-surface histogram was the most representative one for the actual treatment

  4. Clinical symptoms and DNA repair characteristics of xeroderma pigmentosum patients from Germany

    International Nuclear Information System (INIS)

    Thielmann, H.W.; Popanda, O.; Edler, L.; Jung, E.G.

    1991-01-01

    Sixty-one xeroderma pigmentosum (XP) patients living in the Federal Republic of Germany were investigated. Clinical symptoms were correlated with DNA repair parameters measured in fibroblasts grown from skin biopsies. Classification according to the international complementation groups revealed that of the 61 patients 3 belonged to group A, 26 to group C, 16 to group D, 3 to group E, and 2 to group F; 11 were of the XP variant type. A striking clinical aspect was the frequency of histogenetically different skin tumors varying from one XP complementation group to the other: squamous and basal cell carcinomas predominated in XP group C; lentigo maligna melanomas were most frequent in group D; basal cell carcinomas occurred preferentially in group E and XP variants. Three DNA repair parameters were determined for 46 fibroblast strains: colony-forming ability (D0); DNA repair synthesis (G0); and DNA-incising capacity (E0). Dose-response experiments with up to 13 dose levels were performed throughout to achieve sufficient experimental accuracy. DNA-damaging treatments included UV light, the 'UV-like' carcinogen N-acetoxy-2-acetylaminofluorene, and the alkylating carcinogens methyl methanesulfonate and N-methyl-N-nitrosourea. Comparison of clinical signs and repair data was made on the basis of D0, G0, and E0 values of both individual cell strains and weighted means of XP complementation groups. Despite considerable clinical and biochemical heterogeneity within complementation groups distinctive features emerged. In general, D0, G0, and E0 values of all XP strains investigated, including XP variants, were found to be reduced upon treatment with UV light or N-acetoxy-2-acetylaminofluorene

  5. Optimization of radiation therapy, III: a method of assessing complication probabilities from dose-volume histograms

    International Nuclear Information System (INIS)

    Lyman, J.T.; Wolbarst, A.B.

    1987-01-01

    To predict the likelihood of success of a therapeutic strategy, one must be able to assess the effects of the treatment upon both diseased and healthy tissues. This paper proposes a method for determining the probability that a healthy organ that receives a non-uniform distribution of X-irradiation, heat, chemotherapy, or other agent will escape complications. Starting with any given dose distribution, a dose-cumulative-volume histogram for the organ is generated. This is then reduced by an interpolation scheme (involving the volume-weighting of complication probabilities) to a slightly different histogram that corresponds to the same overall likelihood of complications, but which contains one less step. The procedure is repeated, one step at a time, until there remains a final, single-step histogram, for which the complication probability can be determined. The formalism makes use of a complication response function C(D, V) which, for the given treatment schedule, represents the probability of complications arising when the fraction V of the organ receives dose D and the rest of the organ gets none. Although the data required to generate this function are sparse at present, it should be possible to obtain the necessary information from in vivo and clinical studies. Volume effects are taken explicitly into account in two ways: the precise shape of the patient's histogram is employed in the calculation, and the complication response function is a function of the volume

  6. Quality standards for DNA sequence variation databases to improve clinical management under development in Australia

    Directory of Open Access Journals (Sweden)

    B. Bennetts

    2014-09-01

    Full Text Available Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA in collaboration with the Human Genetics Society of Australasia (HGSA, and the Human Variome Project (HVP is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.

  7. AHIMSA - Ad hoc histogram information measure sensing algorithm for feature selection in the context of histogram inspired clustering techniques

    Science.gov (United States)

    Dasarathy, B. V.

    1976-01-01

    An algorithm is proposed for dimensionality reduction in the context of clustering techniques based on histogram analysis. The approach is based on an evaluation of the hills and valleys in the unidimensional histograms along the different features and provides an economical means of assessing the significance of the features in a nonparametric unsupervised data environment. The method has relevance to remote sensing applications.

  8. DNA priming for seasonal influenza vaccine: a phase 1b double-blind randomized clinical trial.

    Directory of Open Access Journals (Sweden)

    Julie E Ledgerwood

    Full Text Available The efficacy of current influenza vaccines is limited in vulnerable populations. DNA vaccines can be produced rapidly, and may offer a potential strategy to improve vaccine immunogenicity, indicated by studies with H5 influenza DNA vaccine prime followed by inactivated vaccine boost.Four sites enrolled healthy adults, randomized to receive 2011/12 seasonal influenza DNA vaccine prime (n=65 or phosphate buffered saline (PBS (n=66 administered intramuscularly with Biojector. All subjects received the 2012/13 seasonal inactivated influenza vaccine, trivalent (IIV3 36 weeks after the priming injection. Vaccine safety and tolerability was the primary objective and measurement of antibody response by hemagglutination inhibition (HAI was the secondary objective.The DNA vaccine prime-IIV3 boost regimen was safe and well tolerated. Significant differences in HAI responses between the DNA vaccine prime and the PBS prime groups were not detected in this study.While DNA priming significantly improved the response to a conventional monovalent H5 vaccine in a previous study, it was not effective in adults using seasonal influenza strains, possibly due to pre-existing immunity to the prime, unmatched prime and boost antigens, or the lengthy 36 week boost interval. Careful optimization of the DNA prime-IIV3 boost regimen as related to antigen matching, interval between vaccinations, and pre-existing immune responses to influenza is likely to be needed in further evaluations of this vaccine strategy. In particular, testing this concept in younger age groups with less prior exposure to seasonal influenza strains may be informative.ClinicalTrials.gov NCT01498718.

  9. Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes.

    Science.gov (United States)

    Aref-Eshghi, Erfan; Rodenhiser, David I; Schenkel, Laila C; Lin, Hanxin; Skinner, Cindy; Ainsworth, Peter; Paré, Guillaume; Hood, Rebecca L; Bulman, Dennis E; Kernohan, Kristin D; Boycott, Kym M; Campeau, Philippe M; Schwartz, Charles; Sadikovic, Bekim

    2018-01-04

    Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  10. Modeling Early Postnatal Brain Growth and Development with CT: Changes in the Brain Radiodensity Histogram from Birth to 2 Years.

    Science.gov (United States)

    Cauley, K A; Hu, Y; Och, J; Yorks, P J; Fielden, S W

    2018-04-01

    The majority of brain growth and development occur in the first 2 years of life. This study investigated these changes by analysis of the brain radiodensity histogram of head CT scans from the clinical population, 0-2 years of age. One hundred twenty consecutive head CTs with normal findings meeting the inclusion criteria from children from birth to 2 years were retrospectively identified from 3 different CT scan platforms. Histogram analysis was performed on brain-extracted images, and histogram mean, mode, full width at half maximum, skewness, kurtosis, and SD were correlated with subject age. The effects of scan platform were investigated. Normative curves were fitted by polynomial regression analysis. Average total brain volume was 360 cm 3 at birth, 948 cm 3 at 1 year, and 1072 cm 3 at 2 years. Total brain tissue density showed an 11% increase in mean density at 1 year and 19% at 2 years. Brain radiodensity histogram skewness was positive at birth, declining logarithmically in the first 200 days of life. The histogram kurtosis also decreased in the first 200 days to approach a normal distribution. Direct segmentation of CT images showed that changes in brain radiodensity histogram skewness correlated with, and can be explained by, a relative increase in gray matter volume and an increase in gray and white matter tissue density that occurs during this period of brain maturation. Normative metrics of the brain radiodensity histogram derived from routine clinical head CT images can be used to develop a model of normal brain development. © 2018 by American Journal of Neuroradiology.

  11. Principal component analysis of the CT density histogram to generate parametric response maps of COPD

    Science.gov (United States)

    Zha, N.; Capaldi, D. P. I.; Pike, D.; McCormack, D. G.; Cunningham, I. A.; Parraga, G.

    2015-03-01

    Pulmonary x-ray computed tomography (CT) may be used to characterize emphysema and airways disease in patients with chronic obstructive pulmonary disease (COPD). One analysis approach - parametric response mapping (PMR) utilizes registered inspiratory and expiratory CT image volumes and CT-density-histogram thresholds, but there is no consensus regarding the threshold values used, or their clinical meaning. Principal-component-analysis (PCA) of the CT density histogram can be exploited to quantify emphysema using data-driven CT-density-histogram thresholds. Thus, the objective of this proof-of-concept demonstration was to develop a PRM approach using PCA-derived thresholds in COPD patients and ex-smokers without airflow limitation. Methods: Fifteen COPD ex-smokers and 5 normal ex-smokers were evaluated. Thoracic CT images were also acquired at full inspiration and full expiration and these images were non-rigidly co-registered. PCA was performed for the CT density histograms, from which the components with the highest eigenvalues greater than one were summed. Since the values of the principal component curve correlate directly with the variability in the sample, the maximum and minimum points on the curve were used as threshold values for the PCA-adjusted PRM technique. Results: A significant correlation was determined between conventional and PCA-adjusted PRM with 3He MRI apparent diffusion coefficient (p<0.001), with CT RA950 (p<0.0001), as well as with 3He MRI ventilation defect percent, a measurement of both small airways disease (p=0.049 and p=0.06, respectively) and emphysema (p=0.02). Conclusions: PRM generated using PCA thresholds of the CT density histogram showed significant correlations with CT and 3He MRI measurements of emphysema, but not airways disease.

  12. CLINICAL-EVALUATION OF A MODIFIED ELISA, USING PHOTOBIOTINYLATED DNA, FOR THE DETECTION OF ANTI-DNA ANTIBODIES

    NARCIS (Netherlands)

    HYLKEMA, MN; HUYGEN, H; KRAMERS, C; VANDERWAL, TJ; DEJONG, J; VANBRUGGEN, MCJ; SWAAK, AJG; BERDEN, JHM; SMEENK, RJT; Hylkema, Machteld

    1994-01-01

    The measurement of anti-dsDNA antibodies is important for the diagnosis and the follow-up of patients with systemic lupus erythematosus (SLE). For routine detection of anti-dsDNA, the Farr assay and the immunofluorescence technique (IFT) on Crithidia luciliae proved to be very useful. The anti-dsDNA

  13. IMPLEMENTASI METODE HISTOGRAM EQUALIZATION UNTUK MENINGKATKAN KUALITAS CITRA DIGITAL

    Directory of Open Access Journals (Sweden)

    Isa Akhlis

    2012-02-01

    Full Text Available Radiografi dapat digunakan untuk membantu mendiagnosis penyakit dalam bidang medis. Umumnya citra radiograf masih tampak kabur sehingga memerlukan pengolahan untuk menghilangkan atau mengurangi kekaburan tersebut. Tujuan penelitian ini adalah mendesain perangkat lunak untuk meningkatkan kualitas citra digital foto Roentgen yaitu dengan meningkatkan kontras citra tersebut. Salah satu metode untuk meningkatkan kontras citra digital adalah dengan menggunakan metode histogram equalization. Metoda tersebut membuat tingkat keabuan citra tersebar merata pada semua tingkat keabuan. Hasil penelitian menunjukkan bahwa metoda histogram equalization dapat digunakan untuk meningkatkan kontras citra.  Hal ini dapat langsung dilihat pada layar monitor.   Kata kunci: citra radiograf,  histogram equalization

  14. HPLOT: the graphics interface package for the HBOOK histogramming package

    International Nuclear Information System (INIS)

    Watkins, H.

    1978-01-01

    The subroutine package HPLOT described in this report, enables the CERN histogramming package HBOOK to produce high-quality pictures by means of high-resolution devices such as plotters. HPLOT can be implemented on any scientific computing system with a Fortran IV compiler and can be interfaced with any graphics package; spectral routines in addition to the basic ones enable users to embellish their histograms. Examples are also given of the use of HPLOT as a graphics package for plotting simple pictures without histograms. (Auth.)

  15. Design of a Clinical Information Management System to Support DNA Analysis Laboratory Operation

    Science.gov (United States)

    Dubay, Christopher J.; Zimmerman, David; Popovich, Bradley

    1995-01-01

    The LabDirector system has been developed at the Oregon Health Sciences University to support the operation of our clinical DNA analysis laboratory. Through an iterative design process which has spanned two years, we have produced a system that is both highly tailored to a clinical genetics production laboratory and flexible in its implementation, to support the rapid growth and change of protocols and methodologies in use in the field. The administrative aspects of the system are integrated with an enterprise schedule management system. The laboratory side of the system is driven by a protocol modeling and execution system. The close integration between these two aspects of the clinical laboratory facilitates smooth operations, and allows management to accurately measure costs and performance. The entire application has been designed and documented to provide utility to a wide range of clinical laboratory environments.

  16. Face recognition algorithm using extended vector quantization histogram features.

    Science.gov (United States)

    Yan, Yan; Lee, Feifei; Wu, Xueqian; Chen, Qiu

    2018-01-01

    In this paper, we propose a face recognition algorithm based on a combination of vector quantization (VQ) and Markov stationary features (MSF). The VQ algorithm has been shown to be an effective method for generating features; it extracts a codevector histogram as a facial feature representation for face recognition. Still, the VQ histogram features are unable to convey spatial structural information, which to some extent limits their usefulness in discrimination. To alleviate this limitation of VQ histograms, we utilize Markov stationary features (MSF) to extend the VQ histogram-based features so as to add spatial structural information. We demonstrate the effectiveness of our proposed algorithm by achieving recognition results superior to those of several state-of-the-art methods on publicly available face databases.

  17. A Modified Image Comparison Algorithm Using Histogram Features

    OpenAIRE

    Al-Oraiqat, Anas M.; Kostyukova, Natalya S.

    2018-01-01

    This article discuss the problem of color image content comparison. Particularly, methods of image content comparison are analyzed, restrictions of color histogram are described and a modified method of images content comparison is proposed. This method uses the color histograms and considers color locations. Testing and analyzing of based and modified algorithms are performed. The modified method shows 97% average precision for a collection containing about 700 images without loss of the adv...

  18. Tumor DNA in cerebral spinal fluid reflects clinical course in a patient with melanoma leptomeningeal brain metastases

    Science.gov (United States)

    Li, Yingmei; Pan, Wenying; Connolly, Ian D.; Reddy, Sunil; Nagpal, Seema

    2017-01-01

    Cerebral spinal fluid (CSF) from brain tumor patients contains tumor cellular and cell-free DNA (cfDNA), which provides a less-invasive and routinely accessible method to obtain tumor genomic information. In this report, we used droplet digital PCR to test mutant tumor DNA in CSF of a patient to monitor the treatment response of metastatic melanoma leptomeningeal disease (LMD). The primary melanoma was known to have a BRAFV600E mutation, and the patient was treated with whole brain radiotherapy and BRAF inhibitors. We collected 9 CSF samples over 6 months. The mutant cfDNA fraction gradually decreased from 53 % (time of diagnosis) to 0 (time of symptom alleviation) over the first 6 time points. Three months after clinical improvement, the patient returned with severe symptoms and the mutant cfDNA was again detected in CSF at high levels. The mutant DNA fraction corresponded well with the patient’s clinical response. We used whole exome sequencing to examine the mutation profiles of the LMD tumor DNA in CSF before therapeutic response and after disease relapse, and discovered a canonical cancer mutation PTENR130* at both time points. The cellular and cfDNA revealed similar mutation profiles, suggesting cfDNA is representative of LMD cells. This study demonstrates the potential of using cellular or cfDNA in CSF to monitor treatment response for LMD. PMID:26961773

  19. Comparison of fastsure tb dna and mgit 960 for the detection of mycobacterium tuberculosis complex in clinical specimens

    International Nuclear Information System (INIS)

    Hussain, A.; Mirza, I.A.; Abbasi, S.A.; Ali, S.; Zia, F.; Ahmed, Z.

    2013-01-01

    Objective: To compare the efficacy of Fastsure TB DNA with fully automated MGIT 960 method for detection of Mycobacterium tuberculosis complex (MTB) in clinical specimens. Study Design: Comparative cross sectional study. Methodology: After decontamination procedure, the clinical specimens were subjected to DNA extraction and amplification. Extracted DNA was separated in a separate tube provided with fastsure TB DNA kit and was then inserted into the cartridge provided and results were observed within 30 minutes. For Processing in MGIT 960, OADC and PANTA were added to the clinical specimens after decontamination and then the tubes were processed in MGIT 960. Results: A total of 80 specimens were tested by both MGIT 960 and fastsure TB DNA. On MGIT 960 system, 57 specimens showed growth of MTB while 23 were negative. On Fastsure TB DNA, 47 Specimens were tested as positive and 33 specimens showed negative result. Sensitivity and specificity of Fastsure TB DNA method was calculated to be 82.45 % and 100 % respectively, while positive and negative predictive values were 100 % and 69.69 % respectively. Conclusion: Fast sure TB DNA is a rapid and accurate method for the detection of Mycobacterium tuberculosis complex (MTB) from clinical specimens. (author)

  20. Expression of DNA repair genes in ovarian cancer samples: biological and clinical considerations.

    Science.gov (United States)

    Ganzinelli, M; Mariani, P; Cattaneo, D; Fossati, R; Fruscio, R; Corso, S; Ricci, F; Broggini, M; Damia, G

    2011-05-01

    The purpose of this study was to investigate retrospectively the mRNA expression of genes involved in different DNA repair pathways implicated in processing platinum-induced damage in 171 chemotherapy-naïve ovarian tumours and correlate the expression of the different genes with clinical parameters. The expression of genes involved in DNA repair pathways (PARP1, ERCC1, XPA, XPF, XPG, BRCA1, FANCA, FANCC, FANCD2, FANCF and PolEta), and in DNA damage transduction (Chk1 and Claspin) was measured by RT-PCR in 13 stage I borderline and 77 stage I and 88 III ovarian carcinomas. ERCC1, XPA, XPF and XPG genes were significantly less expressed in stage III than in stage I carcinoma; BRCA1, FANCA, FANCC, FANCD2 gene expressions were low in borderline tumours, higher in stage I carcinomas and lower in stage III samples. High levels of ERCC1, XPA, FANCC, XPG and PolEta correlated with an increase in Overall Survival (OS) and Progression Free Survival (PFS), whilst high BRCA1 levels were associated with PFS on univariate analysis. With multivariate analyses no genes retained an association when adjusted by stage, grade and residual tumour. A tendency towards a better PFS was observed in patients with the highest level of ERCC1 and BRCA1 after platinum-based therapy than those given both platinum and taxol. The expression of DNA repair genes differed in borderline stage I, stage I and stage III ovarian carcinomas. The role of DNA repair genes in predicting the response in ovarian cancer patients seems far from being established. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Differential diagnosis of normal pressure hydrocephalus by MRI mean diffusivity histogram analysis.

    Science.gov (United States)

    Ivkovic, M; Liu, B; Ahmed, F; Moore, D; Huang, C; Raj, A; Kovanlikaya, I; Heier, L; Relkin, N

    2013-01-01

    Accurate diagnosis of normal pressure hydrocephalus is challenging because the clinical symptoms and radiographic appearance of NPH often overlap those of other conditions, including age-related neurodegenerative disorders such as Alzheimer and Parkinson diseases. We hypothesized that radiologic differences between NPH and AD/PD can be characterized by a robust and objective MR imaging DTI technique that does not require intersubject image registration or operator-defined regions of interest, thus avoiding many pitfalls common in DTI methods. We collected 3T DTI data from 15 patients with probable NPH and 25 controls with AD, PD, or dementia with Lewy bodies. We developed a parametric model for the shape of intracranial mean diffusivity histograms that separates brain and ventricular components from a third component composed mostly of partial volume voxels. To accurately fit the shape of the third component, we constructed a parametric function named the generalized Voss-Dyke function. We then examined the use of the fitting parameters for the differential diagnosis of NPH from AD, PD, and DLB. Using parameters for the MD histogram shape, we distinguished clinically probable NPH from the 3 other disorders with 86% sensitivity and 96% specificity. The technique yielded 86% sensitivity and 88% specificity when differentiating NPH from AD only. An adequate parametric model for the shape of intracranial MD histograms can distinguish NPH from AD, PD, or DLB with high sensitivity and specificity.

  2. Clinical patterns associated with the concurrent detection of anti-HBs and HBV DNA.

    Science.gov (United States)

    Anastasiou, Olympia E; Widera, Marek; Korth, Johannes; Kefalakes, Helenie; Katsounas, Antonios; Hilgard, Gudrun; Gerken, Guido; Canbay, Ali; Ciesek, Sandra; Verheyen, Jens

    2018-02-01

    Simultaneous detection of anti-HBs and HBV DNA is a rare serological combination and has been described in acute and chronic HBV infection. To scrutinize viral and clinical patterns associated with concurrent detection of anti-HBs and HBV DNA. Simultaneous detection of anti-HBs and HBV DNA was observed in 64/1444 (4.4%) patients treated for HBV infection at the University Hospital of Essen from 2006 to 2016 (8 with acute, 20 with reactivated, and 36 chronic HBV infection). Clinical data and laboratory parameters were analyzed. Regions of the small hepatitis B surface antigen (SHB) and the reverse transcriptase (RT) were sequenced using next generation sequencing (NGS). Among the 64 patients with detectable HBV DNA and anti-HBs, 17 were HBsAg negative (HBsAg[-]), and two had acute liver failure. Patients with acute HBV infection had fewer genotype specific amino acid substitutions in the SHB region than patients with reactivated HBV infection (4 [4.5] vs 9 [16.25], P = 0.043). However, we could observe a significantly higher number of mutations in the a-determinant region when comparing chronically infected patients to patients with acute infection (0 [1] vs 1 [1], P = 0.044). The ratio of nonsynonymous to synonymous mutations (Ka/Ks) was on average >1 for the SHB region and 1) in the SHB region indicates that anti-HBs might have exerted selection pressure on the HBsAg. In three cases the diagnosis of acute HBV infection would have been at least delayed by only focusing on HBsAg testing. © 2017 Wiley Periodicals, Inc.

  3. Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women's Cancers.

    Directory of Open Access Journals (Sweden)

    Thomas E Bartlett

    Full Text Available We introduce a novel per-gene measure of intra-gene DNA methylation variability (IGV based on the Illumina Infinium HumanMethylation450 platform, which is prognostic independently of well-known predictors of clinical outcome. Using IGV, we derive a robust gene-panel prognostic signature for ovarian cancer (OC, n = 221, which validates in two independent data sets from Mayo Clinic (n = 198 and TCGA (n = 358, with significance of p = 0.004 in both sets. The OC prognostic signature gene-panel is comprised of four gene groups, which represent distinct biological processes. We show the IGV measurements of these gene groups are most likely a reflection of a mixture of intra-tumour heterogeneity and transcription factor (TF binding/activity. IGV can be used to predict clinical outcome in patients individually, providing a surrogate read-out of hard-to-measure disease processes.

  4. Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women's Cancers.

    Science.gov (United States)

    Bartlett, Thomas E; Jones, Allison; Goode, Ellen L; Fridley, Brooke L; Cunningham, Julie M; Berns, Els M J J; Wik, Elisabeth; Salvesen, Helga B; Davidson, Ben; Trope, Claes G; Lambrechts, Sandrina; Vergote, Ignace; Widschwendter, Martin

    2015-01-01

    We introduce a novel per-gene measure of intra-gene DNA methylation variability (IGV) based on the Illumina Infinium HumanMethylation450 platform, which is prognostic independently of well-known predictors of clinical outcome. Using IGV, we derive a robust gene-panel prognostic signature for ovarian cancer (OC, n = 221), which validates in two independent data sets from Mayo Clinic (n = 198) and TCGA (n = 358), with significance of p = 0.004 in both sets. The OC prognostic signature gene-panel is comprised of four gene groups, which represent distinct biological processes. We show the IGV measurements of these gene groups are most likely a reflection of a mixture of intra-tumour heterogeneity and transcription factor (TF) binding/activity. IGV can be used to predict clinical outcome in patients individually, providing a surrogate read-out of hard-to-measure disease processes.

  5. The clinical utility of HPV DNA testing in cervical cancer screening strategies.

    Science.gov (United States)

    Bhatla, Neerja; Moda, Nidhi

    2009-09-01

    Cervical cancer continues to be the commonest cause of death among women in developing countries, largely due to the failure to the inability to sustain effective cytology-based screening programs. While this burden may come down following implementation of the human papillomavirus (HPV) vaccine, screening will still be required. HPV DNA testing is a promising new technology for cervical cancer prevention and is the most reproducible of all cervical cancer screening tests. Presently, the two assays most widely used for the detection of genital types are the polymerase chain reaction (PCR) and Hybrid Capture 2 assays (hc2). Rapid, affordable tests are expected to be available soon. HPV DNA testing can be used in a variety of clinical scenarios that include primary screening in women older than 30 yr; as an adjunctive test to cytology; in the triage of women with an equivocal cytologic report, e.g., ASC-US; or for follow-up post-treatment for cervical intraepithelial neoplasia (CIN). HPV DNA testing can also be performed on self-collected samples, which allows screening in remote areas and also in women who refuse gynecologic examination.

  6. Steganalytic methods for the detection of histogram shifting data-hiding schemes

    OpenAIRE

    Lerch Hostalot, Daniel

    2011-01-01

    In this paper, some steganalytic techniques designed to detect the existence of hidden messages using histogram shifting methods are presented. Firstly, some techniques to identify specific methods of histogram shifting, based on visible marks on the histogram or abnormal statistical distributions are suggested. Then, we present a general technique capable of detecting all histogram shifting techniques analyzed. This technique is based on the effect of histogram shifting methods on the "volat...

  7. Defect detection based on extreme edge of defective region histogram

    Directory of Open Access Journals (Sweden)

    Zouhir Wakaf

    2018-01-01

    Full Text Available Automatic thresholding has been used by many applications in image processing and pattern recognition systems. Specific attention was given during inspection for quality control purposes in various industries like steel processing and textile manufacturing. Automatic thresholding problem has been addressed well by the commonly used Otsu method, which provides suitable results for thresholding images based on a histogram of bimodal distribution. However, the Otsu method fails when the histogram is unimodal or close to unimodal. Defects have different shapes and sizes, ranging from very small to large. The gray-level distributions of the image histogram can vary between unimodal and multimodal. Furthermore, Otsu-revised methods, like the valley-emphasis method and the background histogram mode extents, which overcome the drawbacks of the Otsu method, require preprocessing steps and fail to use the general threshold for multimodal defects. This study proposes a new automatic thresholding algorithm based on the acquisition of the defective region histogram and the selection of its extreme edge as the threshold value to segment all defective objects in the foreground from the image background. To evaluate the proposed defect-detection method, common standard images for experimentation were used. Experimental results of the proposed method show that the proposed method outperforms the current methods in terms of defect detection.

  8. Clinical applications of circulating tumor DNA and circulating tumor cells in pancreatic cancer.

    Science.gov (United States)

    Riva, Francesca; Dronov, Oleksii I; Khomenko, Dmytro I; Huguet, Florence; Louvet, Christophe; Mariani, Pascale; Stern, Marc-Henri; Lantz, Olivier; Proudhon, Charlotte; Pierga, Jean-Yves; Bidard, Francois-Clement

    2016-03-01

    Pancreatic ductal adenocarcinoma (PDAC) is the most frequent pancreatic cancer type and is characterized by a dismal prognosis due to late diagnosis, local tumor invasion, frequent distant metastases and poor sensitivity to current therapy. In this context, circulating tumor cells and circulating tumor DNA constitute easily accessible blood-borne tumor biomarkers that may prove their clinical interest for screening, early diagnosis and metastatic risk assessment of PDAC. Moreover these markers represent a tool to assess PDAC mutational landscape. In this review, together with key biological findings, we summarize the clinical results obtained using "liquid biopsies" at the different stages of the disease, for early and metastatic diagnosis as well as monitoring during therapy. Copyright © 2016 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  9. Histogram Matching Extends Acceptable Signal Strength Range on Optical Coherence Tomography Images

    Science.gov (United States)

    Chen, Chieh-Li; Ishikawa, Hiroshi; Wollstein, Gadi; Bilonick, Richard A.; Sigal, Ian A.; Kagemann, Larry; Schuman, Joel S.

    2015-01-01

    Purpose. We minimized the influence of image quality variability, as measured by signal strength (SS), on optical coherence tomography (OCT) thickness measurements using the histogram matching (HM) method. Methods. We scanned 12 eyes from 12 healthy subjects with the Cirrus HD-OCT device to obtain a series of OCT images with a wide range of SS (maximal range, 1–10) at the same visit. For each eye, the histogram of an image with the highest SS (best image quality) was set as the reference. We applied HM to the images with lower SS by shaping the input histogram into the reference histogram. Retinal nerve fiber layer (RNFL) thickness was automatically measured before and after HM processing (defined as original and HM measurements), and compared to the device output (device measurements). Nonlinear mixed effects models were used to analyze the relationship between RNFL thickness and SS. In addition, the lowest tolerable SSs, which gave the RNFL thickness within the variability margin of manufacturer recommended SS range (6–10), were determined for device, original, and HM measurements. Results. The HM measurements showed less variability across a wide range of image quality than the original and device measurements (slope = 1.17 vs. 4.89 and 1.72 μm/SS, respectively). The lowest tolerable SS was successfully reduced to 4.5 after HM processing. Conclusions. The HM method successfully extended the acceptable SS range on OCT images. This would qualify more OCT images with low SS for clinical assessment, broadening the OCT application to a wider range of subjects. PMID:26066749

  10. Altered DNA Methylation Patterns Associated With Clinically Relevant Increases in PTSD Symptoms and PTSD Symptom Profiles in Military Personnel.

    Science.gov (United States)

    Martin, Christiana; Cho, Young-Eun; Kim, Hyungsuk; Yun, Sijung; Kanefsky, Rebekah; Lee, Hyunhwa; Mysliwiec, Vincent; Cashion, Ann; Gill, Jessica

    2018-05-01

    Military personnel experience posttraumatic stress disorder (PTSD), which is associated with differential DNA methylation across the whole genome. However, the relationship between these DNA methylation patterns and clinically relevant increases in PTSD severity is not yet clearly understood. The purpose of this study was to identify differences in DNA methylation associated with PTSD symptoms and investigate DNA methylation changes related to increases in the severity of PTSD in military personnel. In this pilot study, a cross-sectional comparison was made between military personnel with PTSD (n = 8) and combat-matched controls without PTSD (n = 6). Symptom measures were obtained, and genome-wide DNA methylation was measured using methylated DNA immunoprecipitation (MeDIP-seq) from whole blood samples at baseline and 3 months later. A longitudinal comparison measured DNA methylation changes in military personnel with clinically relevant increases in PTSD symptoms between time points (PTSD onset) and compared methylation patterns to controls with no clinical changes in PTSD. In military personnel with elevated PTSD symptoms 3 months following baseline, 119 genes exhibited reduced methylation and 8 genes exhibited increased methylation. Genes with reduced methylation in the PTSD-onset group relate to the canonical pathways of netrin signaling, Wnt/Ca + pathway, and axonal guidance signaling. These gene pathways relate to neurological disorders, and the current findings suggest that these epigenetic changes potentially relate to PTSD symptomology. This study provides some novel insights into the role of epigenetic changes in PTSD symptoms and the progression of PTSD symptoms in military personnel.

  11. Clinical significance of changes of expression of anti-dsDNA antibody in serum in patients with SLE

    International Nuclear Information System (INIS)

    Chen Xingguo; Zhang Xiaoli; Liu Chunyan; Cao Jiwei; Du Tongxing; Wang Zizheng

    2008-01-01

    Objective: To investigate the significance of anti-dsDNA antibody in diagnosis and treatment of SLE through measurement of changes of serum anti-dsDNA antibody expression in patients with SLE. Methods: Serum anti-dsDNA antibody was detected with radioisotope method in 60 patients with SLE and 33 controls (consisted of patients with other collagen diseases including Sjogren syndrome, systemic sclerosis, rheumatoid arthritis, polymyositis, mixed connective tissue disease, ankylosing spondylitis). Clinical manifestation and laboratory findings in the SLE patients were studied in detail. Results: (1) Serum anti-dsDNA antibody was positive in 39 of the 60 SLE patients with only two false positive cases in the 33 controls: a sensitivity of 65% and specificity of 93. 3%. (2) In SLE patients, positivity of anti-dsDNA antibody was not correlated with positivity of anti-Sm antibody (P>0.05), but was correlated with positivity of anti-SSA antibody (P<0.05). (3) Incidences of alopecia, skin rashes, oral mucosal ulcer, proteinuria were significantly higher in SLE patients with positive anti-dsDNA antibody than those in SLE patients with negative anti-dsDNA antibody (P<0.05). (4) Incidences of leukopenia and thrombocytopenia were also significantly higher in SLE patients with positive anti-dsDNA antibody (P<0.05). Conclusion: Anti-dsDNA antibody could be taken as a specific marker of SLE and the serum expression were positively correlated with the activity and severity of the disease. (authors)

  12. Histogram bin width selection for time-dependent Poisson processes

    International Nuclear Information System (INIS)

    Koyama, Shinsuke; Shinomoto, Shigeru

    2004-01-01

    In constructing a time histogram of the event sequences derived from a nonstationary point process, we wish to determine the bin width such that the mean squared error of the histogram from the underlying rate of occurrence is minimized. We find that the optimal bin widths obtained for a doubly stochastic Poisson process and a sinusoidally regulated Poisson process exhibit different scaling relations with respect to the number of sequences, time scale and amplitude of rate modulation, but both diverge under similar parametric conditions. This implies that under these conditions, no determination of the time-dependent rate can be made. We also apply the kernel method to these point processes, and find that the optimal kernels do not exhibit any critical phenomena, unlike the time histogram method

  13. Histogram bin width selection for time-dependent Poisson processes

    Energy Technology Data Exchange (ETDEWEB)

    Koyama, Shinsuke; Shinomoto, Shigeru [Department of Physics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502 (Japan)

    2004-07-23

    In constructing a time histogram of the event sequences derived from a nonstationary point process, we wish to determine the bin width such that the mean squared error of the histogram from the underlying rate of occurrence is minimized. We find that the optimal bin widths obtained for a doubly stochastic Poisson process and a sinusoidally regulated Poisson process exhibit different scaling relations with respect to the number of sequences, time scale and amplitude of rate modulation, but both diverge under similar parametric conditions. This implies that under these conditions, no determination of the time-dependent rate can be made. We also apply the kernel method to these point processes, and find that the optimal kernels do not exhibit any critical phenomena, unlike the time histogram method.

  14. Finding significantly connected voxels based on histograms of connection strengths

    DEFF Research Database (Denmark)

    Kasenburg, Niklas; Pedersen, Morten Vester; Darkner, Sune

    2016-01-01

    We explore a new approach for structural connectivity based segmentations of subcortical brain regions. Connectivity based segmentations are usually based on fibre connections from a seed region to predefined target regions. We present a method for finding significantly connected voxels based...... on the distribution of connection strengths. Paths from seed voxels to all voxels in a target region are obtained from a shortest-path tractography. For each seed voxel we approximate the distribution with a histogram of path scores. We hypothesise that the majority of estimated connections are false-positives...... and that their connection strength is distributed differently from true-positive connections. Therefore, an empirical null-distribution is defined for each target region as the average normalized histogram over all voxels in the seed region. Single histograms are then tested against the corresponding null...

  15. 3D Model Retrieval Based on Vector Quantisation Index Histograms

    International Nuclear Information System (INIS)

    Lu, Z M; Luo, H; Pan, J S

    2006-01-01

    This paper proposes a novel technique to retrieval 3D mesh models using vector quantisation index histograms. Firstly, points are sampled uniformly on mesh surface. Secondly, to a point five features representing global and local properties are extracted. Thus feature vectors of points are obtained. Third, we select several models from each class, and employ their feature vectors as a training set. After training using LBG algorithm, a public codebook is constructed. Next, codeword index histograms of the query model and those in database are computed. The last step is to compute the distance between histograms of the query and those of the models in database. Experimental results show the effectiveness of our method

  16. PENGARUH HISTOGRAM EQUALIZATION UNTUK PERBAIKAN KUALITAS CITRA DIGITAL

    Directory of Open Access Journals (Sweden)

    Sisilia Daeng Bakka Mau

    2016-04-01

    Full Text Available Penelitian ini membahas penggunaan metode histogram equalization yang akan digunakan untuk perbaikan kualitas citra. Perbaikan kualitas citra (image enhancement merupakan salah satu proses awal dalam peningkatan mutu citra. Peningkatan mutu citra diperlukan karena seringkali citra yang dijadikan objek pembahasan mempunyai kualitas yang buruk, misalnya citra mengalami derau, kabur, citra terlalu gelap atau terang, citra kurang tajam dan sebagainya. Perbaikan kualitas citra adalah proses memperjelas dan mempertajam ciri atau fitur tertentu dari citra agar citra lebih mudah dipersepsi maupun dianalisa secara lebih teliti. Hasil penelitian ini membuktikan bahwa penggunaan metode histogram equalization dapat digunakan untuk meningkatkan kontras citra dan dapat meningkatkan kualitas citra, sehingga informasi yang ada pada citra lebih jelas terlihat. Kata kunci: perbaikan kualitas citra, histogram equalization, citra digital

  17. The histogram analysis of diffusion-weighted intravoxel incoherent motion (IVIM) imaging for differentiating the gleason grade of prostate cancer.

    Science.gov (United States)

    Zhang, Yu-Dong; Wang, Qing; Wu, Chen-Jiang; Wang, Xiao-Ning; Zhang, Jing; Liu, Hui; Liu, Xi-Sheng; Shi, Hai-Bin

    2015-04-01

    To evaluate histogram analysis of intravoxel incoherent motion (IVIM) for discriminating the Gleason grade of prostate cancer (PCa). A total of 48 patients pathologically confirmed as having clinically significant PCa (size > 0.5 cm) underwent preoperative DW-MRI (b of 0-900 s/mm(2)). Data was post-processed by monoexponential and IVIM model for quantitation of apparent diffusion coefficients (ADCs), perfusion fraction f, diffusivity D and pseudo-diffusivity D*. Histogram analysis was performed by outlining entire-tumour regions of interest (ROIs) from histological-radiological correlation. The ability of imaging indices to differentiate low-grade (LG, Gleason score (GS) ≤6) from intermediate/high-grade (HG, GS > 6) PCa was analysed by ROC regression. Eleven patients had LG tumours (18 foci) and 37 patients had HG tumours (42 foci) on pathology examination. HG tumours had significantly lower ADCs and D in terms of mean, median, 10th and 75th percentiles, combined with higher histogram kurtosis and skewness for ADCs, D and f, than LG PCa (p Histogram D showed relatively higher correlations (ñ = 0.641-0.668 vs. ADCs: 0.544-0.574) with ordinal GS of PCa; and its mean, median and 10th percentile performed better than ADCs did in distinguishing LG from HG PCa. It is feasible to stratify the pathological grade of PCa by IVIM with histogram metrics. D performed better in distinguishing LG from HG tumour than conventional ADCs. • GS had relatively higher correlation with tumour D than ADCs. • Difference of histogram D among two-grade tumours was statistically significant. • D yielded better individual features in demonstrating tumour grade than ADC. • D* and f failed to determine tumour grade of PCa.

  18. Measuring the apparent diffusion coefficient in primary rectal tumors: is there a benefit in performing histogram analyses?

    Science.gov (United States)

    van Heeswijk, Miriam M; Lambregts, Doenja M J; Maas, Monique; Lahaye, Max J; Ayas, Z; Slenter, Jos M G M; Beets, Geerard L; Bakers, Frans C H; Beets-Tan, Regina G H

    2017-06-01

    The apparent diffusion coefficient (ADC) is a potential prognostic imaging marker in rectal cancer. Typically, mean ADC values are used, derived from precise manual whole-volume tumor delineations by experts. The aim was first to explore whether non-precise circular delineation combined with histogram analysis can be a less cumbersome alternative to acquire similar ADC measurements and second to explore whether histogram analyses provide additional prognostic information. Thirty-seven patients who underwent a primary staging MRI including diffusion-weighted imaging (DWI; b0, 25, 50, 100, 500, 1000; 1.5 T) were included. Volumes-of-interest (VOIs) were drawn on b1000-DWI: (a) precise delineation, manually tracing tumor boundaries (2 expert readers), and (b) non-precise delineation, drawing circular VOIs with a wide margin around the tumor (2 non-experts). Mean ADC and histogram metrics (mean, min, max, median, SD, skewness, kurtosis, 5th-95th percentiles) were derived from the VOIs and delineation time was recorded. Measurements were compared between the two methods and correlated with prognostic outcome parameters. Median delineation time reduced from 47-165 s (precise) to 21-43 s (non-precise). The 45th percentile of the non-precise delineation showed the best correlation with the mean ADC from the precise delineation as the reference standard (ICC 0.71-0.75). None of the mean ADC or histogram parameters showed significant prognostic value; only the total tumor volume (VOI) was significantly larger in patients with positive clinical N stage and mesorectal fascia involvement. When performing non-precise tumor delineation, histogram analysis (in specific 45th ADC percentile) may be used as an alternative to obtain similar ADC values as with precise whole tumor delineation. Histogram analyses are not beneficial to obtain additional prognostic information.

  19. VHDL implementation on histogram with ADC CAMAC module

    International Nuclear Information System (INIS)

    Ruby Santhi, R.; Satyanarayana, V.V.V.; Ajith Kumar, B.P.

    2007-01-01

    Modern nuclear spectroscopy systems the data acquisition and analysis in experimental science have been undergoing major changes because of faster speed and higher resolution. The CAMAC module which is described here is FPGA based 8K x 24 bit Histogram Memory integrated with ADC on a single board has been designed and fabricated. This module accepts input from Spectroscopy Amplifier for Pulse Height Analysis and offers all features single spectra for a few selected parameters. These on line histograms are to monitor the progress of the experiments during on line experiments

  20. Integral Histogram with Random Projection for Pedestrian Detection.

    Directory of Open Access Journals (Sweden)

    Chang-Hua Liu

    Full Text Available In this paper, we give a systematic study to report several deep insights into the HOG, one of the most widely used features in the modern computer vision and image processing applications. We first show that, its magnitudes of gradient can be randomly projected with random matrix. To handle over-fitting, an integral histogram based on the differences of randomly selected blocks is proposed. The experiments show that both the random projection and integral histogram outperform the HOG feature obviously. Finally, the two ideas are combined into a new descriptor termed IHRP, which outperforms the HOG feature with less dimensions and higher speed.

  1. Clinical evaluation and mitochondrial DNA sequence analysis in three Chinese families with Leber's hereditary optic neuropathy

    International Nuclear Information System (INIS)

    Qian Yaping; Zhou Xiangtian; Hu Yongwu; Tong Yi; Li Ronghua; Lu Fan; Yang Huanming; Mo Junqin; Qu Jia; Guan Minxin

    2005-01-01

    We report here the clinical, genetic, and molecular characterization of three Chinese families (WZ4, WZ5, and WZ6) with Leber's hereditary optic neuropathy (LHON). Clinical and genetic evaluations revealed the variable severity and age-of-onset in visual impairment in these families. Penetrances of visual impairment in these Chinese families were 33.3%, 35.7%, and 35.5%, respectively, with an average 34.8%. Furthermore, the average age-at-onset in those Chinese families was 17, 20, and 18 years. In addition, the ratios between affected male and female matrilineal relatives in these Chinese families were 3:0, 1:1, and 1.2:1, respectively. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical G11778A mutation associated with LHON in many families. The fact that mtDNA of those pedigrees belonged to different haplogroups F1, D4, and M10 suggested that the G11778A mutation occurred sporadically and multiplied through evolution of the mtDNA in China. However, there was the absence of functionally significant mutations in tRNA and rRNAs or secondary LHON mutations in these Chinese families. The I187T mutation in the ND1, the S99A mutation in the A6, the V254I in CO3, and I58V in ND6 mutation, showing high evolutional conservation, may contribute to the phenotypic expression of the G11778A mutation in the WZ6 pedigree. By contrast, none of mtDNA variants are evolutionarily conserved and implicated to have significantly functional consequence in WZ4 and WZ5 pedigrees. Apparently, these variants do not have a potential modifying role in the development of visual impairment associated with G11778A mutation in those two families. Thus, nuclear modifier gene(s) or environmental factor(s) seem to account for the penetrance and expressivity of LHON in these three Chinese families carrying the G11778A mutation

  2. Effects of direct-to-consumer advertising and clinical guidelines on appropriate use of human papillomavirus DNA tests.

    Science.gov (United States)

    Price, Rebecca Anhang; Frank, Richard G; Cleary, Paul D; Goldie, Sue J

    2011-02-01

    Both clinical guidelines and direct-to-consumer (DTC) advertising influence the use of new health care technologies, but little is known about their relative effects. The introduction of a cervical cancer screening test in 2000 offered a unique opportunity to assess the 2 strategies. To evaluate the effects of clinical guidelines and a targeted DTC advertising campaign on overall and appropriate use of human papillomavirus (HPV) DNA tests. Quasi-experimental study using difference-in-differences analysis. Data were MarketScan private insurance claims for 500,000 women aged 21 to 64 enrolled at least 12 consecutive months from January 2001 through December 2005. Both clinical guidelines and DTC advertising were associated with increases in overall HPV DNA test use. DTC advertising was associated with a statistically significant increase in HPV DNA test use in 2 groups of DTC cities (+5.57%, P advertising was associated with comparable increases in the probability of appropriate and inappropriate use of the HPV DNA test in primary screening. Clinical guideline releases from the American College of Obstetricians and Gynecologists, and by a cosponsored panel, were associated with greater increases in HPV DNA tests for appropriate primary screening than for inappropriate primary screening (β = 0.3347, P advertising was associated with increased overall use of a cervical cancer screening test, whereas clinical guidelines were differentially associated with increased appropriate use. These findings suggest distinct influences of consumer marketing and professional guidelines on the use of health care products and services.

  3. Blood DNA methylation biomarkers predict clinical reactivity in food-sensitized infants.

    Science.gov (United States)

    Martino, David; Dang, Thanh; Sexton-Oates, Alexandra; Prescott, Susan; Tang, Mimi L K; Dharmage, Shyamali; Gurrin, Lyle; Koplin, Jennifer; Ponsonby, Anne-Louise; Allen, Katrina J; Saffery, Richard

    2015-05-01

    The diagnosis of food allergy (FA) can be challenging because approximately half of food-sensitized patients are asymptomatic. Current diagnostic tests are excellent makers of sensitization but poor predictors of clinical reactivity. Thus oral food challenges (OFCs) are required to determine a patient's risk of reactivity. We sought to discover genomic biomarkers of clinical FA with utility for predicting food challenge outcomes. Genome-wide DNA methylation (DNAm) profiling was performed on blood mononuclear cells from volunteers who had undergone objective OFCs, concurrent skin prick tests, and specific IgE tests. Fifty-eight food-sensitized patients (aged 11-15 months) were assessed, half of whom were clinically reactive. Thirteen nonallergic control subjects were also assessed. Reproducibility was assessed in an additional 48 samples by using methylation data from an independent population of patients with clinical FA. Using a supervised learning approach, we discovered a DNAm signature of 96 CpG sites that predict clinical outcomes. Diagnostic scores were derived from these 96 methylation sites, and cutoffs were determined in a sensitivity analysis. Methylation biomarkers outperformed allergen-specific IgE and skin prick tests for predicting OFC outcomes. FA status was correctly predicted in the replication cohort with an accuracy of 79.2%. DNAm biomarkers with clinical utility for predicting food challenge outcomes are readily detectable in blood. The development of this technology in detailed follow-up studies will yield highly innovative diagnostic assays. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  4. Clinical identification of bacteria in human chronic wound infections: culturing vs. 16S ribosomal DNA sequencing

    Directory of Open Access Journals (Sweden)

    Rhoads Daniel D

    2012-11-01

    Full Text Available Abstract Background Chronic wounds affect millions of people and cost billions of dollars in the United States each year. These wounds harbor polymicrobial biofilm communities, which can be difficult to elucidate using culturing methods. Clinical molecular microbiological methods are increasingly being employed to investigate the microbiota of chronic infections, including wounds, as part of standard patient care. However, molecular testing is more sensitive than culturing, which results in markedly different results being reported to clinicians. This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing, and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture. Methods Parallel samples from 51 chronic wounds were studied using aerobic culturing and 16S DNA sequencing for the identification of bacteria. Results One hundred forty-five (145 unique genera were identified using molecular methods, and 68 of these genera were aerotolerant. Fourteen (14 unique genera were identified using aerobic culture methods. One-third (31/92 of the cultures were determined to be Staphylococcus aureus, Pseudomonas aeruginosa, and Enterococcus faecalis with higher relative abundance scores were more likely to be detected by culture as demonstrated with regression modeling. Conclusion Discordance between molecular and culture testing is often observed. However, culture-free 16S ribosomal DNA sequencing and its relative abundance score can provide clinicians with insight into which bacteria are most abundant in a sample and which are most likely to be detected by culture.

  5. Clinical Significance of Plasma Epstein-Barr Virus DNA in Pulmonary Lymphoepithelioma-like Carcinoma (LELC) Patients.

    Science.gov (United States)

    Xie, Mian; Wu, Xiaojun; Wang, Fang; Zhang, Jinjun; Ben, Xiaosong; Zhang, Jiexia; Li, Xiaoxiang

    2018-02-01

    Primary pulmonary lymphoepithelioma-like carcinoma (LELC) is a histologically distinctive subtype of NSCLC and an Epstein-Barr virus (EBV)-associated epithelial neoplasm. We investigated the clinical significance of plasma concentrations of EBV DNA in patients with pulmonary LELC. Two independent sets of plasma samples from a total of 429 patients with patients with pulmonary LELC (287 initial and 142 confirmatory) were available for EBV DNA determination. Plasma samples from the patients were subjected to a real-time quantitative polymerase chain reaction before treatment and 3 months after radical resection. Cutoff points were determined for pretreatment plasma EBV DNA concentration (low disease status and change in EBV DNA concentrations by using nonparametric tests. High EBV DNA concentration was associated with shorter OS in the initial, confirmatory, and combined data sets (combined data set hazard ratio = 3.67, 95% confidence interval: 2.72-4.38, p disease. High EBV DNA concentration was also associated with shorter disease-free survival (DFS) in patients with stage I/II disease. Patients with persistently detectable plasma EBV DNA had significantly poorer OS (p disease progression of pulmonary LELC. High baseline EBV DNA concentration is an independent poor prognostic marker in patients with pulmonary LELC. These results should be confirmed in larger prospective trials. Copyright © 2017 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

  6. Clinical significance of HPV DNA cotesting in Korean women with ASCUS or ASC-H.

    Science.gov (United States)

    Lee, Sanghoon; Kim, Jae Won; Hong, Jin Hwa; Song, Jae Yun; Lee, Jae Kwan; Kim, In Sun; Lee, Nak Woo

    2014-12-01

    The purpose of this study was to evaluate the clinical significance of Human papillomavirus (HPV) DNA cotesting in Korean women with abnormal Papanicolaou (Pap) smear results based on colposcopic pathology. A total of 1012 women underwent liquid-based Pap smears and hybrid capture II HPV DNA tests followed by colposcopy at the Korea University Hospital from January 2007 to May 2012. Of these women, 832 women were included in this retrospective study. The mean patient age was 45.4 ± 13.7 years (range:15-80). The distribution of Pap smear results was normal (4.7%), atypical squamous cells of uncertain significance (ASCUS) (42.1%), low-grade squamous intraepithelial lesion (26.8%), ASC-H (7.0%), and high-grade squamous intraepithelial lesion (HSIL) (19.5%). In women with ASCUS, none of the 87 HPV-negative had ≥cervical intraepithelial neoplasia (CIN2) (P age groups: ASCUS and ASC-H furnish healthcare providers with informative data. There is a lower proportion of ≥CIN2 in HPV-negative women and a higher proportion of ≥CIN2 in HPV-positive. When HPV data were further evaluated by age group, the risk of ≥CIN2 was lower in HPV-negative women, especially in women ≥30. © 2014 Wiley Periodicals, Inc.

  7. Fuzzy Logic-Based Histogram Equalization for Image Contrast Enhancement

    Directory of Open Access Journals (Sweden)

    V. Magudeeswaran

    2013-01-01

    Full Text Available Fuzzy logic-based histogram equalization (FHE is proposed for image contrast enhancement. The FHE consists of two stages. First, fuzzy histogram is computed based on fuzzy set theory to handle the inexactness of gray level values in a better way compared to classical crisp histograms. In the second stage, the fuzzy histogram is divided into two subhistograms based on the median value of the original image and then equalizes them independently to preserve image brightness. The qualitative and quantitative analyses of proposed FHE algorithm are evaluated using two well-known parameters like average information contents (AIC and natural image quality evaluator (NIQE index for various images. From the qualitative and quantitative measures, it is interesting to see that this proposed method provides optimum results by giving better contrast enhancement and preserving the local information of the original image. Experimental result shows that the proposed method can effectively and significantly eliminate washed-out appearance and adverse artifacts induced by several existing methods. The proposed method has been tested using several images and gives better visual quality as compared to the conventional methods.

  8. Hybrid Histogram Descriptor: A Fusion Feature Representation for Image Retrieval.

    Science.gov (United States)

    Feng, Qinghe; Hao, Qiaohong; Chen, Yuqi; Yi, Yugen; Wei, Ying; Dai, Jiangyan

    2018-06-15

    Currently, visual sensors are becoming increasingly affordable and fashionable, acceleratingly the increasing number of image data. Image retrieval has attracted increasing interest due to space exploration, industrial, and biomedical applications. Nevertheless, designing effective feature representation is acknowledged as a hard yet fundamental issue. This paper presents a fusion feature representation called a hybrid histogram descriptor (HHD) for image retrieval. The proposed descriptor comprises two histograms jointly: a perceptually uniform histogram which is extracted by exploiting the color and edge orientation information in perceptually uniform regions; and a motif co-occurrence histogram which is acquired by calculating the probability of a pair of motif patterns. To evaluate the performance, we benchmarked the proposed descriptor on RSSCN7, AID, Outex-00013, Outex-00014 and ETHZ-53 datasets. Experimental results suggest that the proposed descriptor is more effective and robust than ten recent fusion-based descriptors under the content-based image retrieval framework. The computational complexity was also analyzed to give an in-depth evaluation. Furthermore, compared with the state-of-the-art convolutional neural network (CNN)-based descriptors, the proposed descriptor also achieves comparable performance, but does not require any training process.

  9. Histogram equalization with Bayesian estimation for noise robust speech recognition.

    Science.gov (United States)

    Suh, Youngjoo; Kim, Hoirin

    2018-02-01

    The histogram equalization approach is an efficient feature normalization technique for noise robust automatic speech recognition. However, it suffers from performance degradation when some fundamental conditions are not satisfied in the test environment. To remedy these limitations of the original histogram equalization methods, class-based histogram equalization approach has been proposed. Although this approach showed substantial performance improvement under noise environments, it still suffers from performance degradation due to the overfitting problem when test data are insufficient. To address this issue, the proposed histogram equalization technique employs the Bayesian estimation method in the test cumulative distribution function estimation. It was reported in a previous study conducted on the Aurora-4 task that the proposed approach provided substantial performance gains in speech recognition systems based on the acoustic modeling of the Gaussian mixture model-hidden Markov model. In this work, the proposed approach was examined in speech recognition systems with deep neural network-hidden Markov model (DNN-HMM), the current mainstream speech recognition approach where it also showed meaningful performance improvement over the conventional maximum likelihood estimation-based method. The fusion of the proposed features with the mel-frequency cepstral coefficients provided additional performance gains in DNN-HMM systems, which otherwise suffer from performance degradation in the clean test condition.

  10. Improved LSB matching steganography with histogram characters reserved

    Science.gov (United States)

    Chen, Zhihong; Liu, Wenyao

    2008-03-01

    This letter bases on the researches of LSB (least significant bit, i.e. the last bit of a binary pixel value) matching steganographic method and the steganalytic method which aims at histograms of cover images, and proposes a modification to LSB matching. In the LSB matching, if the LSB of the next cover pixel matches the next bit of secret data, do nothing; otherwise, choose to add or subtract one from the cover pixel value at random. In our improved method, a steganographic information table is defined and records the changes which embedded secrete bits introduce in. Through the table, the next LSB which has the same pixel value will be judged to add or subtract one dynamically in order to ensure the histogram's change of cover image is minimized. Therefore, the modified method allows embedding the same payload as the LSB matching but with improved steganographic security and less vulnerability to attacks compared with LSB matching. The experimental results of the new method show that the histograms maintain their attributes, such as peak values and alternative trends, in an acceptable degree and have better performance than LSB matching in the respects of histogram distortion and resistance against existing steganalysis.

  11. MPV17-related mitochondrial DNA maintenance defect: New cases and review of clinical, biochemical, and molecular aspects.

    Science.gov (United States)

    El-Hattab, Ayman W; Wang, Julia; Dai, Hongzheng; Almannai, Mohammed; Staufner, Christian; Alfadhel, Majid; Gambello, Michael J; Prasun, Pankaj; Raza, Saleem; Lyons, Hernando J; Afqi, Manal; Saleh, Mohammed A M; Faqeih, Eissa A; Alzaidan, Hamad I; Alshenqiti, Abduljabbar; Flore, Leigh Anne; Hertecant, Jozef; Sacharow, Stephanie; Barbouth, Deborah S; Murayama, Kei; Shah, Amit A; Lin, Henry C; Wong, Lee-Jun C

    2018-04-01

    Mitochondrial DNA (mtDNA) maintenance defects are a group of diseases caused by deficiency of proteins involved in mtDNA synthesis, mitochondrial nucleotide supply, or mitochondrial dynamics. One of the mtDNA maintenance proteins is MPV17, which is a mitochondrial inner membrane protein involved in importing deoxynucleotides into the mitochondria. In 2006, pathogenic variants in MPV17 were first reported to cause infantile-onset hepatocerebral mtDNA depletion syndrome and Navajo neurohepatopathy. To date, 75 individuals with MPV17-related mtDNA maintenance defect have been reported with 39 different MPV17 pathogenic variants. In this report, we present an additional 25 affected individuals with nine novel MPV17 pathogenic variants. We summarize the clinical features of all 100 affected individuals and review the total 48 MPV17 pathogenic variants. The vast majority of affected individuals presented with an early-onset encephalohepatopathic disease characterized by hepatic and neurological manifestations, failure to thrive, lactic acidemia, and mtDNA depletion detected mainly in liver tissue. Rarely, MPV17 deficiency can cause a late-onset neuromyopathic disease characterized by myopathy and peripheral neuropathy with no or minimal liver involvement. Approximately half of the MPV17 pathogenic variants are missense. A genotype with biallelic missense variants, in particular homozygous p.R50Q, p.P98L, and p.R41Q, can carry a relatively better prognosis. © 2017 Wiley Periodicals, Inc.

  12. 3D facial expression recognition based on histograms of surface differential quantities

    KAUST Repository

    Li, Huibin; Morvan, Jean-Marie; Chen, Liming

    2011-01-01

    . To characterize shape information of the local neighborhood of facial landmarks, we calculate the weighted statistical distributions of surface differential quantities, including histogram of mesh gradient (HoG) and histogram of shape index (HoS). Normal cycle

  13. Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors.

    Directory of Open Access Journals (Sweden)

    Hector Hernandez-Vargas

    Full Text Available BACKGROUND: Hepatocellular carcinoma (HCC is characterized by late detection and fast progression, and it is believed that epigenetic disruption may be the cause of its molecular and clinicopathological heterogeneity. A better understanding of the global deregulation of methylation states and how they correlate with disease progression will aid in the design of strategies for earlier detection and better therapeutic decisions. METHODS AND FINDINGS: We characterized the changes in promoter methylation in a series of 30 HCC tumors and their respective surrounding tissue and identified methylation signatures associated with major risk factors and clinical correlates. A wide panel of cancer-related gene promoters was analyzed using Illumina bead array technology, and CpG sites were then selected according to their ability to classify clinicopathological parameters. An independent series of HCC tumors and matched surrounding tissue was used for validation of the signatures. We were able to develop and validate a signature of methylation in HCC. This signature distinguished HCC from surrounding tissue and from other tumor types, and was independent of risk factors. However, aberrant methylation of an independent subset of promoters was associated with tumor progression and etiological risk factors (HBV or HCV infection and alcohol consumption. Interestingly, distinct methylation of an independent panel of gene promoters was strongly correlated with survival after cancer therapy. CONCLUSION: Our study shows that HCC tumors exhibit specific DNA methylation signatures associated with major risk factors and tumor progression stage, with potential clinical applications in diagnosis and prognosis.

  14. Clinical characteristics of three patients with UVs syndrome, a photosensitive disorder with defective DNA repair

    International Nuclear Information System (INIS)

    Itoh, T.; Yamaizumi, M.; Hiro-oka, M.; Matsui, T.; Matsuno, M.; Ono, T.; Ichihashi, M.

    1996-01-01

    Recently, we established a new category of photosensitive disorder termed UVsup(s) syndrome. Cells from patients with UVsup(s) syndrome have a similar UV sensitivity as xeroderma pigmentosum (XP) cells, but have a normal level of unscheduled DNA synthesis (UDS) unlike XP. UVsup(s) syndrome is distinct from Cockayne syndrome (CS) or XP including XP variant (XP-V) as determined by studies of genetic factors using cell fusion, microinjection, and postreplication repair assays. In this study, we identified three japanese patients with UVsup(s) syndrome: an 11-year-old girl, a 17 year old male, and an 8-year-old boy. The first two patients were siblings, while the third was a case from a different family. All of these patients exhibited acute recurrent sunburn. Common clinical manifestations of the patients were slight erythema and dryness, a number of freckles on sun-exposed areas, and slight telangiectasia only seen on the cheek and nose. Patient 3 showed a lowered minimal erythema dose between 280 and 300 nm. The patients' fibroblasts showed similar characteristics to those in CS, such as UV sensitivity, and a failure of RNA synthesis (RRS) after UV irradiation, despite a normal level of UDS. Thus, UVsup(s) syndrome is a new hereditary photosensitive disorder with clinical manifestations similar to a mild form of Xp but showing the cellular characteristics of CS. (Author)

  15. ADC histogram analysis for adrenal tumor histogram analysis of apparent diffusion coefficient in differentiating adrenal adenoma from pheochromocytoma.

    Science.gov (United States)

    Umanodan, Tomokazu; Fukukura, Yoshihiko; Kumagae, Yuichi; Shindo, Toshikazu; Nakajo, Masatoyo; Takumi, Koji; Nakajo, Masanori; Hakamada, Hiroto; Umanodan, Aya; Yoshiura, Takashi

    2017-04-01

    To determine the diagnostic performance of apparent diffusion coefficient (ADC) histogram analysis in diffusion-weighted (DW) magnetic resonance imaging (MRI) for differentiating adrenal adenoma from pheochromocytoma. We retrospectively evaluated 52 adrenal tumors (39 adenomas and 13 pheochromocytomas) in 47 patients (21 men, 26 women; mean age, 59.3 years; range, 16-86 years) who underwent DW 3.0T MRI. Histogram parameters of ADC (b-values of 0 and 200 [ADC 200 ], 0 and 400 [ADC 400 ], and 0 and 800 s/mm 2 [ADC 800 ])-mean, variance, coefficient of variation (CV), kurtosis, skewness, and entropy-were compared between adrenal adenomas and pheochromocytomas, using the Mann-Whitney U-test. Receiver operating characteristic (ROC) curves for the histogram parameters were generated to differentiate adrenal adenomas from pheochromocytomas. Sensitivity and specificity were calculated by using a threshold criterion that would maximize the average of sensitivity and specificity. Variance and CV of ADC 800 were significantly higher in pheochromocytomas than in adrenal adenomas (P histogram parameters for diagnosing adrenal adenomas (ADC 200 , 0.82; ADC 400 , 0.87; and ADC 800 , 0.92), with sensitivity of 84.6% and specificity of 84.6% (cutoff, ≤2.82) with ADC 200 ; sensitivity of 89.7% and specificity of 84.6% (cutoff, ≤2.77) with ADC 400 ; and sensitivity of 94.9% and specificity of 92.3% (cutoff, ≤2.67) with ADC 800 . ADC histogram analysis of DW MRI can help differentiate adrenal adenoma from pheochromocytoma. 3 J. Magn. Reson. Imaging 2017;45:1195-1203. © 2016 International Society for Magnetic Resonance in Medicine.

  16. Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors.

    Directory of Open Access Journals (Sweden)

    Xinhui Wang

    Full Text Available BACKGROUND: Adenocarcinomas located near the gastroesophageal junction have unclear etiology and are difficult to classify. We used DNA methylation analysis to identify subtype-specific markers and new subgroups of gastroesophageal adenocarcinomas, and studied their association with epidemiological risk factors and clinical outcomes. METHODOLOGY/PRINCIPAL FINDINGS: We used logistic regression models and unsupervised hierarchical cluster analysis of 74 DNA methylation markers on 45 tumor samples (44 patients of esophageal and gastric adenocarcinomas obtained from a population-based case-control study to uncover epigenetic markers and cluster groups of gastroesophageal adenocarcinomas. No distinct epigenetic differences were evident between subtypes of gastric and esophageal cancers. However, we identified two gastroesophageal adenocarcinoma subclusters based on DNA methylation profiles. Group membership was best predicted by GATA5 DNA methylation status. We analyzed the associations between these two epigenetic groups and exposure using logistic regression, and the associations with survival time using Cox regression in a larger set of 317 tumor samples (278 patients. There were more males with esophageal and gastric cardia cancers in Cluster Group 1 characterized by higher GATA5 DNA methylation values (all p<0.05. This group also showed associations of borderline statistical significance with having ever smoked (p-value = 0.07, high body mass index (p-value = 0.06, and symptoms of gastroesophageal reflux (p-value = 0.07. Subjects in cluster Group 1 showed better survival than those in Group 2 after adjusting for tumor differentiation grade, but this was not found to be independent of tumor stage. CONCLUSIONS/SIGNIFICANCE: DNA methylation profiling can be used in population-based studies to identify epigenetic subclasses of gastroesophageal adenocarcinomas and class-specific DNA methylation markers that can be linked to

  17. Concordance of mutation detection in circulating tumor DNA in early clinical trials using different blood collection protocols

    DEFF Research Database (Denmark)

    Ahlborn, Lise B.; Madsen, Mette; Jonson, Lars

    2017-01-01

    in a clinical setting. Here we investigate the concordance between standard blood collection for molecular analysis using immediate separation of plasma, compared to the use of collection tubes allowing for delayed processing. Methods: In this study, we measured the fractional abundance of tumor specific...... patients with advanced solid cancers enrolled in early clinical trials. Results: Concordance in the fractional abundance of mutations in ctDNA isolated from blood collected in either K3EDTA or BCT tubes from patients with different solid cancers was observed. Conclusions: This study indicates that BCT...... mutations (BRAF p.V600E and PIK3CA p.H1047R) in ctDNA isolated from blood samples collected in either cell-stabilizing Cell-Free DNA BCT tubes (delayed processing within 72 hours) or standard K3EDTA tubes (immediate processing within 15 minutes). Twenty-five blood sample pairs (EDTA/BCT) were collected from...

  18. Isobio software: biological dose distribution and biological dose volume histogram from physical dose conversion using linear-quadratic-linear model.

    Science.gov (United States)

    Jaikuna, Tanwiwat; Khadsiri, Phatchareewan; Chawapun, Nisa; Saekho, Suwit; Tharavichitkul, Ekkasit

    2017-02-01

    To develop an in-house software program that is able to calculate and generate the biological dose distribution and biological dose volume histogram by physical dose conversion using the linear-quadratic-linear (LQL) model. The Isobio software was developed using MATLAB version 2014b to calculate and generate the biological dose distribution and biological dose volume histograms. The physical dose from each voxel in treatment planning was extracted through Computational Environment for Radiotherapy Research (CERR), and the accuracy was verified by the differentiation between the dose volume histogram from CERR and the treatment planning system. An equivalent dose in 2 Gy fraction (EQD 2 ) was calculated using biological effective dose (BED) based on the LQL model. The software calculation and the manual calculation were compared for EQD 2 verification with pair t -test statistical analysis using IBM SPSS Statistics version 22 (64-bit). Two and three-dimensional biological dose distribution and biological dose volume histogram were displayed correctly by the Isobio software. Different physical doses were found between CERR and treatment planning system (TPS) in Oncentra, with 3.33% in high-risk clinical target volume (HR-CTV) determined by D 90% , 0.56% in the bladder, 1.74% in the rectum when determined by D 2cc , and less than 1% in Pinnacle. The difference in the EQD 2 between the software calculation and the manual calculation was not significantly different with 0.00% at p -values 0.820, 0.095, and 0.593 for external beam radiation therapy (EBRT) and 0.240, 0.320, and 0.849 for brachytherapy (BT) in HR-CTV, bladder, and rectum, respectively. The Isobio software is a feasible tool to generate the biological dose distribution and biological dose volume histogram for treatment plan evaluation in both EBRT and BT.

  19. Improved dose–volume histogram estimates for radiopharmaceutical therapy by optimizing quantitative SPECT reconstruction parameters

    International Nuclear Information System (INIS)

    Cheng Lishui; Hobbs, Robert F; Sgouros, George; Frey, Eric C; Segars, Paul W

    2013-01-01

    In radiopharmaceutical therapy, an understanding of the dose distribution in normal and target tissues is important for optimizing treatment. Three-dimensional (3D) dosimetry takes into account patient anatomy and the nonuniform uptake of radiopharmaceuticals in tissues. Dose–volume histograms (DVHs) provide a useful summary representation of the 3D dose distribution and have been widely used for external beam treatment planning. Reliable 3D dosimetry requires an accurate 3D radioactivity distribution as the input. However, activity distribution estimates from SPECT are corrupted by noise and partial volume effects (PVEs). In this work, we systematically investigated OS-EM based quantitative SPECT (QSPECT) image reconstruction in terms of its effect on DVHs estimates. A modified 3D NURBS-based Cardiac-Torso (NCAT) phantom that incorporated a non-uniform kidney model and clinically realistic organ activities and biokinetics was used. Projections were generated using a Monte Carlo (MC) simulation; noise effects were studied using 50 noise realizations with clinical count levels. Activity images were reconstructed using QSPECT with compensation for attenuation, scatter and collimator–detector response (CDR). Dose rate distributions were estimated by convolution of the activity image with a voxel S kernel. Cumulative DVHs were calculated from the phantom and QSPECT images and compared both qualitatively and quantitatively. We found that noise, PVEs, and ringing artifacts due to CDR compensation all degraded histogram estimates. Low-pass filtering and early termination of the iterative process were needed to reduce the effects of noise and ringing artifacts on DVHs, but resulted in increased degradations due to PVEs. Large objects with few features, such as the liver, had more accurate histogram estimates and required fewer iterations and more smoothing for optimal results. Smaller objects with fine details, such as the kidneys, required more iterations and less

  20. Improved dose-volume histogram estimates for radiopharmaceutical therapy by optimizing quantitative SPECT reconstruction parameters

    Science.gov (United States)

    Cheng, Lishui; Hobbs, Robert F.; Segars, Paul W.; Sgouros, George; Frey, Eric C.

    2013-06-01

    In radiopharmaceutical therapy, an understanding of the dose distribution in normal and target tissues is important for optimizing treatment. Three-dimensional (3D) dosimetry takes into account patient anatomy and the nonuniform uptake of radiopharmaceuticals in tissues. Dose-volume histograms (DVHs) provide a useful summary representation of the 3D dose distribution and have been widely used for external beam treatment planning. Reliable 3D dosimetry requires an accurate 3D radioactivity distribution as the input. However, activity distribution estimates from SPECT are corrupted by noise and partial volume effects (PVEs). In this work, we systematically investigated OS-EM based quantitative SPECT (QSPECT) image reconstruction in terms of its effect on DVHs estimates. A modified 3D NURBS-based Cardiac-Torso (NCAT) phantom that incorporated a non-uniform kidney model and clinically realistic organ activities and biokinetics was used. Projections were generated using a Monte Carlo (MC) simulation; noise effects were studied using 50 noise realizations with clinical count levels. Activity images were reconstructed using QSPECT with compensation for attenuation, scatter and collimator-detector response (CDR). Dose rate distributions were estimated by convolution of the activity image with a voxel S kernel. Cumulative DVHs were calculated from the phantom and QSPECT images and compared both qualitatively and quantitatively. We found that noise, PVEs, and ringing artifacts due to CDR compensation all degraded histogram estimates. Low-pass filtering and early termination of the iterative process were needed to reduce the effects of noise and ringing artifacts on DVHs, but resulted in increased degradations due to PVEs. Large objects with few features, such as the liver, had more accurate histogram estimates and required fewer iterations and more smoothing for optimal results. Smaller objects with fine details, such as the kidneys, required more iterations and less

  1. Histogram analysis for smartphone-based rapid hematocrit determination

    Science.gov (United States)

    Jalal, Uddin M.; Kim, Sang C.; Shim, Joon S.

    2017-01-01

    A novel and rapid analysis technique using histogram has been proposed for the colorimetric quantification of blood hematocrits. A smartphone-based “Histogram” app for the detection of hematocrits has been developed integrating the smartphone embedded camera with a microfluidic chip via a custom-made optical platform. The developed histogram analysis shows its effectiveness in the automatic detection of sample channel including auto-calibration and can analyze the single-channel as well as multi-channel images. Furthermore, the analyzing method is advantageous to the quantification of blood-hematocrit both in the equal and varying optical conditions. The rapid determination of blood hematocrits carries enormous information regarding physiological disorders, and the use of such reproducible, cost-effective, and standard techniques may effectively help with the diagnosis and prevention of a number of human diseases. PMID:28717569

  2. Histogram Equalization to Model Adaptation for Robust Speech Recognition

    Directory of Open Access Journals (Sweden)

    Suh Youngjoo

    2010-01-01

    Full Text Available We propose a new model adaptation method based on the histogram equalization technique for providing robustness in noisy environments. The trained acoustic mean models of a speech recognizer are adapted into environmentally matched conditions by using the histogram equalization algorithm on a single utterance basis. For more robust speech recognition in the heavily noisy conditions, trained acoustic covariance models are efficiently adapted by the signal-to-noise ratio-dependent linear interpolation between trained covariance models and utterance-level sample covariance models. Speech recognition experiments on both the digit-based Aurora2 task and the large vocabulary-based task showed that the proposed model adaptation approach provides significant performance improvements compared to the baseline speech recognizer trained on the clean speech data.

  3. Multifractal analysis of three-dimensional histogram from color images

    International Nuclear Information System (INIS)

    Chauveau, Julien; Rousseau, David; Richard, Paul; Chapeau-Blondeau, Francois

    2010-01-01

    Natural images, especially color or multicomponent images, are complex information-carrying signals. To contribute to the characterization of this complexity, we investigate the possibility of multiscale organization in the colorimetric structure of natural images. This is realized by means of a multifractal analysis applied to the three-dimensional histogram from natural color images. The observed behaviors are confronted to those of reference models with known multifractal properties. We use for this purpose synthetic random images with trivial monofractal behavior, and multidimensional multiplicative cascades known for their actual multifractal behavior. The behaviors observed on natural images exhibit similarities with those of the multifractal multiplicative cascades and display the signature of elaborate multiscale organizations stemming from the histograms of natural color images. This type of characterization of colorimetric properties can be helpful to various tasks of digital image processing, as for instance modeling, classification, indexing.

  4. A novel parallel architecture for local histogram equalization

    Science.gov (United States)

    Ohannessian, Mesrob I.; Choueiter, Ghinwa F.; Diab, Hassan

    2005-07-01

    Local histogram equalization is an image enhancement algorithm that has found wide application in the pre-processing stage of areas such as computer vision, pattern recognition and medical imaging. The computationally intensive nature of the procedure, however, is a main limitation when real time interactive applications are in question. This work explores the possibility of performing parallel local histogram equalization, using an array of special purpose elementary processors, through an HDL implementation that targets FPGA or ASIC platforms. A novel parallelization scheme is presented and the corresponding architecture is derived. The algorithm is reduced to pixel-level operations. Processing elements are assigned image blocks, to maintain a reasonable performance-cost ratio. To further simplify both processor and memory organizations, a bit-serial access scheme is used. A brief performance assessment is provided to illustrate and quantify the merit of the approach.

  5. Effects of Direct-to-Consumer Advertising and Clinical Guidelines on Appropriate Use of Human Papillomavirus DNA Tests

    Science.gov (United States)

    2011-01-01

    Background Both clinical guidelines and direct-to-consumer (DTC) advertising influence use of new health care technologies, but little is known about their relative effects. The introduction of a cervical cancer screening test in 2000 offered a unique opportunity to assess the two strategies. Objective To evaluate the effects of clinical guidelines and a targeted DTC advertising campaign on overall and appropriate use of human papillomavirus (HPV) DNA tests. Research Design Quasi-experimental study using difference-in-differences analysis. Data were MarketScan private insurance claims for 500,000 women ages 21 to 64 enrolled at least 12 consecutive months from January 2001 through December 2005. Results Both clinical guidelines and DTC advertising were associated with increases in overall HPV DNA test use. DTC advertising was associated with a statistically significant increase in HPV DNA test use in two groups of DTC cities (+5.57 percent, padvertising was associated with comparable increases in the probability of appropriate and inappropriate use of the HPV DNA test in primary screening. Clinical guideline releases from the American College of Obstetricians and Gynecologists, and by a co-sponsored panel, were associated with greater increases in HPV DNA tests for appropriate primary screening than for inappropriate primary screening (β=0.3347, padvertising was associated with increased overall use of a cervical cancer screening test, while clinical guidelines were differentially associated with increased appropriate use. These findings suggest distinct influences of consumer marketing and professional guidelines on the use of health care products and services. PMID:21150798

  6. Histogram specification as a method of density modification

    International Nuclear Information System (INIS)

    Harrison, R.W.

    1988-01-01

    A new method for improving the quality and extending the resolution of Fourier maps is described. The method is based on a histogram analysis of the electron density. The distribution of electron density values in the map is forced to be 'ideal'. The 'ideal' distribution is assumed to be Gaussian. The application of the method to improve the electron density map for the protein Acinetobacter asparaginase, which is a tetrameric enzyme of molecular weight 140000 daltons, is described. (orig.)

  7. Breast density pattern characterization by histogram features and texture descriptors

    OpenAIRE

    Carneiro,Pedro Cunha; Franco,Marcelo Lemos Nunes; Thomaz,Ricardo de Lima; Patrocinio,Ana Claudia

    2017-01-01

    Abstract Introduction Breast cancer is the first leading cause of death for women in Brazil as well as in most countries in the world. Due to the relation between the breast density and the risk of breast cancer, in medical practice, the breast density classification is merely visual and dependent on professional experience, making this task very subjective. The purpose of this paper is to investigate image features based on histograms and Haralick texture descriptors so as to separate mammo...

  8. Motor Oil Classification using Color Histograms and Pattern Recognition Techniques.

    Science.gov (United States)

    Ahmadi, Shiva; Mani-Varnosfaderani, Ahmad; Habibi, Biuck

    2018-04-20

    Motor oil classification is important for quality control and the identification of oil adulteration. In thiswork, we propose a simple, rapid, inexpensive and nondestructive approach based on image analysis and pattern recognition techniques for the classification of nine different types of motor oils according to their corresponding color histograms. For this, we applied color histogram in different color spaces such as red green blue (RGB), grayscale, and hue saturation intensity (HSI) in order to extract features that can help with the classification procedure. These color histograms and their combinations were used as input for model development and then were statistically evaluated by using linear discriminant analysis (LDA), quadratic discriminant analysis (QDA), and support vector machine (SVM) techniques. Here, two common solutions for solving a multiclass classification problem were applied: (1) transformation to binary classification problem using a one-against-all (OAA) approach and (2) extension from binary classifiers to a single globally optimized multilabel classification model. In the OAA strategy, LDA, QDA, and SVM reached up to 97% in terms of accuracy, sensitivity, and specificity for both the training and test sets. In extension from binary case, despite good performances by the SVM classification model, QDA and LDA provided better results up to 92% for RGB-grayscale-HSI color histograms and up to 93% for the HSI color map, respectively. In order to reduce the numbers of independent variables for modeling, a principle component analysis algorithm was used. Our results suggest that the proposed method is promising for the identification and classification of different types of motor oils.

  9. Independent histogram pursuit for segmentation of skin lesions

    DEFF Research Database (Denmark)

    Gomez, D.D.; Butakoff, C.; Ersbøll, Bjarne Kjær

    2008-01-01

    In this paper, an unsupervised algorithm, called the Independent Histogram Pursuit (HIP), for segmenting dermatological lesions is proposed. The algorithm estimates a set of linear combinations of image bands that enhance different structures embedded in the image. In particular, the first estima...... to deal with different types of dermatological lesions. The boundary detection precision using k-means segmentation was close to 97%. The proposed algorithm can be easily combined with the majority of classification algorithms....

  10. Color and Contrast Enhancement by Controlled Piecewise Affine Histogram Equalization

    Directory of Open Access Journals (Sweden)

    Jose-Luis Lisani

    2012-10-01

    Full Text Available This paper presents a simple contrast enhancement algorithm based on histogram equalization (HE. The proposed algorithm performs a piecewise affine transform of the intensity levels of a digital image such that the new cumulative distribution function will be approximately uniform (as with HE, but where the stretching of the range is locally controlled to avoid brutal noise enhancement. We call this algorithm Piecewise Affine Equalization (PAE. Several experiments show that, in general, the new algorithm improves HE results.

  11. Quantification of viral DNA during HIV-1 infection: A review of relevant clinical uses and laboratory methods.

    Science.gov (United States)

    Alidjinou, E K; Bocket, L; Hober, D

    2015-02-01

    Effective antiretroviral therapy usually leads to undetectable HIV-1 RNA in the plasma. However, the virus persists in some cells of infected patients as various DNA forms, both integrated and unintegrated. This reservoir represents the greatest challenge to the complete cure of HIV-1 infection and its characteristics highly impact the course of the disease. The quantification of HIV-1 DNA in blood samples constitutes currently the most practical approach to measure this residual infection. Real-time quantitative PCR (qPCR) is the most common method used for HIV-DNA quantification and many strategies have been developed to measure the different forms of HIV-1 DNA. In the literature, several "in-house" PCR methods have been used and there is a need for standardization to have comparable results. In addition, qPCR is limited for the precise quantification of low levels by background noise. Among new assays in development, digital PCR was shown to allow an accurate quantification of HIV-1 DNA. Total HIV-1 DNA is most commonly measured in clinical routine. The absolute quantification of proviruses and unintegrated forms is more often used for research purposes. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  12. Breast density pattern characterization by histogram features and texture descriptors

    Directory of Open Access Journals (Sweden)

    Pedro Cunha Carneiro

    2017-04-01

    Full Text Available Abstract Introduction Breast cancer is the first leading cause of death for women in Brazil as well as in most countries in the world. Due to the relation between the breast density and the risk of breast cancer, in medical practice, the breast density classification is merely visual and dependent on professional experience, making this task very subjective. The purpose of this paper is to investigate image features based on histograms and Haralick texture descriptors so as to separate mammographic images into categories of breast density using an Artificial Neural Network. Methods We used 307 mammographic images from the INbreast digital database, extracting histogram features and texture descriptors of all mammograms and selecting them with the K-means technique. Then, these groups of selected features were used as inputs of an Artificial Neural Network to classify the images automatically into the four categories reported by radiologists. Results An average accuracy of 92.9% was obtained in a few tests using only some of the Haralick texture descriptors. Also, the accuracy rate increased to 98.95% when texture descriptors were mixed with some features based on a histogram. Conclusion Texture descriptors have proven to be better than gray levels features at differentiating the breast densities in mammographic images. From this paper, it was possible to automate the feature selection and the classification with acceptable error rates since the extraction of the features is suitable to the characteristics of the images involving the problem.

  13. Contrast Enhancement Algorithm Based on Gap Adjustment for Histogram Equalization

    Directory of Open Access Journals (Sweden)

    Chung-Cheng Chiu

    2016-06-01

    Full Text Available Image enhancement methods have been widely used to improve the visual effects of images. Owing to its simplicity and effectiveness histogram equalization (HE is one of the methods used for enhancing image contrast. However, HE may result in over-enhancement and feature loss problems that lead to unnatural look and loss of details in the processed images. Researchers have proposed various HE-based methods to solve the over-enhancement problem; however, they have largely ignored the feature loss problem. Therefore, a contrast enhancement algorithm based on gap adjustment for histogram equalization (CegaHE is proposed. It refers to a visual contrast enhancement algorithm based on histogram equalization (VCEA, which generates visually pleasing enhanced images, and improves the enhancement effects of VCEA. CegaHE adjusts the gaps between two gray values based on the adjustment equation, which takes the properties of human visual perception into consideration, to solve the over-enhancement problem. Besides, it also alleviates the feature loss problem and further enhances the textures in the dark regions of the images to improve the quality of the processed images for human visual perception. Experimental results demonstrate that CegaHE is a reliable method for contrast enhancement and that it significantly outperforms VCEA and other methods.

  14. Contrast Enhancement Algorithm Based on Gap Adjustment for Histogram Equalization

    Science.gov (United States)

    Chiu, Chung-Cheng; Ting, Chih-Chung

    2016-01-01

    Image enhancement methods have been widely used to improve the visual effects of images. Owing to its simplicity and effectiveness histogram equalization (HE) is one of the methods used for enhancing image contrast. However, HE may result in over-enhancement and feature loss problems that lead to unnatural look and loss of details in the processed images. Researchers have proposed various HE-based methods to solve the over-enhancement problem; however, they have largely ignored the feature loss problem. Therefore, a contrast enhancement algorithm based on gap adjustment for histogram equalization (CegaHE) is proposed. It refers to a visual contrast enhancement algorithm based on histogram equalization (VCEA), which generates visually pleasing enhanced images, and improves the enhancement effects of VCEA. CegaHE adjusts the gaps between two gray values based on the adjustment equation, which takes the properties of human visual perception into consideration, to solve the over-enhancement problem. Besides, it also alleviates the feature loss problem and further enhances the textures in the dark regions of the images to improve the quality of the processed images for human visual perception. Experimental results demonstrate that CegaHE is a reliable method for contrast enhancement and that it significantly outperforms VCEA and other methods. PMID:27338412

  15. Failure to attend out-patient clinics: is it in our DNA?

    LENUS (Irish Health Repository)

    Roberts, Kinley

    2012-02-01

    PURPOSE: This paper aims to determine the reasons why patients miss clinic appointments and to ascertain patients\\' views on the implementation of reminder systems and penalty fees to reduce the rates of did not attend (DNAs). Overall, the paper seeks to establish novel ways to run a more efficient out-patient department (OPD) service to improve waiting times and access for patients to limited neurology resources. DESIGN\\/METHODOLOGY\\/APPROACH: A questionnaire-based study was approved by the audit committee and was offered to 204 out-patients attending the neurology clinics over a three-month period (July to September 2009). The patients\\' demographic details and non-attendance records were reviewed. The paper aimed to ascertain, from the patients\\' perspective, why people failed to attend clinic appointments. Each participant was asked their views on how they felt their public hospital service might reduce the number of DNAs at their neurology OPD. FINDINGS: A total of 204 patients took part. Participants had a mean age of 31 years (range 25-75 years) with a modal peak in the 26 to 35 age bracket. Almost 10 per cent of those surveyed admitted to missing a hospital out-patient appointment in the past. The most common reason was that they simply "forgot" (28 per cent). DNA rates by age range were proportionally similar to the overall age profile of attenders. Over 55 per cent said they would like a pre-appointment reminder via a mobile telephone text message, 19 per cent preferred a pre-appointment telephone call, and 19 per cent an e-mail. Of those surveyed, 47 per cent said they would be willing to pay a fee on booking that could be refunded on attending for their appointment. The majority of these felt Euro 20 was the most appropriate amount (39 per cent). The rate of acceptance for various fee amounts was uniform across age ranges. Over half (52 per cent) said that they would agree to a "buddy" system whereby the appointment reminder was sent to the patient

  16. Utility of a Multiplex PCR Assay for Detecting Herpesvirus DNA in Clinical Samples

    Science.gov (United States)

    Druce, Julian; Catton, Mike; Chibo, Doris; Minerds, Kirsty; Tyssen, David; Kostecki, Renata; Maskill, Bill; Leong-Shaw, Wendy; Gerrard, Marie; Birch, Chris

    2002-01-01

    A multiplex PCR was designed to amplify herpes simplex virus types 1 and 2, cytomegalovirus, and varicella-zoster virus DNA present in a diverse range of clinical material. The susceptibility of these viruses to in vivo inhibition by at least one antiviral drug was an important consideration in their inclusion in the multiplex detection system. An aliquot of equine herpesvirus was introduced into each specimen prior to extraction and served as an indicator of potential inhibitors of the PCR and a detector of suboptimal PCR conditions. Compared to virus isolation and immunofluorescence-based antigen detection, the multiplex assay yielded higher detection rates for all viruses represented in the assay. The turnaround time for performance of the assay was markedly reduced compared to those for the other techniques used to identify these viruses. More than 21,000 tests have been performed using the assay. Overall, the multiplex PCR enabled the detection of substantially increased numbers of herpesviruses, in some cases in specimens or anatomical sites where previously they were rarely if ever identified using traditional detection methods. PMID:11980951

  17. Smoking, season, and detection of chlamydia pneumoniae DNA in clinically stable COPD patients

    Directory of Open Access Journals (Sweden)

    Goldsmith Charles H

    2002-07-01

    Full Text Available Abstract Background The prevalence and role of Chlamydia pneumoniae in chronic obstructive pulmonary disease (COPD remain unclear. Methods Peripheral blood mononuclear cells were obtained from 100 outpatients with smoking-related, clinically stable COPD, and induced sputum was obtained in 62 patients. Results Patients had mean age (standard deviation of 65.8 (10.7 years, mean forced expiratory volume in one second of 1.34 (0.61 L, and 61 (61.0% were male. C. pneumoniae nucleic acids were detected by nested polymerase chain reaction in 27 (27.0%. Current smoking (odds ratio {OR} = 2.6, 95% confidence interval {CI}: 1.1, 6.6, P = 0.04, season (November to April (OR = 3.6, 95% CI: 1.4, 9.2, P = 0.007, and chronic sputum production (OR = 6.4, 95% CI: 1.8, 23.2, P = 0.005 were associated with detection of C. pneumoniae DNA. Conclusions Prospective studies are needed to examine the role of C. pneumoniae nucleic acid detection in COPD disease symptoms and progression.

  18. Clinical phenotype associations with various types of anti-dsDNA antibodies in patients with recent onset of rheumatic symptoms. Results from a multicentre observational study

    DEFF Research Database (Denmark)

    Compagno, Michele; Rekvig, Ole P; Bengtsson, Anders A

    2014-01-01

    UNLABELLED: Despite anti-dsDNA antibodies constitute a wide range of specificities, they are considered as the hallmark for systemic lupus erythematosus (SLE). OBJECTIVE: To identify clinical phenotypes associated with anti-dsDNA antibodies, independently of any clinical diagnoses. METHODS...

  19. Non-parametric comparison of histogrammed two-dimensional data distributions using the Energy Test

    International Nuclear Information System (INIS)

    Reid, Ivan D; Lopes, Raul H C; Hobson, Peter R

    2012-01-01

    When monitoring complex experiments, comparison is often made between regularly acquired histograms of data and reference histograms which represent the ideal state of the equipment. With the larger HEP experiments now ramping up, there is a need for automation of this task since the volume of comparisons could overwhelm human operators. However, the two-dimensional histogram comparison tools available in ROOT have been noted in the past to exhibit shortcomings. We discuss a newer comparison test for two-dimensional histograms, based on the Energy Test of Aslan and Zech, which provides more conclusive discrimination between histograms of data coming from different distributions than methods provided in a recent ROOT release.

  20. Clinical implications of monitoring circulating tumor DNA in patients with colorectal cancer

    DEFF Research Database (Denmark)

    Schøler, Lone V; Reinert, Thomas; Ørntoft, Mai-Britt W

    2017-01-01

    .007). Changes in ctDNA levels induced by relapse intervention (n = 19) showed good agreement with changes in tumor volume (κ = 0.41; Spearman ρ = 0.4).Conclusions: Postoperative ctDNA detection provides evidence of residual disease and identifies patients at very high risk of relapse. Longitudinal surveillance...

  1. Feasibility of using microbeads with holographic barcodes to track DNA specimens in the clinical molecular laboratory

    Directory of Open Access Journals (Sweden)

    Jason D. Merker

    2013-07-01

    Full Text Available We demonstrate the feasibility of using glass microbeads with a holographic barcode identifier to track DNA specimens in the molecular pathology laboratory. These beads can be added to peripheral blood specimens and are carried through automated DNA extraction protocols that use magnetic glass particles. We found that an adequate number of microbeads are consistently carried over during genomic DNA extraction to allow specimen identification, that the beads do not interfere with the performance of several different molecular assays, and that the beads and genomic DNA remain stable when stored together under regular storage conditions in the molecular pathology laboratory. The beads function as an internal, easily readable specimen barcode. This approach may be useful for identifying DNA specimens and reducing errors associated with molecular laboratory testing.

  2. Histogram analysis of diffusion kurtosis imaging estimates for in vivo assessment of 2016 WHO glioma grades: A cross-sectional observational study.

    Science.gov (United States)

    Hempel, Johann-Martin; Schittenhelm, Jens; Brendle, Cornelia; Bender, Benjamin; Bier, Georg; Skardelly, Marco; Tabatabai, Ghazaleh; Castaneda Vega, Salvador; Ernemann, Ulrike; Klose, Uwe

    2017-10-01

    To assess the diagnostic performance of histogram analysis of diffusion kurtosis imaging (DKI) maps for in vivo assessment of the 2016 World Health Organization Classification of Tumors of the Central Nervous System (2016 CNS WHO) integrated glioma grades. Seventy-seven patients with histopathologically-confirmed glioma who provided written informed consent were retrospectively assessed between 01/2014 and 03/2017 from a prospective trial approved by the local institutional review board. Ten histogram parameters of mean kurtosis (MK) and mean diffusivity (MD) metrics from DKI were independently assessed by two blinded physicians from a volume of interest around the entire solid tumor. One-way ANOVA was used to compare MK and MD histogram parameter values between 2016 CNS WHO-based tumor grades. Receiver operating characteristic analysis was performed on MK and MD histogram parameters for significant results. The 25th, 50th, 75th, and 90th percentiles of MK and average MK showed significant differences between IDH1/2 wild-type gliomas, IDH1/2 mutated gliomas, and oligodendrogliomas with chromosome 1p/19q loss of heterozygosity and IDH1/2 mutation (pHistogram analysis of DKI can stratify gliomas according to the integrated approach of 2016 CNS WHO. The 50th (median), 75th , and the 90th percentiles showed the highest diagnostic performance. However, the average MK is also robust and feasible in routine clinical practice. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Comparison of real-time and quantitative polymerase chain reaction assays in detection of cytomegalovirus DNA in clinical specimens

    International Nuclear Information System (INIS)

    Gokahmetoglu, S.; Deniz, E.

    2007-01-01

    To compare the real-time (RT) and qualitative (Q) polymerase chain reaction (PCR) assays for detection of Cytomegalovirus (CMV) DNA. The study took place in the Department of Microbiology, Erciyes University, Kayseri and in Iontek Laboratory, Istanbul, Turkey, from August to December 2006. One hundred and seven clinical specimens from 67 patients were included in the study. Cytomegalovirus DNA was investigated using RT-PCR kit (Fluorion Iontek, Turkey) and Q-PCR kit (Fluorion Iontek, Turkey). Deoxyribonucleic acid sequencing was applied to the samples that yielded discrepant results in both assays. Mac Nema's Chi Square test was used for statistical analysis. Of the specimens, 27 were found positive with both assays: 9 with only RT-PCR, and 11 with only Q-PCR assay. Both assays were found negative in 60 of the specimens. There was a good agreement between the 2 assays in 87(81.3%) of the specimens. There was no statistical significant difference between the assays (p>0.05). Two of the 11 samples that RT-PCR negative Q-PCR positive, and 3 of 9 samples that RT-PCR positive Q-PCR negative were found to be CMV DNA positive by DNA sequencing. A good level of concordance between RT-PCR and Q-PCR assays for CMV DNA detection has been found. (author)

  4. The relationship between increased levels of Anti-dsDNA with clinical manifestation in patients with SLE in Haji Adam Malik General Hospital Medan

    Science.gov (United States)

    Marpaung, B.; Patrick, J.

    2018-03-01

    Systemic Lupus Erythematosus (SLE) is an autoimmune rheumatic disease characterized by widespread inflammation and affects any organism the body. Many autoimmune diseases result in autoantibody production, but Anti-dsDNA antibodies are highly specific to SLE. Previous study found that Anti-dsDNA antibodies are associated with severe clinical manifestations of lupus. The aim of this study was to examine the relationship between anti-dsDNA level with clinical features and laboratory findings in SLE patients. This cross-sectional study was conducted in Hospital Haji Adam Malik Medan in May-October 2016.We examine anti-dsDNA, clinical features and kidney laboratory profile in all patient. Data were statistically analyzed.81 SLE patients with median level of anti-dsDNA 294 (6.1-1317). There was no significant relationship between increased level of Anti-dsDNA with clinical manifestations (p>0.05). There were significant relationships between increased level of Anti-dsDNA with renal impairment (p=0.049), urea level (p=0.016), urine protein (p=0.042) and hematology disorder (p=0.005). Arthritis is the most frequent clinical manifestation (96.3%) followed by malar rash (77.8%). Elevated anti-dsDNA level was not related with clinical manifestations but there was significant relationship with hematology disorder, urea, creatinine, and proteinuria in SLE patents.

  5. Sensitivity of volumetric modulated arc therapy patient specific QA results to multileaf collimator errors and correlation to dose volume histogram based metrics.

    LENUS (Irish Health Repository)

    Coleman, Linda

    2013-11-01

    This study investigates the impact of systematic multileaf collimator (MLC) positional errors on gamma analysis results used for quality assurance (QA) of Rapidarc treatments. In addition, this study evaluates the relationship of these gamma analysis results and clinical dose volume histogram metrics (DVH) for Rapidarc treatment plans.

  6. Bin Ratio-Based Histogram Distances and Their Application to Image Classification.

    Science.gov (United States)

    Hu, Weiming; Xie, Nianhua; Hu, Ruiguang; Ling, Haibin; Chen, Qiang; Yan, Shuicheng; Maybank, Stephen

    2014-12-01

    Large variations in image background may cause partial matching and normalization problems for histogram-based representations, i.e., the histograms of the same category may have bins which are significantly different, and normalization may produce large changes in the differences between corresponding bins. In this paper, we deal with this problem by using the ratios between bin values of histograms, rather than bin values' differences which are used in the traditional histogram distances. We propose a bin ratio-based histogram distance (BRD), which is an intra-cross-bin distance, in contrast with previous bin-to-bin distances and cross-bin distances. The BRD is robust to partial matching and histogram normalization, and captures correlations between bins with only a linear computational complexity. We combine the BRD with the ℓ1 histogram distance and the χ(2) histogram distance to generate the ℓ1 BRD and the χ(2) BRD, respectively. These combinations exploit and benefit from the robustness of the BRD under partial matching and the robustness of the ℓ1 and χ(2) distances to small noise. We propose a method for assessing the robustness of histogram distances to partial matching. The BRDs and logistic regression-based histogram fusion are applied to image classification. The experimental results on synthetic data sets show the robustness of the BRDs to partial matching, and the experiments on seven benchmark data sets demonstrate promising results of the BRDs for image classification.

  7. A Comparative Study for Detection of EGFR Mutations in Plasma Cell-Free DNA in Korean Clinical Diagnostic Laboratories

    Directory of Open Access Journals (Sweden)

    Yoonjung Kim

    2018-01-01

    Full Text Available Liquid biopsies to genotype the epidermal growth factor receptor (EGFR for targeted therapy have been implemented in clinical decision-making in the field of lung cancer, but harmonization of detection methods is still scarce among clinical laboratories. We performed a pilot external quality assurance (EQA scheme to harmonize circulating tumor DNA testing among laboratories. For EQA, we created materials containing different levels of spiked cell-free DNA (cfDNA in normal plasma. The limit of detection (LOD of the cobas® EGFR Mutation Test v2 (Roche Molecular Systems was also evaluated. From November 2016 to June 2017, seven clinical diagnostic laboratories participated in the EQA program. The majority (98.94% of results obtained using the cobas assay and next-generation sequencing (NGS were acceptable. Quantitative results from the cobas assay were positively correlated with allele frequencies derived from digital droplet PCR measurements and showed good reproducibility among laboratories. The LOD of the cobas assay was 5~27 copies/mL for p.E746_A750del (exon 19 deletion, 35~70 copies/mL for p.L858R, 18~36 copies/mL for p.T790M, and 15~31 copies/mL for p.A767_V769dup (exon 20 insertion. Deep sequencing of materials (>100,000X depth of coverage resulted in detection of low-level targets present at frequencies of 0.06~0.13%. Our results indicate that the cobas assay is a reliable and rapid method for detecting EGFR mutations in plasma cfDNA. Careful interpretation is particularly important for p.T790M detection in the setting of relapse. Individual laboratories should optimize NGS performance to maximize clinical utility.

  8. Histogram specification as a method of density modification

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, R.W.

    1988-12-01

    A new method for improving the quality and extending the resolution of Fourier maps is described. The method is based on a histogram analysis of the electron density. The distribution of electron density values in the map is forced to be 'ideal'. The 'ideal' distribution is assumed to be Gaussian. The application of the method to improve the electron density map for the protein Acinetobacter asparaginase, which is a tetrameric enzyme of molecular weight 140000 daltons, is described.

  9. Histogram Modification and Wavelet Transform for High Performance Watermarking

    Directory of Open Access Journals (Sweden)

    Ying-Shen Juang

    2012-01-01

    Full Text Available This paper proposes a reversible watermarking technique for natural images. According to the similarity of neighbor coefficients’ values in wavelet domain, most differences between two adjacent pixels are close to zero. The histogram is built based on these difference statistics. As more peak points can be used for secret data hiding, the hiding capacity is improved compared with those conventional methods. Moreover, as the differences concentricity around zero is improved, the transparency of the host image can be increased. Experimental results and comparison show that the proposed method has both advantages in hiding capacity and transparency.

  10. High capacity, high speed histogramming data acquisition memory

    International Nuclear Information System (INIS)

    Epstein, A.; Boulin, C.

    1996-01-01

    A double width CAMAC DRAM store module was developed for use as a histogramming memory in fast time-resolved synchrotron radiation applications to molecular biology. High speed direct memory modify (3 MHz) is accomplished by using a discrete DRAM controller and fast page mode access. The module can be configured using standard SIMMs to sizes of up to 64M-words. The word width is 16 bit and the module can handle overflows by storing the overflow addresses in a dedicated FIFO. Simultaneous front panel DMM/DMI access and CAMAC readout of the overflow addresses is supported

  11. WASP (Write a Scientific Paper) using Excel - 4: Histograms.

    Science.gov (United States)

    Grech, Victor

    2018-02-01

    Plotting data into graphs is a crucial step in data analysis as part of an initial descriptive statistics exercise since it gives the researcher an overview of the shape and nature of the data. Outlier values may also be identified, and these may be incorrect data, or true and important outliers. This paper explains how to access Microsoft Excel's Analysis Toolpak and provides some pointers for the utilisation of the histogram tool within the Toolpak. Copyright © 2018. Published by Elsevier B.V.

  12. Text-Independent Speaker Identification Using the Histogram Transform Model

    DEFF Research Database (Denmark)

    Ma, Zhanyu; Yu, Hong; Tan, Zheng-Hua

    2016-01-01

    In this paper, we propose a novel probabilistic method for the task of text-independent speaker identification (SI). In order to capture the dynamic information during SI, we design a super-MFCCs features by cascading three neighboring Mel-frequency Cepstral coefficients (MFCCs) frames together....... These super-MFCC vectors are utilized for probabilistic model training such that the speaker’s characteristics can be sufficiently captured. The probability density function (PDF) of the aforementioned super-MFCCs features is estimated by the recently proposed histogram transform (HT) method. To recedes...

  13. Prevention of DNA contamination during forensic medical examinations in a clinical forensic medical service: A best practice implementation project.

    Science.gov (United States)

    Lutz, Tasha

    2015-01-01

    Contamination of forensic specimens can have significant and detrimental effects on cases presented in court. In 2010 a wrongful conviction in Australia resulted in an inquiry with 25 recommendations to minimize the risk of DNA contamination of forensic specimens. DNA decontamination practices in a clinical forensic medical service currently attempt to comply with these recommendations. Evaluation of these practices has not been undertaken. The aim of this project was to audit the current DNA decontamination practices of forensic medical and nursing examiners in the forensic medical examination process and implement changes based on the audit findings. A re-audit following implementation would be undertaken to identify change and inform further research. The Joanna Briggs Institute's Practical Application of Clinical Evidence System and Getting Research into Practice were used as the audit tool in this project. A baseline audit was conducted; analysis of this audit process was then undertaken. Following education and awareness training targeted at clinicians, a re-audit was completed. There were a total of 24 audit criteria; the baseline audit reflected 20 of these criteria had 100% compliance. The remaining 4 audit criteria demonstrated compliance between 65% and 90%. Education and awareness training resulted in improved compliance in 2 of the 4 audit criteria, with the remaining 2 having unchanged compliance. The findings demonstrated that education and raising awareness can improve clinical practice; however there are also external factors outside the control of the clinicians that influence compliance with best practice.

  14. SU-C-207A-07: Cumulative 18F-FDG Uptake Histogram Relative to Radiation Dose Volume Histogram of Lung After IMRT Or PSPT and Their Association with Radiation Pneumonitis

    International Nuclear Information System (INIS)

    Shusharina, N; Choi, N; Bortfeld, T; Liao, Z; Mohan, R

    2016-01-01

    Purpose: To determine whether the difference in cumulative 18F-FDG uptake histogram of lung treated with either IMRT or PSPT is associated with radiation pneumonitis (RP) in patients with inoperable stage II and III NSCLC. Methods: We analyzed 24 patients from a prospective randomized trial to compare IMRT (n=12) with vs. PSPT (n=12) for inoperable NSCLC. All patients underwent PET-CT imaging between 35 and 88 days post-therapy. Post-treatment PET-CT was aligned with planning 4D CT to establish a voxel-to-voxel correspondence between post-treatment PET and planning dose images. 18F-FDG uptake as a function of radiation dose to normal lung was obtained for each patient. Distribution of the standard uptake value (SUV) was analyzed using a volume histogram method. The image quantitative characteristics and DVH measures were correlated with clinical symptoms of pneumonitis. Results: Patients with RP were present in both groups: 5 in the IMRT and 6 in the PSPT. The analysis of cumulative SUV histograms showed significantly higher relative volumes of the normal lung having higher SUV uptake in the PSPT patients for both symptomatic and asymptomatic cases (VSUV=2: 10% for IMRT vs 16% for proton RT and VSUV=1: 10% for IMRT vs 23% for proton RT). In addition, the SUV histograms for symptomatic cases in PSPT patients exhibited a significantly longer tail at the highest SUV. The absolute volume of the lung receiving the dose >70 Gy was larger in the PSPT patients. Conclusion: 18F-FDG uptake – radiation dose response correlates with RP in both groups of patients by means of the linear regression slope. SUV is higher for the PSPT patients for both symptomatic and asymptomatic cases. Higher uptake after PSPT patients is explained by larger volumes of the lung receiving high radiation dose.

  15. Differentially Private Event Histogram Publication on Sequences over Graphs

    Institute of Scientific and Technical Information of China (English)

    Ning Wang; Yu Gu; Jia Xu; Fang-Fang Li; Ge Yu

    2017-01-01

    The big data era is coming with strong and ever-growing demands on analyzing personal information and footprints in the cyber world. To enable such analysis without privacy leak risk, differential privacy (DP) has been quickly rising in recent years, as the first practical privacy protection model with rigorous theoretical guarantee. This paper discusses how to publish differentially private histograms on events in time series domain, with sequences of personal events over graphs with events as edges. Such individual-generated sequences commonly appear in formalized industrial workflows, online game logs, and spatial-temporal trajectories. Directly publishing the statistics of sequences may compromise personal privacy. While existing DP mechanisms mainly target at normalized domains with fixed and aligned dimensions, our problem raises new challenges when the sequences could follow arbitrary paths on the graph. To tackle the problem, we reformulate the problem with a three-step framework, which 1) carefully truncates the original sequences, trading off errors introduced by the truncation with those introduced by the noise added to guarantee privacy, 2) decomposes the event graph into path sub-domains based on a group of event pivots, and 3) employs a deeply optimized tree-based histogram construction approach for each sub-domain to benefit with less noise addition. We present a careful analysis on our framework to support thorough optimizations over each step of the framework, and verify the huge improvements of our proposals over state-of-the-art solutions.

  16. Variational Histogram Equalization for Single Color Image Defogging

    Directory of Open Access Journals (Sweden)

    Li Zhou

    2016-01-01

    Full Text Available Foggy images taken in the bad weather inevitably suffer from contrast loss and color distortion. Existing defogging methods merely resort to digging out an accurate scene transmission in ignorance of their unpleasing distortion and high complexity. Different from previous works, we propose a simple but powerful method based on histogram equalization and the physical degradation model. By revising two constraints in a variational histogram equalization framework, the intensity component of a fog-free image can be estimated in HSI color space, since the airlight is inferred through a color attenuation prior in advance. To cut down the time consumption, a general variation filter is proposed to obtain a numerical solution from the revised framework. After getting the estimated intensity component, it is easy to infer the saturation component from the physical degradation model in saturation channel. Accordingly, the fog-free image can be restored with the estimated intensity and saturation components. In the end, the proposed method is tested on several foggy images and assessed by two no-reference indexes. Experimental results reveal that our method is relatively superior to three groups of relevant and state-of-the-art defogging methods.

  17. Visual Contrast Enhancement Algorithm Based on Histogram Equalization

    Directory of Open Access Journals (Sweden)

    Chih-Chung Ting

    2015-07-01

    Full Text Available Image enhancement techniques primarily improve the contrast of an image to lend it a better appearance. One of the popular enhancement methods is histogram equalization (HE because of its simplicity and effectiveness. However, it is rarely applied to consumer electronics products because it can cause excessive contrast enhancement and feature loss problems. These problems make the images processed by HE look unnatural and introduce unwanted artifacts in them. In this study, a visual contrast enhancement algorithm (VCEA based on HE is proposed. VCEA considers the requirements of the human visual perception in order to address the drawbacks of HE. It effectively solves the excessive contrast enhancement problem by adjusting the spaces between two adjacent gray values of the HE histogram. In addition, VCEA reduces the effects of the feature loss problem by using the obtained spaces. Furthermore, VCEA enhances the detailed textures of an image to generate an enhanced image with better visual quality. Experimental results show that images obtained by applying VCEA have higher contrast and are more suited to human visual perception than those processed by HE and other HE-based methods.

  18. Visual Contrast Enhancement Algorithm Based on Histogram Equalization

    Science.gov (United States)

    Ting, Chih-Chung; Wu, Bing-Fei; Chung, Meng-Liang; Chiu, Chung-Cheng; Wu, Ya-Ching

    2015-01-01

    Image enhancement techniques primarily improve the contrast of an image to lend it a better appearance. One of the popular enhancement methods is histogram equalization (HE) because of its simplicity and effectiveness. However, it is rarely applied to consumer electronics products because it can cause excessive contrast enhancement and feature loss problems. These problems make the images processed by HE look unnatural and introduce unwanted artifacts in them. In this study, a visual contrast enhancement algorithm (VCEA) based on HE is proposed. VCEA considers the requirements of the human visual perception in order to address the drawbacks of HE. It effectively solves the excessive contrast enhancement problem by adjusting the spaces between two adjacent gray values of the HE histogram. In addition, VCEA reduces the effects of the feature loss problem by using the obtained spaces. Furthermore, VCEA enhances the detailed textures of an image to generate an enhanced image with better visual quality. Experimental results show that images obtained by applying VCEA have higher contrast and are more suited to human visual perception than those processed by HE and other HE-based methods. PMID:26184219

  19. Accelerated weight histogram method for exploring free energy landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Lindahl, V.; Lidmar, J.; Hess, B. [Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm (Sweden)

    2014-07-28

    Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

  20. Image compression using moving average histogram and RBF network

    International Nuclear Information System (INIS)

    Khowaja, S.; Ismaili, I.A.

    2015-01-01

    Modernization and Globalization have made the multimedia technology as one of the fastest growing field in recent times but optimal use of bandwidth and storage has been one of the topics which attract the research community to work on. Considering that images have a lion share in multimedia communication, efficient image compression technique has become the basic need for optimal use of bandwidth and space. This paper proposes a novel method for image compression based on fusion of moving average histogram and RBF (Radial Basis Function). Proposed technique employs the concept of reducing color intensity levels using moving average histogram technique followed by the correction of color intensity levels using RBF networks at reconstruction phase. Existing methods have used low resolution images for the testing purpose but the proposed method has been tested on various image resolutions to have a clear assessment of the said technique. The proposed method have been tested on 35 images with varying resolution and have been compared with the existing algorithms in terms of CR (Compression Ratio), MSE (Mean Square Error), PSNR (Peak Signal to Noise Ratio), computational complexity. The outcome shows that the proposed methodology is a better trade off technique in terms of compression ratio, PSNR which determines the quality of the image and computational complexity. (author)

  1. Stochastic Learning of Multi-Instance Dictionary for Earth Mover's Distance based Histogram Comparison

    OpenAIRE

    Fan, Jihong; Liang, Ru-Ze

    2016-01-01

    Dictionary plays an important role in multi-instance data representation. It maps bags of instances to histograms. Earth mover's distance (EMD) is the most effective histogram distance metric for the application of multi-instance retrieval. However, up to now, there is no existing multi-instance dictionary learning methods designed for EMD based histogram comparison. To fill this gap, we develop the first EMD-optimal dictionary learning method using stochastic optimization method. In the stoc...

  2. DNA methylation signatures for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer

    DEFF Research Database (Denmark)

    Haldrup, Christa; Mundbjerg, Kamilla; Vestergaard, Else Marie

    2013-01-01

    Purpose Diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, causing overtreatment of indolent PC and risk of delayed treatment of aggressive PC. Here, we identify six novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential. Methods...... Microarray-based screening and bisulfite sequencing of 20 nonmalignant and 29 PC tissue specimens were used to identify new candidate DNA hypermethylation markers for PC. Diagnostic and prognostic potential was evaluated in 35 nonmalignant prostate tissue samples, 293 radical prostatectomy (RP) samples...... into low- and high-methylation subgroups, was trained in cohort 1 (HR, 1.91; 95% CI, 1.26 to 2.90) and validated in cohort 2 (HR, 2.33; 95% CI, 1.31 to 4.13). Conclusion We identified six novel candidate DNA methylation markers for PC. C1orf114 hypermethylation and a three-gene methylation signature were...

  3. DNA methylation patterns of genes related to immune response in the different clinical forms of oral lichen planus.

    Science.gov (United States)

    Cruz, Aline Fernanda; de Resende, Renata Gonçalves; de Lacerda, Júlio César Tanos; Pereira, Núbia Braga; Melo, Leonardo Augusto; Diniz, Marina Gonçalves; Gomes, Carolina Cavalieri; Gomez, Ricardo Santiago

    2018-01-01

    The oral lichen planus is a chronic inflammatory disease. Although its aetiology is not well understood, the role of T lymphocytes in its inflammatory events is recognised. Identifying the epigenetic mechanisms involved in the pathogenesis of this immune-mediated condition is fundamental for understanding the inflammatory reaction that occurs in the disease. The purpose of this work was to evaluate the methylation pattern of 21 immune response-related genes in the different clinical forms of oral lichen planus. A cross-sectional study was performed to analyse the DNA methylation patterns in three distinct groups of oral lichen planus: (i) reticular/plaque lesions; (ii) erosive lesions; (iii) normal oral mucosa (control group). After DNA extraction from biopsies, the samples were submitted to digestions by methylation-sensitive and methylation-dependent enzymes and double digestion. The relative percentage of methylated DNA for each gene was provided using real-time polymerase chain reaction arrays. Hypermethylation of the STAT5A gene was observed only in the control group (59.0%). A higher hypermethylation of the ELANE gene was found in reticular/plaque lesions (72.1%) compared to the erosive lesions (50.0%). Our results show variations in the methylation profile of immune response-related genes, according to the clinical type of oral lichen planus after comparing with the normal oral mucosa. Further studies are necessary to validate these findings using gene expression analysis. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Using histograms to introduce randomization in the generation of ensembles of decision trees

    Science.gov (United States)

    Kamath, Chandrika; Cantu-Paz, Erick; Littau, David

    2005-02-22

    A system for decision tree ensembles that includes a module to read the data, a module to create a histogram, a module to evaluate a potential split according to some criterion using the histogram, a module to select a split point randomly in an interval around the best split, a module to split the data, and a module to combine multiple decision trees in ensembles. The decision tree method includes the steps of reading the data; creating a histogram; evaluating a potential split according to some criterion using the histogram, selecting a split point randomly in an interval around the best split, splitting the data, and combining multiple decision trees in ensembles.

  5. Ternary monolayers as DNA recognition interfaces for direct and sensitive electrochemical detection in untreated clinical samples

    Czech Academy of Sciences Publication Activity Database

    Campuzano, S.; Kuralay, F.; Lobo-Castanón, M.J.; Bartošík, Martin; Vyavahare, K.; Paleček, Emil; Haake, D.A.; Wang, J.

    2011-01-01

    Roč. 26, č. 8 (2011), s. 3577-3583 ISSN 0956-5663 R&D Projects: GA MŠk(CZ) ME09038 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : electrochemical detection * DNA hybridization * self-assembled monolayer Subject RIV: BO - Biophysics Impact factor: 5.602, year: 2011

  6. Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women’s Cancers

    Science.gov (United States)

    Bartlett, Thomas E.; Jones, Allison; Goode, Ellen L.; Fridley, Brooke L.; Cunningham, Julie M.; Berns, Els M. J. J.; Wik, Elisabeth; Salvesen, Helga B.; Davidson, Ben; Trope, Claes G.; Lambrechts, Sandrina; Vergote, Ignace; Widschwendter, Martin

    2015-01-01

    We introduce a novel per-gene measure of intra-gene DNA methylation variability (IGV) based on the Illumina Infinium HumanMethylation450 platform, which is prognostic independently of well-known predictors of clinical outcome. Using IGV, we derive a robust gene-panel prognostic signature for ovarian cancer (OC, n = 221), which validates in two independent data sets from Mayo Clinic (n = 198) and TCGA (n = 358), with significance of p = 0.004 in both sets. The OC prognostic signature gene-panel is comprised of four gene groups, which represent distinct biological processes. We show the IGV measurements of these gene groups are most likely a reflection of a mixture of intra-tumour heterogeneity and transcription factor (TF) binding/activity. IGV can be used to predict clinical outcome in patients individually, providing a surrogate read-out of hard-to-measure disease processes. PMID:26629914

  7. Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

    Directory of Open Access Journals (Sweden)

    Nelson Laura D

    2012-06-01

    Full Text Available Abstract Background Tri- and tetra-nucleotide repeats in mammalian genomes can induce formation of alternative non-B DNA structures such as triplexes and guanine (G-quadruplexes. These structures can induce mutagenesis, chromosomal translocations and genomic instability. We wanted to determine if proteins that bind triplex DNA structures are quantitatively or qualitatively different between colorectal tumor and adjacent normal tissue and if this binding activity correlates with patient clinical characteristics. Methods Extracts from 63 human colorectal tumor and adjacent normal tissues were examined by gel shifts (EMSA for triplex DNA-binding proteins, which were correlated with clinicopathological tumor characteristics using the Mann-Whitney U, Spearman’s rho, Kaplan-Meier and Mantel-Cox log-rank tests. Biotinylated triplex DNA and streptavidin agarose affinity binding were used to purify triplex-binding proteins in RKO cells. Western blotting and reverse-phase protein array were used to measure protein expression in tissue extracts. Results Increased triplex DNA-binding activity in tumor extracts correlated significantly with lymphatic disease, metastasis, and reduced overall survival. We identified three multifunctional splicing factors with biotinylated triplex DNA affinity: U2AF65 in cytoplasmic extracts, and PSF and p54nrb in nuclear extracts. Super-shift EMSA with anti-U2AF65 antibodies produced a shifted band of the major EMSA H3 complex, identifying U2AF65 as the protein present in the major EMSA band. U2AF65 expression correlated significantly with EMSA H3 values in all extracts and was higher in extracts from Stage III/IV vs. Stage I/II colon tumors (p = 0.024. EMSA H3 values and U2AF65 expression also correlated significantly with GSK3 beta, beta-catenin, and NF- B p65 expression, whereas p54nrb and PSF expression correlated with c-Myc, cyclin D1, and CDK4. EMSA values and expression of all three splicing factors correlated

  8. TOP-DRAWER, Histograms, Scatterplots, Curve-Smoothing

    International Nuclear Information System (INIS)

    Chaffee, R.B.

    1988-01-01

    Description of program or function: TOP DRAWER produces histograms, scatterplots, data points with error bars and plots symbols, and curves passing through data points, with elaborate titles. It also does smoothing and calculates frequency distributions. There is little facility, however, for arithmetic manipulation. Because of its restricted applicability, TOP DRAWER can be controlled by a relatively simple set of commands, and this control is further simplified by the choice of reasonable default values for all parameters. Despite this emphasis on simplicity, TOP DRAWER plots are of exceptional quality and are suitable for publication. Input is normally from card-image records, although a set of subroutines is provided to accommodate FORTRAN calls. The program contains switches which can be set to generate code suitable for execution on IBM, DECX VAX, and PRIME computers

  9. Steam leak detection method in pipeline using histogram analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Se Oh; Jeon, Hyeong Seop; Son, Ki Sung; Chae, Gyung Sun [Saean Engineering Corp, Seoul (Korea, Republic of); Park, Jong Won [Dept. of Information Communications Engineering, Chungnam NationalUnversity, Daejeon (Korea, Republic of)

    2015-10-15

    Leak detection in a pipeline usually involves acoustic emission sensors such as contact type sensors. These contact type sensors pose difficulties for installation and cannot operate in areas having high temperature and radiation. Therefore, recently, many researchers have studied the leak detection phenomenon by using a camera. Leak detection by using a camera has the advantages of long distance monitoring and wide area surveillance. However, the conventional leak detection method by using difference images often mistakes the vibration of a structure for a leak. In this paper, we propose a method for steam leakage detection by using the moving average of difference images and histogram analysis. The proposed method can separate the leakage and the vibration of a structure. The working performance of the proposed method is verified by comparing with experimental results.

  10. Histogram plots and cutoff energies for nuclear discrete levels

    International Nuclear Information System (INIS)

    Belgya, T.; Molnar, G.; Fazekas, B.; Oestoer, J.

    1997-05-01

    Discrete level schemes for 1277 nuclei, from 6 Li through 251 Es, extracted from the Evaluated Nuclear Structure Data File were analyzed. Cutoff energies (U max ), indicating the upper limit of level scheme completeness, were deduced from the inspection of histograms of the cumulative number of levels. Parameters of the constant-temperature level density formula (nuclear temperature T and energy shift U 0 ) were obtained by means of the least square fit of the formula to the known levels below cutoff energy. The results are tabulated for all 1277 nuclei allowing for an easy and reliable application of the constant-temperature level density approach. A complete set of cumulative plots of discrete levels is also provided. (author). 5 figs, 2 tabs

  11. TSimpleAnalysis: histogramming many trees in parallel

    CERN Document Server

    Giommi, Luca

    2016-01-01

    I worked inside the ROOT team of EP-SFT group. My project focuses on writing a ROOT class that has the aim of creating histograms from a TChain. The name of the class is TSimpleAnalysis and it is already integrated in ROOT. The work that I have done was to write the source, the header le of the class and also a python script, that allows to the user to use the class through the command line. This represents a great improvement respect to the usual user code that counts lines and lines of code to do the same thing. (Link for the class: https://root.cern.ch/doc/master/classTSimpleAnalysis.html)

  12. Fast Graph Partitioning Active Contours for Image Segmentation Using Histograms

    Directory of Open Access Journals (Sweden)

    Nath SumitK

    2009-01-01

    Full Text Available Abstract We present a method to improve the accuracy and speed, as well as significantly reduce the memory requirements, for the recently proposed Graph Partitioning Active Contours (GPACs algorithm for image segmentation in the work of Sumengen and Manjunath (2006. Instead of computing an approximate but still expensive dissimilarity matrix of quadratic size, , for a 2D image of size and regular image tiles of size , we use fixed length histograms and an intensity-based symmetric-centrosymmetric extensor matrix to jointly compute terms associated with the complete dissimilarity matrix. This computationally efficient reformulation of GPAC using a very small memory footprint offers two distinct advantages over the original implementation. It speeds up convergence of the evolving active contour and seamlessly extends performance of GPAC to multidimensional images.

  13. The effect of energy spectrum change on DNA damage in and out of field in 10-MV clinical photon beams.

    Science.gov (United States)

    Ezzati, A O; Xiao, Y; Sohrabpour, M; Studenski, M T

    2015-01-01

    The aim of this study was to quantify the DNA damage induced in a clinical megavoltage photon beam at various depths in and out of the field. MCNPX was used to simulate 10 × 10 and 20 × 20 cm(2) 10-MV photon beams from a clinical linear accelerator. Photon and electron spectra were collected in a water phantom at depths of 2.5, 12.5 and 22.5 cm on the central axis and at off-axis points out to 10 cm. These spectra were used as an input to a validated microdosimetric Monte Carlo code, MCDS, to calculate the RBE of induced DSB in DNA at points in and out of the primary radiation field at three depths. There was an observable difference in the energy spectra for photons and electrons for points in the primary radiation field and those points out of field. In the out-of-field region, the mean energy for the photon and electron spectra decreased by a factor of about six and three from the in-field mean energy, respectively. Despite the differences in spectra and mean energy, the change in RBE was photon and electron spectra, these changes do not correlate with a change in RBE in a clinical MV photon beam as the electron spectra are dominated by electrons with energies >20 keV.

  14. DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights

    Directory of Open Access Journals (Sweden)

    Soledad Gómez

    2015-09-01

    We have analyzed the DNA methylome of neuroblastoma using high-density microarrays (Infinium Human Methylation 450k BeadChip to define the epigenetic landscape of this pediatric tumor and its potential clinicopathological impact. Here, we provide the detail of methods and quality control parameters of the microarray data used for the study. Methylation data has been deposited at NCBI Gene Expression Omnibus data repository, accession number GSE54719; superseries record GSE54721.

  15. Inactivation of the DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents.

    Science.gov (United States)

    Esteller, M; Garcia-Foncillas, J; Andion, E; Goodman, S N; Hidalgo, O F; Vanaclocha, V; Baylin, S B; Herman, J G

    2000-11-09

    The DNA-repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) inhibits the killing of tumor cells by alkylating agents. MGMT activity is controlled by a promoter; methylation of the promoter silences the gene in cancer, and the cells no longer produce MGMT. We examined gliomas to determine whether methylation of the MGMT promoter is related to the responsiveness of the tumor to alkylating agents. We analyzed the MGMT promoter in tumor DNA by a methylation-specific polymerase-chain-reaction assay. The gliomas were obtained from patients who had been treated with carmustine (1,3-bis(2-chloroethyl)-1-nitrosourea, or BCNU). The molecular data were correlated with the clinical outcome. The MGMT promoter was methylated in gliomas from 19 of 47 patients (40 percent). This finding was associated with regression of the tumor and prolonged overall and disease-free survival. It was an independent and stronger prognostic factor than age, stage, tumor grade, or performance status. Methylation of the MGMT promoter in gliomas is a useful predictor of the responsiveness of the tumors to alkylating agents.

  16. Symbol recognition via statistical integration of pixel-level constraint histograms: a new descriptor.

    Science.gov (United States)

    Yang, Su

    2005-02-01

    A new descriptor for symbol recognition is proposed. 1) A histogram is constructed for every pixel to figure out the distribution of the constraints among the other pixels. 2) All the histograms are statistically integrated to form a feature vector with fixed dimension. The robustness and invariance were experimentally confirmed.

  17. Hand Vein Images Enhancement Based on Local Gray-level Information Histogram

    Directory of Open Access Journals (Sweden)

    Jun Wang

    2015-06-01

    Full Text Available Based on the Histogram equalization theory, this paper presents a novel concept of histogram to realize the contrast enhancement of hand vein images, avoiding the lost of topological vein structure or importing the fake vein information. Firstly, we propose the concept of gray-level information histogram, the fundamental characteristic of which is that the amplitudes of the components can objectively reflect the contribution of the gray levels and information to the representation of image information. Then, we propose the histogram equalization method that is composed of an automatic histogram separation module and an intensity transformation module, and the histogram separation module is a combination of the proposed prompt multiple threshold procedure and an optimum peak signal-to-noise (PSNR calculation to separate the histogram into small-scale detail, the use of the intensity transformation module can enhance the vein images with vein topological structure and gray information preservation for each generated sub-histogram. Experimental results show that the proposed method can achieve extremely good contrast enhancement effect.

  18. Infrared Contrast Enhancement Through Log-Power Histogram Modification

    NARCIS (Netherlands)

    Toet, A.; Wu, T.

    2015-01-01

    A simple power-logarithm histogram modification operator is proposed to enhance infrared (IR) image contrast. The algorithm combines a logarithm operator that smoothes the input image histogram while retaining the relative ordering of the original bins, with a power operator that restores the

  19. Thresholding using two-dimensional histogram and watershed algorithm in the luggage inspection system

    International Nuclear Information System (INIS)

    Chen Jingyun; Cong Peng; Song Qi

    2006-01-01

    The authors present a new DR image segmentation method based on two-dimensional histogram and watershed algorithm. The authors use watershed algorithm to locate threshold on the vertical projection plane of two-dimensional histogram. This method is applied to the segmentation of DR images produced by luggage inspection system with DR-CT. The advantage of this method is also analyzed. (authors)

  20. Curvature histogram features for retrieval of images of smooth 3D objects

    International Nuclear Information System (INIS)

    Zhdanov, I; Scherbakov, O; Potapov, A; Peterson, M

    2014-01-01

    We consider image features on the base of histograms of oriented gradients (HOG) with addition of contour curvature histogram (HOG-CH), and also compare it with results of known scale-invariant feature transform (SIFT) approach in application to retrieval of images of smooth 3D objects.

  1. Cross-interval histogram analysis of neuronal activity on multi-electrode arrays

    NARCIS (Netherlands)

    Castellone, P.; Rutten, Wim; Marani, Enrico

    2003-01-01

    Cross-neuron-interval histogram (CNIH) analysis has been performed in order to study correlated activity and connectivity between pairs of neurons in a spontaneously active developing cultured network of rat cortical cells. Thirty-eight histograms could be analyzed using two parameters, one for the

  2. Treatment plan evaluation using dose-volume histogram (DVH) and spatial dose-volume histogram (zDVH)

    International Nuclear Information System (INIS)

    Cheng, C.-W.; Das, Indra J.

    1999-01-01

    Objective: The dose-volume histogram (DVH) has been accepted as a tool for treatment-plan evaluation. However, DVH lacks spatial information. A new concept, the z-dependent dose-volume histogram (zDVH), is presented as a supplement to the DVH in three-dimensional (3D) treatment planning to provide the spatial variation, as well as the size and magnitude of the different dose regions within a region of interest. Materials and Methods: Three-dimensional dose calculations were carried out with various plans for three disease sites: lung, breast, and prostate. DVHs were calculated for the entire volume. A zDVH is defined as a differential dose-volume histogram with respect to a computed tomographic (CT) slice position. In this study, zDVHs were calculated for each CT slice in the treatment field. DVHs and zDVHs were compared. Results: In the irradiation of lung, DVH calculation indicated that the treatment plan satisfied the dose-volume constraint placed on the lung and zDVH of the lung revealed that a sizable fraction of the lung centered about the central axis (CAX) received a significant dose, a situation that warranted a modification of the treatment plan due to the removal of one lung. In the irradiation of breast with tangential fields, the DVH showed that about 7% of the breast volume received at least 110% of the prescribed dose (PD) and about 11% of the breast received less than 98% PD. However, the zDVHs of the breast volume in each of seven planes showed the existence of high-dose regions of 34% and 15%, respectively, of the volume in the two caudal-most planes and cold spots of about 40% in the two cephalic planes. In the treatment planning of prostate, DVHs showed that about 15% of the bladder and 40% of the rectum received 102% PD, whereas about 30% of the bladder and 50% of the rectum received the full dose. Taking into account the hollow structure of both the bladder and the rectum, the dose-surface histograms (DSH) showed larger hot-spot volume, about

  3. Neutron stars as X-ray burst sources. II. Burst energy histograms and why they burst

    International Nuclear Information System (INIS)

    Baan, W.A.

    1979-01-01

    In this work we explore some of the implications of a model for X-ray burst sources where bursts are caused by Kruskal-Schwarzschild instabilities at the magnetopause of an accreting and rotating neutron star. A number of simplifying assumptions are made in order to test the model using observed burst-energy histograms for the rapid burster MXB 1730--335. The predicted histograms have a correct general shape, but it appears that other effects are important as well, and that mode competition, for instance, may suppress the histograms at high burst energies. An explanation is ventured for the enhancement in the histogram at the highest burst energies, which produces the bimodal shape in high accretion rate histograms. Quantitative criteria are given for deciding when accreting neutron stars are steady sources or burst sources, and these criteria are tested using the X-ray pulsars

  4. Whole-Lesion Histogram Analysis of Apparent Diffusion Coefficient for the Assessment of Cervical Cancer.

    Science.gov (United States)

    Guan, Yue; Shi, Hua; Chen, Ying; Liu, Song; Li, Weifeng; Jiang, Zhuoran; Wang, Huanhuan; He, Jian; Zhou, Zhengyang; Ge, Yun

    2016-01-01

    The aim of this study was to explore the application of whole-lesion histogram analysis of apparent diffusion coefficient (ADC) values of cervical cancer. A total of 54 women (mean age, 53 years) with cervical cancers underwent 3-T diffusion-weighted imaging with b values of 0 and 800 s/mm prospectively. Whole-lesion histogram analysis of ADC values was performed. Paired sample t test was used to compare differences in ADC histogram parameters between cervical cancers and normal cervical tissues. Receiver operating characteristic curves were constructed to identify the optimal threshold of each parameter. All histogram parameters in this study including ADCmean, ADCmin, ADC10%-ADC90%, mode, skewness, and kurtosis of cervical cancers were significantly lower than those of normal cervical tissues (all P histogram analysis of ADC maps is useful in the assessment of cervical cancer.

  5. Identification of ssDNA aptamers specific to clinical isolates of Streptococcus mutans strains with different cariogenicity.

    Science.gov (United States)

    Cui, Wei; Liu, Jiaojiao; Su, Donghua; Hu, Danyang; Hou, Shuai; Hu, Tongnan; Yang, Jiyong; Luo, Yanping; Xi, Qing; Chu, Bingfeng; Wang, Chenglong

    2016-06-01

    Streptococcus mutans, a Gram-positive facultative anaerobic bacterium, is considered to be a major etiological factor for dental caries. In this study, plaques from dental enamel surfaces of caries-active and caries-free individuals were obtained and cultivated for S. mutans isolation. Morphology examination, biochemical characterization, and polymerase chain reaction were performed to identify S. mutans The cariogenicity of S. mutans strains isolated from clinical specimens was evaluated by testing the acidogenicity, aciduricity, extracellular polysaccharide production, and adhesion ability of the bacteria. Finally, subtractive SELEX (systematic evolution of ligands by exponential enrichment) technology targeting whole intact cells was used to screen for ssDNA aptamers specific to the strains with high cariogenicity. After nine rounds of subtractive SELEX, sufficient pool enrichment was achieved as shown by radioactive isotope analysis. The enriched pool was cloned and sequenced randomly, followed by MEME online and RNA structure software analysis of the sequences. Results from the flow cytometry indicated that aptamers H1, H16, H4, L1, L10, and H19 could discriminate highly cariogenic S. mutans strains from poorly cariogenic strains. Among these, Aptamer H19 had the strongest binding capacity with cariogenic S. mutans strains with a dissociation constant of 69.45 ± 38.53 nM. In conclusion, ssDNA aptamers specific to highly cariogenic clinical S. mutans strains were successfully obtained. These ssDNA aptamers might be used for the early diagnosis and treatment of dental caries. © The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Differentiation of adrenal adenomas from nonadenomas using CT histogram analysis method: A prospective study

    International Nuclear Information System (INIS)

    Halefoglu, Ahmet Mesrur; Bas, Nagihan; Yasar, Ahmet; Basak, Muzaffer

    2010-01-01

    negative pixels yielded high correlation with mean attenuation decreases, both on unenhanced and delayed contrast-enhanced CT. Our sensitivity was 90.9% for the 10% negative pixel percentage threshold compared to 77.2% sensitivity for ≤10 HU mean attenuation threshold for unenhanced CT. Both methods gave a 100% specificity for the diagnosis of adenoma. We also obtained a 37.9% sensitivity for 5% negative pixel threshold and a slightly lower sensitivity of 28.8% for 10% negative pixel threshold compared to the 12.1% sensitivity of ≤10 HU mean attenuation threshold while maintaining 100% specificity for contrast-enhanced CT. Conclusion: The CT histogram analysis is a simple and easily applicable method which provides higher sensitivity than the commonly used 10 HU threshold mean attenuation method of unenhanced CT and can replace it for the diagnosis of an adenoma. But with contrast-enhanced CT, although 100% specificity is being maintained, the sensitivities obtained are very poor for each method and is therefore likely to limit CT histogram analysis to be used as a clinically useful adjunct in the diagnosis of adenoma.

  7. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome.

    Directory of Open Access Journals (Sweden)

    Maribel Forero-Castro

    Full Text Available Identifying additional genetic alterations associated with poor prognosis in acute lymphoblastic leukemia (ALL is still a challenge.To characterize the presence of additional DNA copy number alterations (CNAs in children and adults with ALL by whole-genome oligonucleotide array (aCGH analysis, and to identify their associations with clinical features and outcome. Array-CGH was carried out in 265 newly diagnosed ALLs (142 children and 123 adults. The NimbleGen CGH 12x135K array (Roche was used to analyze genetic gains and losses. CNAs were analyzed with GISTIC and aCGHweb software. Clinical and biological variables were analyzed. Three of the patients showed chromothripsis (cth6, cth14q and cth15q. CNAs were associated with age, phenotype, genetic subtype and overall survival (OS. In the whole cohort of children, the losses on 14q32.33 (p = 0.019 and 15q13.2 (p = 0.04 were related to shorter OS. In the group of children without good- or poor-risk cytogenetics, the gain on 1p36.11 was a prognostic marker independently associated with shorter OS. In adults, the gains on 19q13.2 (p = 0.001 and Xp21.1 (p = 0.029, and the loss of 17p (p = 0.014 were independent markers of poor prognosis with respect to OS. In summary, CNAs are frequent in ALL and are associated with clinical parameters and survival. Genome-wide DNA copy number analysis allows the identification of genetic markers that predict clinical outcome, suggesting that detection of these genetic lesions will be useful in the management of patients newly diagnosed with ALL.

  8. Comparison of manual methods of extracting genomic DNA from dried blood spots collected on different cards: implications for clinical practice.

    Science.gov (United States)

    Molteni, C G; Terranova, L; Zampiero, A; Galeone, C; Principi, N; Esposito, S

    2013-01-01

    Isolating genomic DNA from blood samples is essential when studying the associations between genetic variants and susceptibility to a given clinical condition, or its severity. This study of three extraction techniques and two types of commercially available cards involved 219 children attending our outpatient pediatric clinic for follow-up laboratory tests after they had been hospitalised. An aliquot of venous blood was drawn into plastic tubes without additives and, after several inversions, 80 microL were put on circles of common paper cards and Whatman FTA-treated cards. Three extraction methods were compared: the Qiagen Investigator, Gensolve, and Masterpure. The best method in terms of final DNA yield was Masterpure, which led to a significantly higher yield regardless of the type of card (p less than 0.001), followed by Qiagen Investigator and Gensolve. Masterpure was also the best in terms of price, seemed to be simple and reliable, and required less hands-on time than other techniques. These conclusions support the use of Masterpure in studies that evaluate the associations between genetic variants and the severity or prevalence of infectious diseases.

  9. Clinical Development of a Cytomegalovirus DNA Vaccine: From Product Concept to Pivotal Phase 3 Trial

    Directory of Open Access Journals (Sweden)

    Michele Gerber

    2013-09-01

    Full Text Available 2013 marks a milestone year for plasmid DNA vaccine development as a first-in-class cytomegalovirus (CMV DNA vaccine enters pivotal phase 3 testing. This vaccine consists of two plasmids expressing CMV antigens glycoprotein B (gB and phosphoprotein 65 (pp65 formulated with a CRL1005 poloxamer and benzalkonium chloride (BAK delivery system designed to enhance plasmid expression. The vaccine’s planned initial indication under investigation is for prevention of CMV reactivation in CMV-seropositive (CMV+ recipients of an allogeneic hematopoietic stem cell transplant (HCT. A randomized, double-blind placebo-controlled phase 2 proof-of-concept study provided initial evidence of the safety of this product in CMV+ HCT recipients who underwent immune ablation conditioning regimens. This study revealed a significant reduction in viral load endpoints and increased frequencies of pp65-specific interferon-γ-producing T cells in vaccine recipients compared to placebo recipients. The results of this endpoint-defining trial provided the basis for defining the primary and secondary endpoints of a global phase 3 trial in HCT recipients. A case study is presented here describing the development history of this vaccine from product concept to initiation of the phase 3 trial.

  10. Clinical Development of a Cytomegalovirus DNA Vaccine: From Product Concept to Pivotal Phase 3 Trial.

    Science.gov (United States)

    Smith, Larry R; Wloch, Mary K; Chaplin, Jennifer A; Gerber, Michele; Rolland, Alain P

    2013-09-25

    2013 marks a milestone year for plasmid DNA vaccine development as a first-in-class cytomegalovirus (CMV) DNA vaccine enters pivotal phase 3 testing. This vaccine consists of two plasmids expressing CMV antigens glycoprotein B (gB) and phosphoprotein 65 (pp65) formulated with a CRL1005 poloxamer and benzalkonium chloride (BAK) delivery system designed to enhance plasmid expression. The vaccine's planned initial indication under investigation is for prevention of CMV reactivation in CMV-seropositive (CMV⁺) recipients of an allogeneic hematopoietic stem cell transplant (HCT). A randomized, double-blind placebo-controlled phase 2 proof-of-concept study provided initial evidence of the safety of this product in CMV⁺ HCT recipients who underwent immune ablation conditioning regimens. This study revealed a significant reduction in viral load endpoints and increased frequencies of pp65-specific interferon-γ-producing T cells in vaccine recipients compared to placebo recipients. The results of this endpoint-defining trial provided the basis for defining the primary and secondary endpoints of a global phase 3 trial in HCT recipients. A case study is presented here describing the development history of this vaccine from product concept to initiation of the phase 3 trial.

  11. Stochastic learning of multi-instance dictionary for earth mover’s distance-based histogram comparison

    KAUST Repository

    Fan, Jihong; Liang, Ru-Ze

    2016-01-01

    Dictionary plays an important role in multi-instance data representation. It maps bags of instances to histograms. Earth mover’s distance (EMD) is the most effective histogram distance metric for the application of multi-instance retrieval. However

  12. Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    International Nuclear Information System (INIS)

    Sadi, Al Muktafi; Wang, Dong-Yu; Youngson, Bruce J; Miller, Naomi; Boerner, Scott; Done, Susan J; Leong, Wey L

    2011-01-01

    The ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications. A modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens. Compared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients. We

  13. Clinical risk factors, DNA variants, and the development of type 2 diabetes

    DEFF Research Database (Denmark)

    Lyssenko, Valeriya; Jonsson, Anna Elisabet; Almgren, Peter

    2008-01-01

    Type 2 diabetes mellitus is thought to develop from an interaction between environmental and genetic factors. We examined whether clinical or genetic factors or both could predict progression to diabetes in two prospective cohorts.......Type 2 diabetes mellitus is thought to develop from an interaction between environmental and genetic factors. We examined whether clinical or genetic factors or both could predict progression to diabetes in two prospective cohorts....

  14. Histogram-based ionogram displays and their application to autoscaling

    Science.gov (United States)

    Lynn, Kenneth J. W.

    2018-03-01

    A simple method is described for displaying and auto scaling the basic ionogram parameters foF2 and h'F2 as well as some additional layer parameters from digital ionograms. The technique employed is based on forming frequency and height histograms in each ionogram. This technique has now been applied specifically to ionograms produced by the IPS5D ionosonde developed and operated by the Australian Space Weather Service (SWS). The SWS ionograms are archived in a cleaned format and readily available from the SWS internet site. However, the method is applicable to any ionosonde which produces ionograms in a digital format at a useful signal-to-noise level. The most novel feature of the technique for autoscaling is its simplicity and the avoidance of the mathematical imaging and line fitting techniques often used. The program arose from the necessity to display many days of ionogram output to allow the location of specific types of ionospheric event such as ionospheric storms, travelling ionospheric disturbances and repetitive ionospheric height changes for further investigation and measurement. Examples and applications of the method are given including the removal of sporadic E and spread F.

  15. Efficient Scalable Median Filtering Using Histogram-Based Operations.

    Science.gov (United States)

    Green, Oded

    2018-05-01

    Median filtering is a smoothing technique for noise removal in images. While there are various implementations of median filtering for a single-core CPU, there are few implementations for accelerators and multi-core systems. Many parallel implementations of median filtering use a sorting algorithm for rearranging the values within a filtering window and taking the median of the sorted value. While using sorting algorithms allows for simple parallel implementations, the cost of the sorting becomes prohibitive as the filtering windows grow. This makes such algorithms, sequential and parallel alike, inefficient. In this work, we introduce the first software parallel median filtering that is non-sorting-based. The new algorithm uses efficient histogram-based operations. These reduce the computational requirements of the new algorithm while also accessing the image fewer times. We show an implementation of our algorithm for both the CPU and NVIDIA's CUDA supported graphics processing unit (GPU). The new algorithm is compared with several other leading CPU and GPU implementations. The CPU implementation has near perfect linear scaling with a speedup on a quad-core system. The GPU implementation is several orders of magnitude faster than the other GPU implementations for mid-size median filters. For small kernels, and , comparison-based approaches are preferable as fewer operations are required. Lastly, the new algorithm is open-source and can be found in the OpenCV library.

  16. Landmark Detection in Orbital Images Using Salience Histograms

    Science.gov (United States)

    Wagstaff, Kiri L.; Panetta, Julian; Schorghofer, Norbert; Greeley, Ronald; PendletonHoffer, Mary; bunte, Melissa

    2010-01-01

    NASA's planetary missions have collected, and continue to collect, massive volumes of orbital imagery. The volume is such that it is difficult to manually review all of the data and determine its significance. As a result, images are indexed and searchable by location and date but generally not by their content. A new automated method analyzes images and identifies "landmarks," or visually salient features such as gullies, craters, dust devil tracks, and the like. This technique uses a statistical measure of salience derived from information theory, so it is not associated with any specific landmark type. It identifies regions that are unusual or that stand out from their surroundings, so the resulting landmarks are context-sensitive areas that can be used to recognize the same area when it is encountered again. A machine learning classifier is used to identify the type of each discovered landmark. Using a specified window size, an intensity histogram is computed for each such window within the larger image (sliding the window across the image). Next, a salience map is computed that specifies, for each pixel, the salience of the window centered at that pixel. The salience map is thresholded to identify landmark contours (polygons) using the upper quartile of salience values. Descriptive attributes are extracted for each landmark polygon: size, perimeter, mean intensity, standard deviation of intensity, and shape features derived from an ellipse fit.

  17. Multifractal diffusion entropy analysis: Optimal bin width of probability histograms

    Science.gov (United States)

    Jizba, Petr; Korbel, Jan

    2014-11-01

    In the framework of Multifractal Diffusion Entropy Analysis we propose a method for choosing an optimal bin-width in histograms generated from underlying probability distributions of interest. The method presented uses techniques of Rényi’s entropy and the mean squared error analysis to discuss the conditions under which the error in the multifractal spectrum estimation is minimal. We illustrate the utility of our approach by focusing on a scaling behavior of financial time series. In particular, we analyze the S&P500 stock index as sampled at a daily rate in the time period 1950-2013. In order to demonstrate a strength of the method proposed we compare the multifractal δ-spectrum for various bin-widths and show the robustness of the method, especially for large values of q. For such values, other methods in use, e.g., those based on moment estimation, tend to fail for heavy-tailed data or data with long correlations. Connection between the δ-spectrum and Rényi’s q parameter is also discussed and elucidated on a simple example of multiscale time series.

  18. Using the Bootstrap Method for a Statistical Significance Test of Differences between Summary Histograms

    Science.gov (United States)

    Xu, Kuan-Man

    2006-01-01

    A new method is proposed to compare statistical differences between summary histograms, which are the histograms summed over a large ensemble of individual histograms. It consists of choosing a distance statistic for measuring the difference between summary histograms and using a bootstrap procedure to calculate the statistical significance level. Bootstrapping is an approach to statistical inference that makes few assumptions about the underlying probability distribution that describes the data. Three distance statistics are compared in this study. They are the Euclidean distance, the Jeffries-Matusita distance and the Kuiper distance. The data used in testing the bootstrap method are satellite measurements of cloud systems called cloud objects. Each cloud object is defined as a contiguous region/patch composed of individual footprints or fields of view. A histogram of measured values over footprints is generated for each parameter of each cloud object and then summary histograms are accumulated over all individual histograms in a given cloud-object size category. The results of statistical hypothesis tests using all three distances as test statistics are generally similar, indicating the validity of the proposed method. The Euclidean distance is determined to be most suitable after comparing the statistical tests of several parameters with distinct probability distributions among three cloud-object size categories. Impacts on the statistical significance levels resulting from differences in the total lengths of satellite footprint data between two size categories are also discussed.

  19. Parameterization of the Age-Dependent Whole Brain Apparent Diffusion Coefficient Histogram

    Science.gov (United States)

    Batra, Marion; Nägele, Thomas

    2015-01-01

    Purpose. The distribution of apparent diffusion coefficient (ADC) values in the brain can be used to characterize age effects and pathological changes of the brain tissue. The aim of this study was the parameterization of the whole brain ADC histogram by an advanced model with influence of age considered. Methods. Whole brain ADC histograms were calculated for all data and for seven age groups between 10 and 80 years. Modeling of the histograms was performed for two parts of the histogram separately: the brain tissue part was modeled by two Gaussian curves, while the remaining part was fitted by the sum of a Gaussian curve, a biexponential decay, and a straight line. Results. A consistent fitting of the histograms of all age groups was possible with the proposed model. Conclusions. This study confirms the strong dependence of the whole brain ADC histograms on the age of the examined subjects. The proposed model can be used to characterize changes of the whole brain ADC histogram in certain diseases under consideration of age effects. PMID:26609526

  20. Histogram analysis of T2*-based pharmacokinetic imaging in cerebral glioma grading.

    Science.gov (United States)

    Liu, Hua-Shan; Chiang, Shih-Wei; Chung, Hsiao-Wen; Tsai, Ping-Huei; Hsu, Fei-Ting; Cho, Nai-Yu; Wang, Chao-Ying; Chou, Ming-Chung; Chen, Cheng-Yu

    2018-03-01

    To investigate the feasibility of histogram analysis of the T2*-based permeability parameter volume transfer constant (K trans ) for glioma grading and to explore the diagnostic performance of the histogram analysis of K trans and blood plasma volume (v p ). We recruited 31 and 11 patients with high- and low-grade gliomas, respectively. The histogram parameters of K trans and v p , derived from the first-pass pharmacokinetic modeling based on the T2* dynamic susceptibility-weighted contrast-enhanced perfusion-weighted magnetic resonance imaging (T2* DSC-PW-MRI) from the entire tumor volume, were evaluated for differentiating glioma grades. Histogram parameters of K trans and v p showed significant differences between high- and low-grade gliomas and exhibited significant correlations with tumor grades. The mean K trans derived from the T2* DSC-PW-MRI had the highest sensitivity and specificity for differentiating high-grade gliomas from low-grade gliomas compared with other histogram parameters of K trans and v p . Histogram analysis of T2*-based pharmacokinetic imaging is useful for cerebral glioma grading. The histogram parameters of the entire tumor K trans measurement can provide increased accuracy with additional information regarding microvascular permeability changes for identifying high-grade brain tumors. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Parameterization of the Age-Dependent Whole Brain Apparent Diffusion Coefficient Histogram

    Directory of Open Access Journals (Sweden)

    Uwe Klose

    2015-01-01

    Full Text Available Purpose. The distribution of apparent diffusion coefficient (ADC values in the brain can be used to characterize age effects and pathological changes of the brain tissue. The aim of this study was the parameterization of the whole brain ADC histogram by an advanced model with influence of age considered. Methods. Whole brain ADC histograms were calculated for all data and for seven age groups between 10 and 80 years. Modeling of the histograms was performed for two parts of the histogram separately: the brain tissue part was modeled by two Gaussian curves, while the remaining part was fitted by the sum of a Gaussian curve, a biexponential decay, and a straight line. Results. A consistent fitting of the histograms of all age groups was possible with the proposed model. Conclusions. This study confirms the strong dependence of the whole brain ADC histograms on the age of the examined subjects. The proposed model can be used to characterize changes of the whole brain ADC histogram in certain diseases under consideration of age effects.

  2. Quadrant Dynamic with Automatic Plateau Limit Histogram Equalization for Image Enhancement

    Directory of Open Access Journals (Sweden)

    P. Jagatheeswari

    2014-01-01

    Full Text Available The fundamental and important preprocessing stage in image processing is the image contrast enhancement technique. Histogram equalization is an effective contrast enhancement technique. In this paper, a histogram equalization based technique called quadrant dynamic with automatic plateau limit histogram equalization (QDAPLHE is introduced. In this method, a hybrid of dynamic and clipped histogram equalization methods are used to increase the brightness preservation and to reduce the overenhancement. Initially, the proposed QDAPLHE algorithm passes the input image through a median filter to remove the noises present in the image. Then the histogram of the filtered image is divided into four subhistograms while maintaining second separated point as the mean brightness. Then the clipping process is implemented by calculating automatically the plateau limit as the clipped level. The clipped portion of the histogram is modified to reduce the loss of image intensity value. Finally the clipped portion is redistributed uniformly to the entire dynamic range and the conventional histogram equalization is executed in each subhistogram independently. Based on the qualitative and the quantitative analysis, the QDAPLHE method outperforms some existing methods in literature.

  3. Molecular and clinical characterization of the myopathic form of mitochondrial DNA depletion syndrome caused by mutations in the thymidine kinase (TK2) gene.

    Science.gov (United States)

    Chanprasert, Sirisak; Wang, Jing; Weng, Shao-Wen; Enns, Gregory M; Boué, Daniel R; Wong, Brenda L; Mendell, Jerry R; Perry, Deborah A; Sahenk, Zarife; Craigen, William J; Alcala, Francisco J Climent; Pascual, Juan M; Melancon, Serge; Zhang, Victor Wei; Scaglia, Fernando; Wong, Lee-Jun C

    2013-01-01

    Mitochondrial DNA (mtDNA) depletion syndromes (MDSs) are a clinically and molecularly heterogeneous group of mitochondrial cytopathies characterized by severe mtDNA copy number reduction in affected tissues. Clinically, MDSs are mainly categorized as myopathic, encephalomyopathic, hepatocerebral, or multi-systemic forms. To date, the myopathic form of MDS is mainly caused by mutations in the TK2 gene, which encodes thymidine kinase 2, the first and rate limiting step enzyme in the phosphorylation of pyrimidine nucleosides. We analyzed 9 unrelated families with 11 affected subjects exhibiting the myopathic form of MDS, by sequencing the TK2 gene. Twelve mutations including 4 novel mutations were detected in 9 families. Skeletal muscle specimens were available from 7 out of 11 subjects. Respiratory chain enzymatic activities in skeletal muscle were measured in 6 subjects, and enzymatic activities were reduced in 3 subjects. Quantitative analysis of mtDNA content in skeletal muscle was performed in 5 subjects, and marked mtDNA content reduction was observed in each. In addition, we outline the molecular and clinical characteristics of this syndrome in a total of 52 patients including those previously reported, and a total of 36 TK2 mutations are summarized. Clinically, hypotonia and proximal muscle weakness are the major phenotypes present in all subjects. In summary, our study expands the molecular and clinical spectrum associated with TK2 deficiency. © 2013.

  4. An evaluation of an improved method for computing histograms in dynamic tracer studies using positron-emission tomography

    International Nuclear Information System (INIS)

    Ollinger, J.M.; Snyder, D.L.

    1986-01-01

    A method for computing approximate minimum-mean-square-error estimates of histograms from list-mode data for use in dynamic tracer studies is evaluated. Parameters estimated from these histograms are significantly more accurate than those estimated from histograms computed by a commonly used method

  5. Clinical heterogeneity within xeroderma pigmentosum associated with mutations in the DNA repair and transcription gene ERCC3

    Energy Technology Data Exchange (ETDEWEB)

    Vermeulen, W.; Kleijer, W.J.; Bootsma, D.; Hoeijmakers, J.H.J.; Weeda, G. (Erasmus Univ., Rotterdam (Netherlands)); Scott, R.J.; Rodgers, S.; Mueller, H.J. (Univ. Hospital, Basel (Switzerland)); Cole, J.; Arlett, C.F. (Univ. of Sussex, Brighton (United Kingdom))

    1994-02-01

    The human DNA excision repair gene ERCC3 specifically corrects the nucleotide excision repair (NER) defect of xeroderma pigmentosum (XP) complementation group B. In addition to its function in NER, the ERCC3 DNA helicase was recently identified as one of the components of the human BTF2/TFIIH transcription factor complex, which is required for initiation of transcription of class II genes. To date, a single patient (XP11BE) has been assigned to this XP group B (XP-B), with the remarkable conjunction of two autosomal recessive DNA repair deficiency disorders: XP and Cockayne syndrome (CS). The intriguing involvement of the ERCC3 protein in the vital process of transcription may provide an explanation for the rarity, severity, and wide spectrum of clinical features in this complementation group. Here the authors report the identification of two new XP-B patients: XPCS1BA and XPCS2BA (siblings), by microneedle injection of the cloned ERCC3 repair gene as well as by cell hybridization. Molecular analysis of the ERCC3 gene in both patients revealed a single base substitution causing a missense mutation in a region that is completely conserved in yeast, Drosophila, mouse, and human ERCC3. As in patient XP11BE, the expression of only one allele (paternal) is detected. The mutation causes a virtually complete inactivation of the NER function of the protein. Despite this severe NER defect, both patients display a late onset of neurologic impairment, mild cutaneous symptoms, and a striking absence of skin tumors even at an age of >40 years. Analysis of the frequency of hprt[sup [minus

  6. Differences in Bordetella pertussis DNA load according to clinical and epidemiological characteristics of patients with whooping cough.

    Science.gov (United States)

    Brotons, Pedro; de Paz, Hector D; Toledo, Diana; Villanova, Marta; Plans, Pedro; Jordan, Iolanda; Dominguez, Angela; Jane, Mireia; Godoy, Pere; Muñoz-Almagro, Carmen

    2016-04-01

    To identify associations between nasopharyngeal Bordetella pertussis DNA load and clinical and epidemiological characteristics and evaluate DNA load prognostic value in pertussis severity. Prospective observational multi-centre study including nasopharyngeal samples positive to pertussis DNA by real-time PCR collected from children and adult patients in more than 200 health centres of Catalonia (Spain) during 2012-2013. B. pertussis load was inversely correlated with age (rho = -0.32, p < 0.001), time to diagnosis (rho = -0.33, p < 0.001) and number of symptoms (rho = 0.13, p = 0.002). Median bacterial load was significantly higher in inpatients versus outpatients (4.91 vs. 2.55 log10 CFU/mL, p < 0.001), patients with complications versus those without (6.05 vs. 2.82 log10 CFU/mL, p < 0.001), disease incidence in summer and autumn versus spring and winter (3.50 vs. 2.21 log10 CFU/mL, p = 0.002), and unvaccinated-partially vaccinated patients versus vaccinated (4.20 vs. 2.76 log10 CFU/mL, p = 0.004). A logistic regression model including bacterial load and other candidate prognostic factors showed good prediction for hospital care (AUC = 0.94) although only age and unvaccinated status were found to be prognostic factors. We observed strong positive associations of nasopharyngeal bacterial load with severity outcomes of hospitalisation and occurrence of complications. Bacterial load and other independent variables contributed to an accurate prognostic model for hospitalisation. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  7. HEp-2 Cell Classification Using Shape Index Histograms With Donut-Shaped Spatial Pooling

    DEFF Research Database (Denmark)

    Larsen, Anders Boesen Lindbo; Vestergaard, Jacob Schack; Larsen, Rasmus

    2014-01-01

    We present a new method for automatic classification of indirect immunoflourescence images of HEp-2 cells into different staining pattern classes. Our method is based on a new texture measure called shape index histograms that captures second-order image structure at multiple scales. Moreover, we...... datasets. Our results show that shape index histograms are superior to other popular texture descriptors for HEp-2 cell classification. Moreover, when comparing to other automated systems for HEp-2 cell classification we show that shape index histograms are very competitive; especially considering...

  8. An alternative to γ histograms for ROI-based quantitative dose comparisons

    International Nuclear Information System (INIS)

    Dvorak, P

    2009-01-01

    An alternative to gamma (γ) histograms for ROI-based quantitative comparisons of dose distributions using the γ concept is proposed. The method provides minimum values of dose difference and distance-to-agreement such that a pre-set fraction of the region of interest passes the γ test. Compared to standard γ histograms, the method provides more information in terms of pass rate per γ calculation. This is achieved at negligible additional calculation cost and without loss of accuracy. The presented method is proposed as a useful and complementary alternative to standard γ histograms, increasing both the quantity and quality of information for use in acceptance or rejection decisions. (note)

  9. Dose Volume Histogram analysis for rectum and urethral reaction of prostate cancer

    International Nuclear Information System (INIS)

    Yanagi, Takeshi; Tsuji, Hiroshi; Kamada, Tadashi; Tsujii, Hirohiko

    2005-01-01

    The aim of this study is to evaluate the clinically relevant parameters for rectum and urethral reaction using DVH (dose volume histogram) in carbon ion radiotherapy of prostate cancer. In this year, we studied the urinary reaction mainly. 35 patients with prostate cancer were treated with carbon ion beams between June 1995 and December 1997. The applied dose was escalated from 54.0 GyE to 72.0 GyE in fixed 20 fractions. Clinical urinary reaction and rectum reaction were reviewed using Radiation Therapy Oncology Group (RTOG) scoring system for acute reactions, RTOG/European Organization for Research and Treatment of Cancer (EORTC) scoring system for late reactions. Taking the ROI (region of interest) for DVH of urethra, we used surrogate one that was derived from the observation of MR images. 35 patients were analyzed for acute urinary reaction and 34 for late urinary reaction in the study of this year. DVH analysis suggested difference among the grades for acute and late reactions. These analysis appears to be a useful tool for predicting the urinary reactions. (author)

  10. Histogram-driven cupping correction (HDCC) in CT

    Science.gov (United States)

    Kyriakou, Y.; Meyer, M.; Lapp, R.; Kalender, W. A.

    2010-04-01

    Typical cupping correction methods are pre-processing methods which require either pre-calibration measurements or simulations of standard objects to approximate and correct for beam hardening and scatter. Some of them require the knowledge of spectra, detector characteristics, etc. The aim of this work was to develop a practical histogram-driven cupping correction (HDCC) method to post-process the reconstructed images. We use a polynomial representation of the raw-data generated by forward projection of the reconstructed images; forward and backprojection are performed on graphics processing units (GPU). The coefficients of the polynomial are optimized using a simplex minimization of the joint entropy of the CT image and its gradient. The algorithm was evaluated using simulations and measurements of homogeneous and inhomogeneous phantoms. For the measurements a C-arm flat-detector CT (FD-CT) system with a 30×40 cm2 detector, a kilovoltage on board imager (radiation therapy simulator) and a micro-CT system were used. The algorithm reduced cupping artifacts both in simulations and measurements using a fourth-order polynomial and was in good agreement to the reference. The minimization algorithm required less than 70 iterations to adjust the coefficients only performing a linear combination of basis images, thus executing without time consuming operations. HDCC reduced cupping artifacts without the necessity of pre-calibration or other scan information enabling a retrospective improvement of CT image homogeneity. However, the method can work with other cupping correction algorithms or in a calibration manner, as well.

  11. Norrie disease resulting from a gene deletion: clinical features and DNA studies.

    OpenAIRE

    Donnai, D; Mountford, R C; Read, A P

    1988-01-01

    We describe a family in which two boys with Norrie disease have a deletion of the DXS7 locus. The deletion does not extend as far distally as the OTC or DXS84 loci. A full clinical description of the patients is given to help establish the range of manifestations of Norrie disease. There is no evidence of any other X linked disease in our patients.

  12. Norrie disease resulting from a gene deletion: clinical features and DNA studies.

    Science.gov (United States)

    Donnai, D; Mountford, R C; Read, A P

    1988-02-01

    We describe a family in which two boys with Norrie disease have a deletion of the DXS7 locus. The deletion does not extend as far distally as the OTC or DXS84 loci. A full clinical description of the patients is given to help establish the range of manifestations of Norrie disease. There is no evidence of any other X linked disease in our patients.

  13. [Characteristic and clinical significance of DNA methyltransferase 3B overexpression in endometrial carcinoma].

    Science.gov (United States)

    Dong, Y; Zhou, M; Ba, X J; Si, J W; Li, W T; Wang, Y; Li, D; Li, T

    2016-10-18

    To determine the clinicopathological significance of the DNA methyltransferase 3B (DNMT3B) overexpression in endometrial carcinomas and to evaluate its correlation with hormone receptor status. Immunohistochemistry was performed to assess the expression of DNMT3B and hormone receptors in 104 endometrial carcinomas. DNMT3B overexpression occurred frequently in endometrioid carcinoma (EC, 54.8%) more than in nonendometrioid carcinoma (NEC, 30.0%) with statistical significance (P=0.028). Furthermore, there was a trend that EC with worse clinico-pathological variables and shorter survival had a higher DNMT3B expression, and the correlation between DNMT3B and tumor grade reached statistical significance (P=0.019).A negative correlation between DNMT3B and estrogen receptor (ER) or progesterone receptor (PR) expression was found in EC. NMT3B overexpression occurred frequently in the ER or PR negative subgroups (78.9%, 86.7%) more than in the positive subgroups (47.7%, 47.8%) with statistical significance (P=0.016, P=0.006). In addition, the DNMT3B overexpression increased in tumors with both ER and PR negative expression (92.9%, P=0.002). However, no such correlation was found in NEC (P>0.05). Sequence analyses demonstrated multiple ER and PR binding sites in the promoter regions of DNMT3B gene. This study showed that the expression of DNMT3B in EC and NEC was different. DNMT3B overexpression in EC was associated with the worse clinicopathological variables and might have predictive value. The methylation status of EC and NEC maybe different. In addition, in EC, DNMT3B overexpression negatively correlated with ER or PR expression. In NEC, the correlation between DNMT3B and ER or PR status was not present.

  14. Whole-genome DNA methylation status associated with clinical PTSD measures of OIF/OEF veterans

    Science.gov (United States)

    Hammamieh, R; Chakraborty, N; Gautam, A; Muhie, S; Yang, R; Donohue, D; Kumar, R; Daigle, B J; Zhang, Y; Amara, D A; Miller, S-A; Srinivasan, S; Flory, J; Yehuda, R; Petzold, L; Wolkowitz, O M; Mellon, S H; Hood, L; Doyle, F J; Marmar, C; Jett, M

    2017-01-01

    Emerging knowledge suggests that post-traumatic stress disorder (PTSD) pathophysiology is linked to the patients’ epigenetic changes, but comprehensive studies examining genome-wide methylation have not been performed. In this study, we examined genome-wide DNA methylation in peripheral whole blood in combat veterans with and without PTSD to ascertain differentially methylated probes. Discovery was initially made in a training sample comprising 48 male Operation Enduring Freedom (OEF)/Operation Iraqi Freedom (OIF) veterans with PTSD and 51 age/ethnicity/gender-matched combat-exposed PTSD-negative controls. Agilent whole-genome array detected ~5600 differentially methylated CpG islands (CpGI) annotated to ~2800 differently methylated genes (DMGs). The majority (84.5%) of these CpGIs were hypermethylated in the PTSD cases. Functional analysis was performed using the DMGs encoding the promoter-bound CpGIs to identify networks related to PTSD. The identified networks were further validated by an independent test set comprising 31 PTSD+/29 PTSD− veterans. Targeted bisulfite sequencing was also used to confirm the methylation status of 20 DMGs shown to be highly perturbed in the training set. To improve the statistical power and mitigate the assay bias and batch effects, a union set combining both training and test set was assayed using a different platform from Illumina. The pathways curated from this analysis confirmed 65% of the pool of pathways mined from training and test sets. The results highlight the importance of assay methodology and use of independent samples for discovery and validation of differentially methylated genes mined from whole blood. Nonetheless, the current study demonstrates that several important epigenetically altered networks may distinguish combat-exposed veterans with and without PTSD. PMID:28696412

  15. Reliability Study Regarding the Use of Histogram Similarity Methods for Damage Detection

    Directory of Open Access Journals (Sweden)

    Nicoleta Gillich

    2013-01-01

    Full Text Available The paper analyses the reliability of three dissimilarity estimators to compare histograms, as support for a frequency-based damage detection method, able to identify structural changes in beam-like structures. First a brief presentation of the own developed damage detection method is made, with focus on damage localization. It consists actually in comparing a histogram derived from measurement results, with a large series of histograms, namely the damage location indexes for all locations along the beam, obtained by calculus. We tested some dissimilarity estimators like the Minkowski-form Distances, the Kullback-Leibler Divergence and the Histogram Intersection and found the Minkowski Distance as the method providing best results. It was tested for numerous locations, using real measurement results and with results artificially debased by noise, proving its reliability.

  16. Image Enhancement via Subimage Histogram Equalization Based on Mean and Variance

    Directory of Open Access Journals (Sweden)

    Liyun Zhuang

    2017-01-01

    Full Text Available This paper puts forward a novel image enhancement method via Mean and Variance based Subimage Histogram Equalization (MVSIHE, which effectively increases the contrast of the input image with brightness and details well preserved compared with some other methods based on histogram equalization (HE. Firstly, the histogram of input image is divided into four segments based on the mean and variance of luminance component, and the histogram bins of each segment are modified and equalized, respectively. Secondly, the result is obtained via the concatenation of the processed subhistograms. Lastly, the normalization method is deployed on intensity levels, and the integration of the processed image with the input image is performed. 100 benchmark images from a public image database named CVG-UGR-Database are used for comparison with other state-of-the-art methods. The experiment results show that the algorithm can not only enhance image information effectively but also well preserve brightness and details of the original image.

  17. Adaptive Histogram Equalization Based Image Forensics Using Statistics of DC DCT Coefficients

    Directory of Open Access Journals (Sweden)

    Neetu Singh

    2018-01-01

    Full Text Available The vulnerability of digital images is growing towards manipulation. This motivated an area of research to deal with digital image forgeries. The certifying origin and content of digital images is an open problem in the multimedia world. One of the ways to find the truth of images is finding the presence of any type of contrast enhancement. In this work, novel and simple machine learning tool is proposed to detect the presence of histogram equalization using statistical parameters of DC Discrete Cosine Transform (DCT coefficients. The statistical parameters of the Gaussian Mixture Model (GMM fitted to DC DCT coefficients are used as features for classifying original and histogram equalized images. An SVM classifier has been developed to classify original and histogram equalized image which can detect histogram equalized image with accuracy greater than 95% when false rate is less than 5%.

  18. Histograms of Arecibo World Days Measurements and Linear-H Fits Between 1985 and 1995

    National Research Council Canada - National Science Library

    Melendez-Alvira, D

    1998-01-01

    This document presents histograms of linear-H model fits to electron density profiles measured with the incoherent scatter radar of the Arecibo Observatory in Puerto Rico during the World Days between 1985 and 1995...

  19. Image Enhancement via Subimage Histogram Equalization Based on Mean and Variance

    Science.gov (United States)

    2017-01-01

    This paper puts forward a novel image enhancement method via Mean and Variance based Subimage Histogram Equalization (MVSIHE), which effectively increases the contrast of the input image with brightness and details well preserved compared with some other methods based on histogram equalization (HE). Firstly, the histogram of input image is divided into four segments based on the mean and variance of luminance component, and the histogram bins of each segment are modified and equalized, respectively. Secondly, the result is obtained via the concatenation of the processed subhistograms. Lastly, the normalization method is deployed on intensity levels, and the integration of the processed image with the input image is performed. 100 benchmark images from a public image database named CVG-UGR-Database are used for comparison with other state-of-the-art methods. The experiment results show that the algorithm can not only enhance image information effectively but also well preserve brightness and details of the original image. PMID:29403529

  20. Dose-volume histograms for optimization of treatment plans illustrated by the example of oesophagus carcinoma

    International Nuclear Information System (INIS)

    Roth, J.; Huenig, R.; Huegli, C.

    1995-01-01

    Using the example of oesophagus carcinoma, dose-volume histograms for diverse treatment techniques are calculated and judged by means of multiplanar isodose representations. The selected treatment plans are ranked with the aid of the dose-volume histograms. We distinguish the tissue inside and outside of the target volume. The description of the spatial dose distribution in dependence of the different volumes and the respective fractions of the tumor dose therein with the help of dose-volume histograms brings about a correlation between the physical parameters and the biological effects. In addition one has to bear in mind the consequences of measures that influence the reaction and the side-effects of radiotherapy (e.g. chemotherapy), i.e. the recuperation of the tissues that were irradiated intentionally or inevitably. Taking all that into account it is evident that the dose-volume histograms are a powerful tool for assessing the quality of treatment plans. (orig./MG) [de

  1. Efficient Human Action and Gait Analysis Using Multiresolution Motion Energy Histogram

    Directory of Open Access Journals (Sweden)

    Kuo-Chin Fan

    2010-01-01

    Full Text Available Average Motion Energy (AME image is a good way to describe human motions. However, it has to face the computation efficiency problem with the increasing number of database templates. In this paper, we propose a histogram-based approach to improve the computation efficiency. We convert the human action/gait recognition problem to a histogram matching problem. In order to speed up the recognition process, we adopt a multiresolution structure on the Motion Energy Histogram (MEH. To utilize the multiresolution structure more efficiently, we propose an automated uneven partitioning method which is achieved by utilizing the quadtree decomposition results of MEH. In that case, the computation time is only relevant to the number of partitioned histogram bins, which is much less than the AME method. Two applications, action recognition and gait classification, are conducted in the experiments to demonstrate the feasibility and validity of the proposed approach.

  2. Image Enhancement via Subimage Histogram Equalization Based on Mean and Variance.

    Science.gov (United States)

    Zhuang, Liyun; Guan, Yepeng

    2017-01-01

    This paper puts forward a novel image enhancement method via Mean and Variance based Subimage Histogram Equalization (MVSIHE), which effectively increases the contrast of the input image with brightness and details well preserved compared with some other methods based on histogram equalization (HE). Firstly, the histogram of input image is divided into four segments based on the mean and variance of luminance component, and the histogram bins of each segment are modified and equalized, respectively. Secondly, the result is obtained via the concatenation of the processed subhistograms. Lastly, the normalization method is deployed on intensity levels, and the integration of the processed image with the input image is performed. 100 benchmark images from a public image database named CVG-UGR-Database are used for comparison with other state-of-the-art methods. The experiment results show that the algorithm can not only enhance image information effectively but also well preserve brightness and details of the original image.

  3. Comparison of the analytical and clinical performances of Abbott RealTime High Risk HPV, Hybrid Capture 2, and DNA Chip assays in gynecology patients.

    Science.gov (United States)

    Park, Seungman; Kang, Youjin; Kim, Dong Geun; Kim, Eui-Chong; Park, Sung Sup; Seong, Moon-Woo

    2013-08-01

    The detection of high-risk (HR) HPV in cervical cancer screening is important for early diagnosis of cervical cancer or pre-cancerous lesions. We evaluated the analytical and clinical performances of 3 HR HPV assays in Gynecology patients. A total of 991 specimens were included in this study: 787 specimens for use with a Hybrid Capture 2 (HC2) and 204 specimens for a HPV DNA microarray (DNA Chip). All specimens were tested using an Abbott RealTime High Risk HPV assay (Real-time HR), PGMY PCR, and sequence analysis. Clinical sensitivities for severe abnormal cytology (severe than high-grade squamous intraepithelial lesion) were 81.8% for Real-time HR, 77.3% for HC2, and 66.7% for DNA Chip, and clinical sensitivities for severe abnormal histology (cervical intraepithelial neoplasia grade 2+) were 91.7% for HC2, 87.5% for Real-time HR, and 73.3% for DNA Chip. As compared to results of the sequence analysis, HC2, Real-time HR, and DNA Chip showed concordance rates of 94.3% (115/122), 90.0% (117/130), and 61.5% (16/26), respectively. The HC2 assay and Real-time HR assay showed comparable results to each other in both clinical and analytical performances, while the DNA Chip assay showed poor clinical and analytical performances. The Real-time HR assay can be a good alternative option for HR HPV testing with advantages of allowing full automation and simultaneous genotyping of HR types 16 and 18. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Histogram based analysis of lung perfusion of children after congenital diaphragmatic hernia repair.

    Science.gov (United States)

    Kassner, Nora; Weis, Meike; Zahn, Katrin; Schaible, Thomas; Schoenberg, Stefan O; Schad, Lothar R; Zöllner, Frank G

    2018-05-01

    To investigate a histogram based approach to characterize the distribution of perfusion in the whole left and right lung by descriptive statistics and to show how histograms could be used to visually explore perfusion defects in two year old children after Congenital Diaphragmatic Hernia (CDH) repair. 28 children (age of 24.2±1.7months; all left sided hernia; 9 after extracorporeal membrane oxygenation therapy) underwent quantitative DCE-MRI of the lung. Segmentations of left and right lung were manually drawn to mask the calculated pulmonary blood flow maps and then to derive histograms for each lung side. Individual and group wise analysis of histograms of left and right lung was performed. Ipsilateral and contralateral lung show significant difference in shape and descriptive statistics derived from the histogram (Wilcoxon signed-rank test, phistogram derived parameters. Histogram analysis can be a valuable tool to characterize and visualize whole lung perfusion of children after CDH repair. It allows for several possibilities to analyze the data, either describing the perfusion differences between the right and left lung but also to explore and visualize localized perfusion patterns in the 3D lung volume. Subgroup analysis will be possible given sufficient sample sizes. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. ADC histogram analysis of muscle lymphoma - Correlation with histopathology in a rare entity.

    Science.gov (United States)

    Meyer, Hans-Jonas; Pazaitis, Nikolaos; Surov, Alexey

    2018-06-21

    Diffusion weighted imaging (DWI) is able to reflect histopathology architecture. A novel imaging approach, namely histogram analysis, is used to further characterize lesion on MRI. The purpose of this study is to correlate histogram parameters derived from apparent diffusion coefficient- (ADC) maps with histopathology parameters in muscle lymphoma. Eight patients (mean age 64.8 years, range 45-72 years) with histopathologically confirmed muscle lymphoma were retrospectively identified. Cell count, total nucleic and average nucleic areas were estimated using ImageJ. Additionally, Ki67-index was calculated. DWI was obtained on a 1.5T scanner by using the b values of 0 and 1000 s/mm2. Histogram analysis was performed as a whole lesion measurement by using a custom-made Matlabbased application. The correlation analysis revealed statistically significant correlation between cell count and ADCmean (p=-0.76, P=0.03) as well with ADCp75 (p=-0.79, P=0.02). Kurtosis and entropy correlated with average nucleic area (p=-0.81, P=0.02, p=0.88, P=0.007, respectively). None of the analyzed ADC parameters correlated with total nucleic area and with Ki67-index. This study identified significant correlations between cellularity and histogram parameters derived from ADC maps in muscle lymphoma. Thus, histogram analysis parameters reflect histopathology in muscle tumors. Advances in knowledge: Whole lesion ADC histogram analysis is able to reflect histopathology parameters in muscle lymphomas.

  6. Histogram-based quantitative evaluation of endobronchial ultrasonography images of peripheral pulmonary lesion.

    Science.gov (United States)

    Morikawa, Kei; Kurimoto, Noriaki; Inoue, Takeo; Mineshita, Masamichi; Miyazawa, Teruomi

    2015-01-01

    Endobronchial ultrasonography using a guide sheath (EBUS-GS) is an increasingly common bronchoscopic technique, but currently, no methods have been established to quantitatively evaluate EBUS images of peripheral pulmonary lesions. The purpose of this study was to evaluate whether histogram data collected from EBUS-GS images can contribute to the diagnosis of lung cancer. Histogram-based analyses focusing on the brightness of EBUS images were retrospectively conducted: 60 patients (38 lung cancer; 22 inflammatory diseases), with clear EBUS images were included. For each patient, a 400-pixel region of interest was selected, typically located at a 3- to 5-mm radius from the probe, from recorded EBUS images during bronchoscopy. Histogram height, width, height/width ratio, standard deviation, kurtosis and skewness were investigated as diagnostic indicators. Median histogram height, width, height/width ratio and standard deviation were significantly different between lung cancer and benign lesions (all p histogram standard deviation. Histogram standard deviation appears to be the most useful characteristic for diagnosing lung cancer using EBUS images. © 2015 S. Karger AG, Basel.

  7. DE-STRIPING FOR TDICCD REMOTE SENSING IMAGE BASED ON STATISTICAL FEATURES OF HISTOGRAM

    Directory of Open Access Journals (Sweden)

    H.-T. Gao

    2016-06-01

    Full Text Available Aim to striping noise brought by non-uniform response of remote sensing TDI CCD, a novel de-striping method based on statistical features of image histogram is put forward. By analysing the distribution of histograms,the centroid of histogram is selected to be an eigenvalue representing uniformity of ground objects,histogrammic centroid of whole image and each pixels are calculated first,the differences between them are regard as rough correction coefficients, then in order to avoid the sensitivity caused by single parameter and considering the strong continuity and pertinence of ground objects between two adjacent pixels,correlation coefficient of the histograms is introduces to reflect the similarities between them,fine correction coefficient is obtained by searching around the rough correction coefficient,additionally,in view of the influence of bright cloud on histogram,an automatic cloud detection based on multi-feature including grey level,texture,fractal dimension and edge is used to pre-process image.Two 0-level panchromatic images of SJ-9A satellite with obvious strip noise are processed by proposed method to evaluate the performance, results show that the visual quality of images are improved because the strip noise is entirely removed,we quantitatively analyse the result by calculating the non-uniformity ,which has reached about 1% and is better than histogram matching method.

  8. Antibodies to uv light denatured DNA in systemic lupus erythematosus: detection by filter radioimmunoassay and clinical correlations

    Energy Technology Data Exchange (ETDEWEB)

    Davis, P; Russell, A S; Percy, J S

    1976-12-01

    Antibodies to ultraviolet light denatured DNA (UV DNA) have been measured in patients with systemic lupus erythematosus (SLE) and normal subjects, using a millipore filter radioimmunoassay. High levels of UV DNA binding were only found in patients with SLE. The presence of UV DNA antibodies correlated well with the presence of native DNA antibodies, although immunodiffusion studies and inhibition techniques showed these antibodies to be immunologically distinct in many cases. Forty-one percent of the SLE patients had had photosensitivity at some stage of their disease, but there was a poor correlation between this symptom and the presence of UV DNA antibodies. Although UV DNA is known to be a potent immunogen, none of the results from this study suggests that antibodies to UV DNA are more than another example of the broad spectrum of antinuclear antibodies seen in SLE.

  9. Clinical characteristics of three patients with UV{sup s} syndrome, a photosensitive disorder with defective DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, T.; Yamaizumi, M.; Hiro-oka, M.; Matsui, T.; Matsuno, M.; Ono, T. [Kumamoto Univ. (Japan). School of Medicine; Ichihashi, M. [Kobe Univ. (Japan). School of Medicine

    1996-06-01

    Recently, we established a new category of photosensitive disorder termed UVsup(s) syndrome. Cells from patients with UVsup(s) syndrome have a similar UV sensitivity as xeroderma pigmentosum (XP) cells, but have a normal level of unscheduled DNA synthesis (UDS) unlike XP. UVsup(s) syndrome is distinct from Cockayne syndrome (CS) or XP including XP variant (XP-V) as determined by studies of genetic factors using cell fusion, microinjection, and postreplication repair assays. In this study, we identified three japanese patients with UVsup(s) syndrome: an 11-year-old girl, a 17 year old male, and an 8-year-old boy. The first two patients were siblings, while the third was a case from a different family. All of these patients exhibited acute recurrent sunburn. Common clinical manifestations of the patients were slight erythema and dryness, a number of freckles on sun-exposed areas, and slight telangiectasia only seen on the cheek and nose. Patient 3 showed a lowered minimal erythema dose between 280 and 300 nm. The patients` fibroblasts showed similar characteristics to those in CS, such as UV sensitivity, and a failure of RNA synthesis (RRS) after UV irradiation, despite a normal level of UDS. Thus, UVsup(s) syndrome is a new hereditary photosensitive disorder with clinical manifestations similar to a mild form of Xp but showing the cellular characteristics of CS. (Author).

  10. The Social Media DNA of Mayo Clinic-and Health Care.

    Science.gov (United States)

    Kotsenas, Amy L; Aase, Lee; Arce, Makala; Timimi, Farris K; Dacy, Matthew; Young, Colleen; Wald, John T

    2018-01-01

    Hippocrates' admonition and the medical community's aversion to risk have caused many physicians and institutions to resist participation in modern social media sites such as Facebook (Facebook, Inc, Menlo Park, California, USA), Twitter (Twitter Inc, San Francisco, California, USA), and YouTube (San Mateo, California, USA). However, because Mayo Clinic's founders were champions of analog social networking, it was among the earliest hospitals worldwide to create official accounts on these digital platforms. A proper understanding of the traditional mechanisms of knowledge diffusion in medicine and of the nature of social media sites should help professionals see and embrace the opportunities for positive engagement in social media. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  11. Equivalent uniform dose concept evaluated by theoretical dose volume histograms for thoracic irradiation.

    Science.gov (United States)

    Dumas, J L; Lorchel, F; Perrot, Y; Aletti, P; Noel, A; Wolf, D; Courvoisier, P; Bosset, J F

    2007-03-01

    The goal of our study was to quantify the limits of the EUD models for use in score functions in inverse planning software, and for clinical application. We focused on oesophagus cancer irradiation. Our evaluation was based on theoretical dose volume histograms (DVH), and we analyzed them using volumetric and linear quadratic EUD models, average and maximum dose concepts, the linear quadratic model and the differential area between each DVH. We evaluated our models using theoretical and more complex DVHs for the above regions of interest. We studied three types of DVH for the target volume: the first followed the ICRU dose homogeneity recommendations; the second was built out of the first requirements and the same average dose was built in for all cases; the third was truncated by a small dose hole. We also built theoretical DVHs for the organs at risk, in order to evaluate the limits of, and the ways to use both EUD(1) and EUD/LQ models, comparing them to the traditional ways of scoring a treatment plan. For each volume of interest we built theoretical treatment plans with differences in the fractionation. We concluded that both volumetric and linear quadratic EUDs should be used. Volumetric EUD(1) takes into account neither hot-cold spot compensation nor the differences in fractionation, but it is more sensitive to the increase of the irradiated volume. With linear quadratic EUD/LQ, a volumetric analysis of fractionation variation effort can be performed.

  12. Brachytherapy dose-volume histogram computations using optimized stratified sampling methods

    International Nuclear Information System (INIS)

    Karouzakis, K.; Lahanas, M.; Milickovic, N.; Giannouli, S.; Baltas, D.; Zamboglou, N.

    2002-01-01

    A stratified sampling method for the efficient repeated computation of dose-volume histograms (DVHs) in brachytherapy is presented as used for anatomy based brachytherapy optimization methods. The aim of the method is to reduce the number of sampling points required for the calculation of DVHs for the body and the PTV. From the DVHs are derived the quantities such as Conformity Index COIN and COIN integrals. This is achieved by using partial uniform distributed sampling points with a density in each region obtained from a survey of the gradients or the variance of the dose distribution in these regions. The shape of the sampling regions is adapted to the patient anatomy and the shape and size of the implant. For the application of this method a single preprocessing step is necessary which requires only a few seconds. Ten clinical implants were used to study the appropriate number of sampling points, given a required accuracy for quantities such as cumulative DVHs, COIN indices and COIN integrals. We found that DVHs of very large tissue volumes surrounding the PTV, and also COIN distributions, can be obtained using a factor of 5-10 times smaller the number of sampling points in comparison with uniform distributed points

  13. Clinically relevant radioresistant cells efficiently repair DNA double-strand breaks induced by X-rays

    International Nuclear Information System (INIS)

    Kuwahara, Yoshikazu; Baba, Taisuke; Nakagawa, Hironobu; Shimura, Tsutomu; Yamamoto, Yoichiro; Fukumoto, Manabu; Li Li; Ohkubo, Yasuhito

    2009-01-01

    Radiotherapy is one of the major therapeutic modalities for eradicating malignant tumors. However, the existence of radioresistant cells remains one of the most critical obstacles in radiotherapy and radiochemotherapy. Standard radiotherapy for tumor treatment consists of approximately 2 Gy once a day, 5 days a week, over a period of 5-8 weeks. To understand the characteristics of radioresistant cells and to develop more effective radiotherapy, we established a novel radioresistant cell line, HepG2-8960-R with clinical relevance from parental HepG2 cells by long-term fractionated exposure to 2 Gy of X-rays. HepG2-8960-R cells continued to proliferate with daily exposure to 2 Gy X-rays for more than 30 days, while all parental HepG2 cells ceased. After exposure to fractionated 2 Gy X-rays, induction frequencies of micronuclei and remaining foci of γ-H2AX in HepG2-8960-R were less than those in HepG2. Flow cytometric analysis revealed that the proportion of cells in S- and G2/M-phase of the cell cycle was higher in HepG2-8960-R than in HepG2. These suggest that the response of clinically relevant radioresistant (CRR) cells to fractionated radiation is not merely an accumulated response to each fractionated radiation. This is the first report on the establishment of a CRR cell line from an isogenic parental cell line. (author)

  14. Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma.

    Science.gov (United States)

    Wiestler, Benedikt; Capper, David; Sill, Martin; Jones, David T W; Hovestadt, Volker; Sturm, Dominik; Koelsche, Christian; Bertoni, Anna; Schweizer, Leonille; Korshunov, Andrey; Weiß, Elisa K; Schliesser, Maximilian G; Radbruch, Alexander; Herold-Mende, Christel; Roth, Patrick; Unterberg, Andreas; Hartmann, Christian; Pietsch, Torsten; Reifenberger, Guido; Lichter, Peter; Radlwimmer, Bernhard; Platten, Michael; Pfister, Stefan M; von Deimling, Andreas; Weller, Michael; Wick, Wolfgang

    2014-10-01

    The outcome of patients with anaplastic gliomas varies considerably. Whether a molecular classification of anaplastic gliomas based on large-scale genomic or epigenomic analyses is superior to histopathology for reflecting distinct biological groups, predicting outcomes and guiding therapy decisions has yet to be determined. Epigenome-wide DNA methylation analysis, using a platform which also allows the detection of copy-number aberrations, was performed in a cohort of 228 patients with anaplastic gliomas (astrocytomas, oligoastrocytomas, and oligodendrogliomas), including 115 patients of the NOA-04 trial. We further compared these tumors with a group of 55 glioblastomas. Unsupervised clustering of DNA methylation patterns revealed two main groups correlated with IDH status: CpG island methylator phenotype (CIMP) positive (77.5 %) or negative (22.5 %). CIMP(pos) (IDH mutant) tumors showed a further separation based on copy-number status of chromosome arms 1p and 19q. CIMP(neg) (IDH wild type) tumors showed hallmark copy-number alterations of glioblastomas, and clustered together with CIMP(neg) glioblastomas without forming separate groups based on WHO grade. Notably, there was no molecular evidence for a distinct biological entity representing anaplastic oligoastrocytoma. Tumor classification based on CIMP and 1p/19q status was significantly associated with survival, allowing a better prediction of outcome than the current histopathological classification: patients with CIMP(pos) tumors with 1p/19q codeletion (CIMP-codel) had the best prognosis, followed by patients with CIMP(pos) tumors but intact 1p/19q status (CIMP-non-codel). Patients with CIMP(neg) anaplastic gliomas (GBM-like) had the worst prognosis. Collectively, our data suggest that anaplastic gliomas can be grouped by IDH and 1p/19q status into three molecular groups that show clear links to underlying biology and a significant association with clinical outcome in a prospective trial cohort.

  15. Newborn Congenital Cytomegalovirus Screening Based on Clinical Manifestations and Evaluation of DNA-based Assays for In Vitro Diagnostics.

    Science.gov (United States)

    Fujii, Tomoyuki; Oka, Akira; Morioka, Ichiro; Moriuchi, Hiroyuki; Koyano, Shin; Yamada, Hideto; Saito, Shigeru; Sameshima, Hiroshi; Nagamatsu, Takeshi; Tsuchida, Shinya; Inoue, Naoki

    2017-10-01

    To establish a strategy for congenital cytomegalovirus (cCMV) screening and to establish confirmatory assays approved as in vitro diagnostics by the regulatory authorities, we evaluated the clinical risks and performance of diagnostic assays developed by commercial companies, since cCMV infection has significant clinical consequences. Newborns with clinical manifestations considered to be consequences of cCMV infection (n = 575) were screened for the presence of cytomegalovirus (CMV) DNA in urine specimens collected onto filter paper placed in their diapers using the polymerase chain reaction-based assay reported previously. Liquid urine specimens were obtained from all of 20 CMV-positive newborns and 107 of the CMV-negative newborns identified in the screening. We used these 127 specimens, as well as 12 from cCMV cases identified in a previous study and 41 from healthy newborns, to compare the performance of 2 commercial assays and 1 in-house assay. The risk-based screening allowed the identification of cCMV cases at least 10-fold more efficiently than our previous universal screening, although there appears to be a limit to the identification of asymptomatically infected newborns. Although CMV-specific IgM during pregnancy was found frequently in mothers of cCMV newborns, CMV-IgM alone is not an effective diagnostic marker. The urine-filter-based assay and the 3 diagnostic assays yielded identical results. Although risk-based and universal newborn screening strategies for cCMV infection each have their respective advantages and disadvantages, urine-filter-based assay followed by confirmatory in vitro diagnostics assays is able to identify cCMV cases efficiently.

  16. DNA Mismatch Repair Deficiency in Rectal Cancer: Benchmarking Its Impact on Prognosis, Neoadjuvant Response Prediction, and Clinical Cancer Genetics.

    Science.gov (United States)

    de Rosa, Nicole; Rodriguez-Bigas, Miguel A; Chang, George J; Veerapong, Jula; Borras, Ester; Krishnan, Sunil; Bednarski, Brian; Messick, Craig A; Skibber, John M; Feig, Barry W; Lynch, Patrick M; Vilar, Eduardo; You, Y Nancy

    2016-09-01

    DNA mismatch repair deficiency (dMMR) hallmarks consensus molecular subtype 1 of colorectal cancer. It is being routinely tested, but little is known about dMMR rectal cancers. The efficacy of novel treatment strategies cannot be established without benchmarking the outcomes of dMMR rectal cancer with current therapy. We aimed to delineate the impact of dMMR on prognosis, the predicted response to fluoropyrimidine-based neoadjuvant therapy, and implications of germline alterations in the MMR genes in rectal cancer. Between 1992 and 2012, 62 patients with dMMR rectal cancers underwent multimodality therapy. Oncologic treatment and outcomes as well as clinical genetics work-up were examined. Overall and rectal cancer-specific survival were calculated by the Kaplan-Meier method. The median age at diagnosis was 41 years. MMR deficiency was most commonly due to alterations in MSH2 (53%) or MSH6 (23%). After a median follow-up of 6.8 years, the 5-year rectal cancer-specific survival was 100% for stage I and II, 85.1% for stage III, and 60.0% for stage IV disease. Fluoropyrimidine-based neoadjuvant chemoradiation was associated with a complete pathologic response rate of 27.6%. The extent of surgical resection was influenced by synchronous colonic disease at presentation, tumor height, clinical stage, and pelvic radiation. An informed decision for a limited resection focusing on proctectomy did not compromise overall survival. Five of the 11 (45.5%) deaths during follow-up were due to extracolorectal malignancies. dMMR rectal cancer had excellent prognosis and pathologic response with current multimodality therapy including an individualized surgical treatment plan. Identification of a dMMR rectal cancer should trigger germline testing, followed by lifelong surveillance for both colorectal and extracolorectal malignancies. We herein provide genotype-specific outcome benchmarks for comparison with novel interventions. © 2016 by American Society of Clinical Oncology.

  17. Validation of liquid biopsy: plasma cell-free DNA testing in clinical management of advanced non-small cell lung cancer

    Directory of Open Access Journals (Sweden)

    Veldore VH

    2018-01-01

    Full Text Available Vidya H Veldore,1,* Anuradha Choughule,2,* Tejaswi Routhu,1 Nitin Mandloi,1 Vanita Noronha,2 Amit Joshi,2 Amit Dutt,3 Ravi Gupta,1 Ramprasad Vedam,1 Kumar Prabhash2 1MedGenome Labs Private Ltd,, Bangalore, India; 2Tata Memorial Centre, Parel, Mumbai, India; 3The Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai, Maharashtra, India *These authors contributed equally to this work Abstract: Plasma cell-free tumor DNA, or circulating tumor DNA (ctDNA, from liquid biopsy is a potential source of tumor genetic material, in the absence of tissue biopsy, for EGFR testing. Our validation study reiterates the clinical utility of ctDNA next generation sequencing (NGS for EGFR mutation testing in non-small cell lung cancer (NSCLC. A total of 163 NSCLC cases were included in the validation, of which 132 patients had paired tissue biopsy and ctDNA. We chose to validate ctDNA using deep sequencing with custom designed bioinformatics methods that could detect somatic mutations at allele frequencies as low as 0.01%. Benchmarking allele specific real time PCR as one of the standard methods for tissue-based EGFR mutation testing, the ctDNA NGS test was validated on all the plasma derived cell-free DNA samples. We observed a high concordance (96.96% between tissue biopsy and ctDNA for oncogenic driver mutations in Exon 19 and Exon 21 of the EGFR gene. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of the assay were 91.1%, 100% 100%, 95.6%, and 97%, respectively. A false negative rate of 3% was observed. A subset of mutations was also verified on droplet digital PCR. Sixteen percent EGFR mutation positivity was observed in patients where only liquid biopsy was available, thus creating options for targeted therapy. This is the first and largest study from India, demonstrating successful validation of circulating cell-free DNA as a clinically

  18. Can histogram analysis of MR images predict aggressiveness in pancreatic neuroendocrine tumors?

    Science.gov (United States)

    De Robertis, Riccardo; Maris, Bogdan; Cardobi, Nicolò; Tinazzi Martini, Paolo; Gobbo, Stefano; Capelli, Paola; Ortolani, Silvia; Cingarlini, Sara; Paiella, Salvatore; Landoni, Luca; Butturini, Giovanni; Regi, Paolo; Scarpa, Aldo; Tortora, Giampaolo; D'Onofrio, Mirko

    2018-06-01

    To evaluate MRI derived whole-tumour histogram analysis parameters in predicting pancreatic neuroendocrine neoplasm (panNEN) grade and aggressiveness. Pre-operative MR of 42 consecutive patients with panNEN >1 cm were retrospectively analysed. T1-/T2-weighted images and ADC maps were analysed. Histogram-derived parameters were compared to histopathological features using the Mann-Whitney U test. Diagnostic accuracy was assessed by ROC-AUC analysis; sensitivity and specificity were assessed for each histogram parameter. ADC entropy was significantly higher in G2-3 tumours with ROC-AUC 0.757; sensitivity and specificity were 83.3 % (95 % CI: 61.2-94.5) and 61.1 % (95 % CI: 36.1-81.7). ADC kurtosis was higher in panNENs with vascular involvement, nodal and hepatic metastases (p= .008, .021 and .008; ROC-AUC= 0.820, 0.709 and 0.820); sensitivity and specificity were: 85.7/74.3 % (95 % CI: 42-99.2 /56.4-86.9), 36.8/96.5 % (95 % CI: 17.2-61.4 /76-99.8) and 100/62.8 % (95 % CI: 56.1-100/44.9-78.1). No significant differences between groups were found for other histogram-derived parameters (p >.05). Whole-tumour histogram analysis of ADC maps may be helpful in predicting tumour grade, vascular involvement, nodal and liver metastases in panNENs. ADC entropy and ADC kurtosis are the most accurate parameters for identification of panNENs with malignant behaviour. • Whole-tumour ADC histogram analysis can predict aggressiveness in pancreatic neuroendocrine neoplasms. • ADC entropy and kurtosis are higher in aggressive tumours. • ADC histogram analysis can quantify tumour diffusion heterogeneity. • Non-invasive quantification of tumour heterogeneity can provide adjunctive information for prognostication.

  19. Intravoxel incoherent motion (IVIM histogram biomarkers for prediction of neoadjuvant treatment response in breast cancer patients

    Directory of Open Access Journals (Sweden)

    Gene Y. Cho

    Full Text Available Objective: To examine the prognostic capabilities of intravoxel incoherent motion (IVIM metrics and their ability to predict response to neoadjuvant treatment (NAT. Additionally, to observe changes in IVIM metrics between pre- and post-treatment MRI. Methods: This IRB-approved, HIPAA-compliant retrospective study observed 31 breast cancer patients (32 lesions. Patients underwent standard bilateral breast MRI along with diffusion-weighted imaging before and after NAT. Six patients underwent an additional IVIM-MRI scan 12–14 weeks after initial scan and 2 cycles of treatment. In addition to apparent diffusion coefficients (ADC from monoexponential decay, IVIM mean values (tissue diffusivity Dt, perfusion fraction fp, and pseudodiffusivity Dp and histogram metrics were derived using a biexponential model. An additional filter identified voxels of highly vascular tumor tissue (VTT, excluding necrotic or normal tissue. Clinical data include histology of biopsy and clinical response to treatment through RECIST assessment. Comparisons of treatment response were made using Wilcoxon rank-sum tests. Results: Average, kurtosis, and skewness of pseudodiffusion Dp significantly differentiated RECIST responders from nonresponders. ADC and Dt values generally increased (∼70% and VTT% values generally decreased (∼20% post-treatment. Conclusion: Dp metrics showed prognostic capabilities; slow and heterogeneous pseudodiffusion offer poor prognosis. Baseline ADC/Dt parameters were not significant predictors of response. This work suggests that IVIM mean values and heterogeneity metrics may have prognostic value in the setting of breast cancer NAT. Keywords: Breast cancer, Diffusion weighted MRI, Intravoxel incoherent motion, Neoadjuvant treatment, Response evaluation criteria in solid tumors

  20. DNA damage and repair in peripheral blood lymphocytes from healthy individuals and cancer patients: a pilot study on the implications in the clinical response to chemotherapy.

    Science.gov (United States)

    Nadin, Silvina Beatriz; Vargas-Roig, Laura M; Drago, Gisela; Ibarra, Jorge; Ciocca, Daniel R

    2006-07-28

    Drug resistance is considered the main impediment to successful cancer chemotherapy. The quest for a method useful to predict individual responses to chemotherapy prior to treatment is highly desired. This study was designed to determine the individual influences of doxorubicin and cisplatin on the degree of DNA damage, DNA repair and hMSH2 and the hMLH1 protein expression in peripheral blood lymphocytes (PBL) and their correlations with the clinical response. PBL were obtained from 25 cancer patients (pre- and post-chemotherapy) and from 10 healthy persons, cultured and exposed to doxorubicin or cisplatin. Cells were collected at T0 (immediately after drug treatment) and 24h after damage (T24). The alkaline comet assay was employed to assess the DNA damage and repair function, and immunocytochemistry to study hMLH1 and hMSH2 expression. Clinical response was evaluated after three cycles of chemotherapy. Pre-chemotherapy PBL from cancer patients showed significantly higher levels of basal DNA damage than healthy persons, with appreciable interindividual variations between them. The in vivo administration of antineoplasic drugs was accompanied by significant DNA damage, and an increased in the number of apoptotic cells. Cancer patients with complete response showed a high number of apoptotic cells. The DNA migration increased at T0 and at T24 in cisplatin-treated patients, reflecting a decreased rate of cisplatin adducts repair than that observed in healthy individuals. The ability to repair DNA lesions in doxorubicin-damaged cells was very similar between healthy individuals and cancer patients. Cisplatin-treated patients that died by the disease showed lower DNA migration than the mean value. The expression of hMLH1 and hMSH2 was practically identical between healthy individuals and cancer patients. Nevertheless, chemotherapy induced a depletion mostly of hMLH1. In 83% of cisplatin-treated patients with CR the hMLH1 and hMSH2 expression at T24 was higher than the

  1. DSP+FPGA-based real-time histogram equalization system of infrared image

    Science.gov (United States)

    Gu, Dongsheng; Yang, Nansheng; Pi, Defu; Hua, Min; Shen, Xiaoyan; Zhang, Ruolan

    2001-10-01

    Histogram Modification is a simple but effective method to enhance an infrared image. There are several methods to equalize an infrared image's histogram due to the different characteristics of the different infrared images, such as the traditional HE (Histogram Equalization) method, and the improved HP (Histogram Projection) and PE (Plateau Equalization) method and so on. If to realize these methods in a single system, the system must have a mass of memory and extremely fast speed. In our system, we introduce a DSP + FPGA based real-time procession technology to do these things together. FPGA is used to realize the common part of these methods while DSP is to do the different part. The choice of methods and the parameter can be input by a keyboard or a computer. By this means, the function of the system is powerful while it is easy to operate and maintain. In this article, we give out the diagram of the system and the soft flow chart of the methods. And at the end of it, we give out the infrared image and its histogram before and after the process of HE method.

  2. Particle swarm optimization-based local entropy weighted histogram equalization for infrared image enhancement

    Science.gov (United States)

    Wan, Minjie; Gu, Guohua; Qian, Weixian; Ren, Kan; Chen, Qian; Maldague, Xavier

    2018-06-01

    Infrared image enhancement plays a significant role in intelligent urban surveillance systems for smart city applications. Unlike existing methods only exaggerating the global contrast, we propose a particle swam optimization-based local entropy weighted histogram equalization which involves the enhancement of both local details and fore-and background contrast. First of all, a novel local entropy weighted histogram depicting the distribution of detail information is calculated based on a modified hyperbolic tangent function. Then, the histogram is divided into two parts via a threshold maximizing the inter-class variance in order to improve the contrasts of foreground and background, respectively. To avoid over-enhancement and noise amplification, double plateau thresholds of the presented histogram are formulated by means of particle swarm optimization algorithm. Lastly, each sub-image is equalized independently according to the constrained sub-local entropy weighted histogram. Comparative experiments implemented on real infrared images prove that our algorithm outperforms other state-of-the-art methods in terms of both visual and quantized evaluations.

  3. Histogram Curve Matching Approaches for Object-based Image Classification of Land Cover and Land Use

    Science.gov (United States)

    Toure, Sory I.; Stow, Douglas A.; Weeks, John R.; Kumar, Sunil

    2013-01-01

    The classification of image-objects is usually done using parametric statistical measures of central tendency and/or dispersion (e.g., mean or standard deviation). The objectives of this study were to analyze digital number histograms of image objects and evaluate classifications measures exploiting characteristic signatures of such histograms. Two histograms matching classifiers were evaluated and compared to the standard nearest neighbor to mean classifier. An ADS40 airborne multispectral image of San Diego, California was used for assessing the utility of curve matching classifiers in a geographic object-based image analysis (GEOBIA) approach. The classifications were performed with data sets having 0.5 m, 2.5 m, and 5 m spatial resolutions. Results show that histograms are reliable features for characterizing classes. Also, both histogram matching classifiers consistently performed better than the one based on the standard nearest neighbor to mean rule. The highest classification accuracies were produced with images having 2.5 m spatial resolution. PMID:24403648

  4. Histogram Analysis of Diffusion Tensor Imaging Parameters in Pediatric Cerebellar Tumors.

    Science.gov (United States)

    Wagner, Matthias W; Narayan, Anand K; Bosemani, Thangamadhan; Huisman, Thierry A G M; Poretti, Andrea

    2016-05-01

    Apparent diffusion coefficient (ADC) values have been shown to assist in differentiating cerebellar pilocytic astrocytomas and medulloblastomas. Previous studies have applied only ADC measurements and calculated the mean/median values. Here we investigated the value of diffusion tensor imaging (DTI) histogram characteristics of the entire tumor for differentiation of cerebellar pilocytic astrocytomas and medulloblastomas. Presurgical DTI data were analyzed with a region of interest (ROI) approach to include the entire tumor. For each tumor, histogram-derived metrics including the 25th percentile, 75th percentile, and skewness were calculated for fractional anisotropy (FA) and mean (MD), axial (AD), and radial (RD) diffusivity. The histogram metrics were used as primary predictors of interest in a logistic regression model. Statistical significance levels were set at p histogram skewness showed statistically significant differences for MD between low- and high-grade tumors (P = .008). The 25th percentile for MD yields the best results for the presurgical differentiation between pediatric cerebellar pilocytic astrocytomas and medulloblastomas. The analysis of other DTI metrics does not provide additional diagnostic value. Our study confirms the diagnostic value of the quantitative histogram analysis of DTI data in pediatric neuro-oncology. Copyright © 2015 by the American Society of Neuroimaging.

  5. Value of MR histogram analyses for prediction of microvascular invasion of hepatocellular carcinoma.

    Science.gov (United States)

    Huang, Ya-Qin; Liang, He-Yue; Yang, Zhao-Xia; Ding, Ying; Zeng, Meng-Su; Rao, Sheng-Xiang

    2016-06-01

    The objective is to explore the value of preoperative magnetic resonance (MR) histogram analyses in predicting microvascular invasion (MVI) of hepatocellular carcinoma (HCC).Fifty-one patients with histologically confirmed HCC who underwent diffusion-weighted and contrast-enhanced MR imaging were included. Histogram analyses were performed and mean, variance, skewness, kurtosis, 1th, 10th, 50th, 90th, and 99th percentiles were derived. Quantitative histogram parameters were compared between HCCs with and without MVI. Receiver operating characteristics (ROC) analyses were generated to compare the diagnostic performance of tumor size, histogram analyses of apparent diffusion coefficient (ADC) maps, and MR enhancement.The mean, 1th, 10th, and 50th percentiles of ADC maps, and the mean, variance. 1th, 10th, 50th, 90th, and 99th percentiles of the portal venous phase (PVP) images were significantly different between the groups with and without MVI (P histogram analyses-in particular for 1th percentile for PVP images-held promise for prediction of MVI of HCC.

  6. Improved Steganographic Method Preserving Pixel-Value Differencing Histogram with Modulus Function

    Directory of Open Access Journals (Sweden)

    Lee Hae-Yeoun

    2010-01-01

    Full Text Available Abstract We herein advance a secure steganographic algorithm that uses a turnover policy and a novel adjusting process. Although the method of Wang et al. uses Pixel-Value Differencing (PVD and their modulus function provides high capacity and good image quality, the embedding process causes a number of artifacts, such as abnormal increases and fluctuations in the PVD histogram, which may reveal the existence of the hidden message. In order to enhance the security of the algorithm, a turnover policy is used that prevents abnormal increases in the histogram values and a novel adjusting process is devised to remove the fluctuations at the border of the subrange in the PVD histogram. The proposed method therefore eliminates all the weaknesses of the PVD steganographic methods thus far proposed and guarantees secure communication. In the experiments described herein, the proposed algorithm is compared with other PVD steganographic algorithms by using well-known steganalysis techniques, such as RS-analysis, steganalysis for LSB matching, and histogram-based attacks. The results support our contention that the proposed method enhances security by keeping the PVD histogram similar to the cover, while also providing high embedding capacity and good imperceptibility to the naked eye.

  7. Improved Steganographic Method Preserving Pixel-Value Differencing Histogram with Modulus Function

    Directory of Open Access Journals (Sweden)

    Heung-Kyu Lee

    2010-01-01

    Full Text Available We herein advance a secure steganographic algorithm that uses a turnover policy and a novel adjusting process. Although the method of Wang et al. uses Pixel-Value Differencing (PVD and their modulus function provides high capacity and good image quality, the embedding process causes a number of artifacts, such as abnormal increases and fluctuations in the PVD histogram, which may reveal the existence of the hidden message. In order to enhance the security of the algorithm, a turnover policy is used that prevents abnormal increases in the histogram values and a novel adjusting process is devised to remove the fluctuations at the border of the subrange in the PVD histogram. The proposed method therefore eliminates all the weaknesses of the PVD steganographic methods thus far proposed and guarantees secure communication. In the experiments described herein, the proposed algorithm is compared with other PVD steganographic algorithms by using well-known steganalysis techniques, such as RS-analysis, steganalysis for LSB matching, and histogram-based attacks. The results support our contention that the proposed method enhances security by keeping the PVD histogram similar to the cover, while also providing high embedding capacity and good imperceptibility to the naked eye.

  8. Histogram analysis of noise performance on fractional anisotropy brain MR image with different diffusion gradient numbers

    International Nuclear Information System (INIS)

    Chang, Yong Min; Kim, Yong Sun; Kang, Duk Sik; Lee, Young Joo; Sohn, Chul Ho; Woo, Seung Koo; Suh, Kyung Jin

    2005-01-01

    We wished to analyze, qualitatively and quantitatively, the noise performance of fractional anisotropy brain images along with the different diffusion gradient numbers by using the histogram method. Diffusion tensor images were acquired using a 3.0 T MR scanner from ten normal volunteers who had no neurological symptoms. The single-shot spin-echo EPI with a Stejskal-Tanner type diffusion gradient scheme was employed for the diffusion tensor measurement. With a b-valuee of 1000 s/mm 2 , the diffusion tensor images were obtained for 6, 11, 23, 35 and 47 diffusion gradient directions. FA images were generated for each DTI scheme. The histograms were then obtained at selected ROIs for the anatomical structures on the FA image. At the same ROI location, the mean FA value and the standard deviation of the mean FA value were calculated. The quality of the FA image was improved as the number of diffusion gradient directions increased by showing better contrast between the WM and GM. The histogram showed that the variance of FA values was reduced as the number of diffusion gradient directions increased. This histogram analysis was in good agreement with the result obtained using quantitative analysis. The image quality of the FA map was significantly improved as the number of diffusion gradient directions increased. The histogram analysis well demonstrated that the improvement in the FA images resulted from the reduction in the variance of the FA values included in the ROI

  9. "I think we've got too many tests!": Prenatal providers' reflections on ethical and clinical challenges in the practice integration of cell-free DNA screening.

    Science.gov (United States)

    Gammon, B L; Kraft, S A; Michie, M; Allyse, M

    2016-01-01

    The recent introduction of cell-free DNA-based non-invasive prenatal screening (cfDNA screening) into clinical practice was expected to revolutionize prenatal testing. cfDNA screening for fetal aneuploidy has demonstrated higher test sensitivity and specificity for some conditions than conventional serum screening and can be conducted early in the pregnancy. However, it is not clear whether and how clinical practices are assimilating this new type of testing into their informed consent and counselling processes. Since the introduction of cfDNA screening into practice in 2011, the uptake and scope have increased dramatically. Prenatal care providers are under pressure to stay up to date with rapidly changing cfDNA screening panels, manage increasing patient demands, and keep up with changing test costs, all while attempting to use the technology responsibly and ethically. While clinical literature on cfDNA screening has shown benefits for specific patient populations, it has also identified significant misunderstandings among providers and patients alike about the power of the technology. The unique features of cfDNA screening, in comparison to established prenatal testing technologies, have implications for informed decision-making and genetic counselling that must be addressed to ensure ethical practice. This study explored the experiences of prenatal care providers at the forefront of non-invasive genetic screening in the United States to understand how this testing changes the practice of prenatal medicine. We aimed to learn how the experience of providing and offering this testing differs from established prenatal testing methodologies. These differences may necessitate changes to patient education and consent procedures to maintain ethical practice. We used the online American Congress of Obstetricians and Gynecologists Physician Directory to identify a systematic sample of five prenatal care providers in each U.S. state and the District of Columbia. Beginning

  10. Repeatability of derived parameters from histograms following non-Gaussian diffusion modelling of diffusion-weighted imaging in a paediatric oncological cohort

    Energy Technology Data Exchange (ETDEWEB)

    Jerome, Neil P.; Miyazaki, Keiko; Collins, David J.; Orton, Matthew R.; D' Arcy, James A.; Leach, Martin O. [Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London (United Kingdom); Wallace, Toni; Koh, Dow-Mu [Royal Marsden NHS Foundation Trust, Department of Radiology, Sutton, Surrey (United Kingdom); Moreno, Lucas [The Institute of Cancer Research, Paediatric Drug Development Team, Division of Cancer Therapeutics and Clinical Studies, London (United Kingdom); Hospital Nino Jesus, Madrid (Spain); Royal Marsden NHS Foundation Trust, Paediatric Drug Development Unit, Children and Young People' s Unit, Sutton, Surrey (United Kingdom); Pearson, Andrew D.J.; Marshall, Lynley V.; Carceller, Fernando; Zacharoulis, Stergios [The Institute of Cancer Research, Paediatric Drug Development Team, Division of Cancer Therapeutics and Clinical Studies, London (United Kingdom); Royal Marsden NHS Foundation Trust, Paediatric Drug Development Unit, Children and Young People' s Unit, Sutton, Surrey (United Kingdom)

    2017-01-15

    To examine repeatability of parameters derived from non-Gaussian diffusion models in data acquired in children with solid tumours. Paediatric patients (<16 years, n = 17) were scanned twice, 24 h apart, using DWI (6 b-values, 0-1000 mm{sup -2} s) at 1.5 T in a prospective study. Tumour ROIs were drawn (3 slices) and all data fitted using IVIM, stretched exponential, and kurtosis models; percentage coefficients of variation (CV) calculated for each parameter at all ROI histogram centiles, including the medians. The values for ADC, D, DDC{sub α}, α, and DDC{sub K} gave CV < 10 % down to the 5th centile, with sharp CV increases below 5th and above 95th centile. K, f, and D* showed increased CV (>30 %) over the histogram. ADC, D, DDC{sub α}, and DDC{sub K} were strongly correlated (ρ > 0.9), DDC{sub α} and α were not correlated (ρ = 0.083). Perfusion- and kurtosis-related parameters displayed larger, more variable CV across the histogram, indicating observed clinical changes outside of D/DDC in these models should be interpreted with caution. Centiles below 5th for all parameters show high CV and are unreliable as diffusion metrics. The stretched exponential model behaved well for both DDC{sub α} and α, making it a strong candidate for modelling multiple-b-value diffusion imaging data. (orig.)

  11. Clinical response to chemotherapy in locally advanced breast cancer was not associated with several polymorphisms in detoxification enzymes and DNA repair genes.

    Science.gov (United States)

    Saadat, Mostafa; Khalili, Maryam; Nasiri, Meysam; Rajaei, Mehrdad; Omidvari, Shahpour; Saadat, Iraj

    2012-03-02

    The main aim of the present study was to investigate the association between several genetic polymorphisms (in glutathione S-transferase members and DNA repair genes) and clinical response to chemotherapy in locally advanced breast cancer. A sequential series of 101 patients were prospectively included in this study. Clinical assessment of treatment was accomplished by comparing initial tumor size with preoperative tumor size using revised RECIST guideline (version 1.1). Clinical response was regarded as a response or no response. There was no difference between non-responders and responders for the prevalence of genotypes of the study polymorphisms. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  13. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  14. Apparent diffusion coefficient histogram metrics correlate with survival in diffuse intrinsic pontine glioma: a report from the Pediatric Brain Tumor Consortium

    Science.gov (United States)

    Poussaint, Tina Young; Vajapeyam, Sridhar; Ricci, Kelsey I.; Panigrahy, Ashok; Kocak, Mehmet; Kun, Larry E.; Boyett, James M.; Pollack, Ian F.; Fouladi, Maryam

    2016-01-01

    Background Diffuse intrinsic pontine glioma (DIPG) is associated with poor survival regardless of therapy. We used volumetric apparent diffusion coefficient (ADC) histogram metrics to determine associations with progression-free survival (PFS) and overall survival (OS) at baseline and after radiation therapy (RT). Methods Baseline and post-RT quantitative ADC histograms were generated from fluid-attenuated inversion recovery (FLAIR) images and enhancement regions of interest. Metrics assessed included number of peaks (ie, unimodal or bimodal), mean and median ADC, standard deviation, mode, skewness, and kurtosis. Results Based on FLAIR images, the majority of tumors had unimodal peaks with significantly shorter average survival. Pre-RT FLAIR mean, mode, and median values were significantly associated with decreased risk of progression; higher pre-RT ADC values had longer PFS on average. Pre-RT FLAIR skewness and standard deviation were significantly associated with increased risk of progression; higher pre-RT FLAIR skewness and standard deviation had shorter PFS. Nonenhancing tumors at baseline showed higher ADC FLAIR mean values, lower kurtosis, and higher PFS. For enhancing tumors at baseline, bimodal enhancement histograms had much worse PFS and OS than unimodal cases and significantly lower mean peak values. Enhancement in tumors only after RT led to significantly shorter PFS and OS than in patients with baseline or no baseline enhancement. Conclusions ADC histogram metrics in DIPG demonstrate significant correlations between diffusion metrics and survival, with lower diffusion values (increased cellularity), increased skewness, and enhancement associated with shorter survival, requiring future investigations in large DIPG clinical trials. PMID:26487690

  15. Epstein-Barr virus antibodies in serum and DNA load in saliva are not associated with radiological or clinical disease activity in patients with early multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    René M Gieß

    Full Text Available To investigate the association of Epstein-Barr virus (EBV nuclear antigen-1 (EBNA-1 and viral capsid antigen (VCA immunoglobulin (IgG antibodies in serum as well as EBV DNA load in saliva with radiological and clinical disease activity in patients with clinically isolated syndrome (CIS and early relapsing-remitting MS (RRMS.EBNA-1 and VCA immunoglobulin (IgG antibodies were determined in serum of 100 patients with CIS/early RRMS and 60 healthy controls. EBV DNA load was measured in saliva of 48 patients and 50 controls. Patients underwent clinical assessment with the Expanded Disability Status Scale (EDSS and 3 Tesla magnetic resonance imaging at baseline and after a median of 20 months of follow-up (n = 63 for MRI, n = 71 for EDSS. The association of EBV parameters with occurrence of a second relapse, indicating conversion to clinically definite MS (CDMS, was evaluated over a median of 35 months of follow-up after the first clinical event (n = 89.EBNA-1 IgG antibody frequency (p = 0.00005 and EBNA-1 and VCA IgG antibody levels (p<0.0001 for both were higher in patients than in controls. EBV DNA load in saliva did not differ between groups. Neither EBV antibody levels nor DNA load in saliva were associated with baseline or follow-up number or volume of T2-weighted (T2w or contrast enhancing lesions, number of Barkhof criteria or the EDSS, or with the number of new T2w lesions, T2w lesion volume change or EDSS change on follow-up. Likewise, levels of EBV IgG antibodies in serum and DNA load in saliva were not associated with conversion to CDMS.While these findings confirm the association of EBV infection with early MS, neither EBNA-1 nor VCA IgG antibodies in serum nor EBV DNA load in saliva were associated with radiological or clinical disease activity in patients with CIS/early RRMS. These data are compatible with the concept that EBV may be a trigger for MS acting very early during the development of the disease.

  16. Infrared face recognition based on LBP histogram and KW feature selection

    Science.gov (United States)

    Xie, Zhihua

    2014-07-01

    The conventional LBP-based feature as represented by the local binary pattern (LBP) histogram still has room for performance improvements. This paper focuses on the dimension reduction of LBP micro-patterns and proposes an improved infrared face recognition method based on LBP histogram representation. To extract the local robust features in infrared face images, LBP is chosen to get the composition of micro-patterns of sub-blocks. Based on statistical test theory, Kruskal-Wallis (KW) feature selection method is proposed to get the LBP patterns which are suitable for infrared face recognition. The experimental results show combination of LBP and KW features selection improves the performance of infrared face recognition, the proposed method outperforms the traditional methods based on LBP histogram, discrete cosine transform(DCT) or principal component analysis(PCA).

  17. ANALISA PENINGKATAN KUALITAS CITRA BAWAH AIR BERBASIS KOREKSI GAMMA dan HISTOGRAM EQUALIZATION

    Directory of Open Access Journals (Sweden)

    Aria Hendrawan

    2016-11-01

    Full Text Available Underwater image of water quality in the dark, it depends on the depth of water at the time of image acquisition or image. The results of the image quality is adversely affecting the results matching the image pairs underwater with SIFT algorithm. This research aims to use the method of image preprocessing and Histogram Equalization Gamma Correction that works to improve the quality of images underwater. The results showed 27.76% increase using image preprocessing Gamma Correction and Histogram Equalization compared with no increase in image quality. Results of paired t-test has the null hypothesis is rejected so that there is a significant difference between the application of Gamma Correction Histogram Equalization with and without image enhancement.

  18. A novel JPEG steganography method based on modulus function with histogram analysis

    Directory of Open Access Journals (Sweden)

    V. Banoci

    2012-06-01

    Full Text Available In this paper, we present a novel steganographic method for embedding of secret data in still grayscale JPEG image. In order to provide large capacity of the proposed method while maintaining good visual quality of stego-image, the embedding process is performed in quantized transform coefficients of Discrete Cosine transform (DCT by modifying coefficients according to modulo function, what gives to the steganography system blind extraction predisposition. After-embedding histogram of proposed Modulo Histogram Fitting (MHF method is analyzed to secure steganography system against steganalysis attacks. In addition, AES ciphering was implemented to increase security and improve histogram after-embedding characteristics of proposed steganography system as experimental results show.

  19. Histogram analysis of apparent diffusion coefficient maps for differentiating primary CNS lymphomas from tumefactive demyelinating lesions.

    Science.gov (United States)

    Lu, Shan Shan; Kim, Sang Joon; Kim, Namkug; Kim, Ho Sung; Choi, Choong Gon; Lim, Young Min

    2015-04-01

    This study intended to investigate the usefulness of histogram analysis of apparent diffusion coefficient (ADC) maps for discriminating primary CNS lymphomas (PCNSLs), especially atypical PCNSLs, from tumefactive demyelinating lesions (TDLs). Forty-seven patients with PCNSLs and 18 with TDLs were enrolled in our study. Hyperintense lesions seen on T2-weighted images were defined as ROIs after ADC maps were registered to the corresponding T2-weighted image. ADC histograms were calculated from the ROIs containing the entire lesion on every section and on a voxel-by-voxel basis. The ADC histogram parameters were compared among all PCNSLs and TDLs as well as between the subgroup of atypical PCNSLs and TDLs. ROC curves were constructed to evaluate the diagnostic performance of the histogram parameters and to determine the optimum thresholds. The differences between the PCNSLs and TDLs were found in the minimum ADC values (ADCmin) and in the 5th and 10th percentiles (ADC5% and ADC10%) of the cumulative ADC histograms. However, no statistical significance was found in the mean ADC value or in the ADC value concerning the mode, kurtosis, and skewness. The ADCmin, ADC5%, and ADC10% were also lower in atypical PCNSLs than in TDLs. ADCmin was the best indicator for discriminating atypical PCNSLs from TDLs, with a threshold of 556×10(-6) mm2/s (sensitivity, 81.3 %; specificity, 88.9%). Histogram analysis of ADC maps may help to discriminate PCNSLs from TDLs and may be particularly useful in differentiating atypical PCNSLs from TDLs.

  20. Glioma grade assessment by using histogram analysis of diffusion tensor imaging-derived maps

    International Nuclear Information System (INIS)

    Jakab, Andras; Berenyi, Ervin; Molnar, Peter; Emri, Miklos

    2011-01-01

    Current endeavors in neuro-oncology include morphological validation of imaging methods by histology, including molecular and immunohistochemical techniques. Diffusion tensor imaging (DTI) is an up-to-date methodology of intracranial diagnostics that has gained importance in studies of neoplasia. Our aim was to assess the feasibility of discriminant analysis applied to histograms of preoperative diffusion tensor imaging-derived images for the prediction of glioma grade validated by histomorphology. Tumors of 40 consecutive patients included 13 grade II astrocytomas, seven oligoastrocytomas, six grade II oligodendrogliomas, three grade III oligoastrocytomas, and 11 glioblastoma multiformes. Preoperative DTI data comprised: unweighted (B 0 ) images, fractional anisotropy, longitudinal and radial diffusivity maps, directionally averaged diffusion-weighted imaging, and trace images. Sampling consisted of generating histograms for gross tumor volumes; 25 histogram bins per scalar map were calculated. The histogram bins that allowed the most precise determination of low-grade (LG) or high-grade (HG) classification were selected by multivariate discriminant analysis. Accuracy of the model was defined by the success rate of the leave-one-out cross-validation. Statistical descriptors of voxel value distribution did not differ between LG and HG tumors and did not allow classification. The histogram model had 88.5% specificity and 85.7% sensitivity in the separation of LG and HG gliomas; specificity was improved when cases with oligodendroglial components were omitted. Constructing histograms of preoperative radiological images over the tumor volume allows representation of the grade and enables discrimination of LG and HG gliomas which has been confirmed by histopathology. (orig.)

  1. Diagnosis of canine visceral leishmaniasis with radiolabelled probes: comparison of the kDNA PCR-hybridization with three molecular methods in different clinical samples

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Aline Leandra C.; Ferreira, Sidney A.; Carregal, Virginia M.; Andrade, Antero Silva R., E-mail: antero@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil). Lab. de Radiobiologia; Melo, Maria N., E-mail: melo@icb.ufmg.br [Departamento de Parasitologia. Instituto de Ciencias Biologicas. Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil)

    2011-07-01

    Leishmania (Leishmania) chagasi is responsible for visceral leishmaniasis (VL) in Brazil and the dog is the main domestic reservoir. Disease control is based on the elimination of infected animals and the use of a sensitive and specific diagnostic test is necessary. The Brazilian VL control program emphasizes serologic surveys, mainly using the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescence antibody test (IFAT), followed by the elimination of the seropositive dogs. However, these techniques present limitations in terms of sensitivity and specificity. The Polymerase Chain Reaction (PCR) associated to hybridization with DNA probes labeled with {sup 32}P has been recognized as a valuable tool for Leishmania identification. In this study, the sensitivity of kDNA PCR hybridization method was compared with three other molecular methods: Internal Transcribed Spacer 1 Nested PCR (ITS-1nPCR), Leishmania nested PCR (LnPCR) and Seminested kDNA PCR (kDNA snPCR). The comparison was performed in different clinical specimens: conjunctival swab, skin, blood and bone marrow. A group of thirty symptomatic dogs, positive in the parasitological and serological tests, was used. When. The techniques targeting kDNA mini-circles (kDNA snPCR and KDNA PCR-hybridization) showed the worst result for blood samples. The KDNA-PCR hybridization showed the best sensitivity for conjunctival swab. By comparing the samples on the basis of positivity obtained by the sum of all methods, the blood showed the worst outcome (71/120).The bone marrow showed the highest positivity (106/120), followed by conjunctival swab (100/120) and skin (89/120). Since the bone marrow samples are unsuitable for routine epidemiological surveys, the conjunctival swab was recommended because it allows high sensitivity, especially when associated with kDNA PCR hybridization method, and is a noninvasive sampling method. (author)

  2. Diagnosis of canine visceral leishmaniasis with radiolabelled probes: comparison of the kDNA PCR-hybridization with three molecular methods in different clinical samples

    International Nuclear Information System (INIS)

    Ferreira, Aline Leandra C.; Ferreira, Sidney A.; Carregal, Virginia M.; Andrade, Antero Silva R.

    2011-01-01

    Leishmania (Leishmania) chagasi is responsible for visceral leishmaniasis (VL) in Brazil and the dog is the main domestic reservoir. Disease control is based on the elimination of infected animals and the use of a sensitive and specific diagnostic test is necessary. The Brazilian VL control program emphasizes serologic surveys, mainly using the enzyme-linked immunosorbent assay (ELISA) and the immunofluorescence antibody test (IFAT), followed by the elimination of the seropositive dogs. However, these techniques present limitations in terms of sensitivity and specificity. The Polymerase Chain Reaction (PCR) associated to hybridization with DNA probes labeled with 32 P has been recognized as a valuable tool for Leishmania identification. In this study, the sensitivity of kDNA PCR hybridization method was compared with three other molecular methods: Internal Transcribed Spacer 1 Nested PCR (ITS-1nPCR), Leishmania nested PCR (LnPCR) and Seminested kDNA PCR (kDNA snPCR). The comparison was performed in different clinical specimens: conjunctival swab, skin, blood and bone marrow. A group of thirty symptomatic dogs, positive in the parasitological and serological tests, was used. When. The techniques targeting kDNA mini-circles (kDNA snPCR and KDNA PCR-hybridization) showed the worst result for blood samples. The KDNA-PCR hybridization showed the best sensitivity for conjunctival swab. By comparing the samples on the basis of positivity obtained by the sum of all methods, the blood showed the worst outcome (71/120).The bone marrow showed the highest positivity (106/120), followed by conjunctival swab (100/120) and skin (89/120). Since the bone marrow samples are unsuitable for routine epidemiological surveys, the conjunctival swab was recommended because it allows high sensitivity, especially when associated with kDNA PCR hybridization method, and is a noninvasive sampling method. (author)

  3. Comparison of dose length, area, and volume histograms as quantifiers of urethral dose in prostate brachytherapy

    International Nuclear Information System (INIS)

    Butler, Wayne M.; Merrick, Gregory S.; Dorsey, Anthony T.; Hagedorn, Brenda M.

    2000-01-01

    cooler than 125 I implants over most of the range of clinical interest, from 100% to 150% of mPD. Conclusion: Dose gradients in prostate implants result in the observed ordering of DAH, DVH, and DLH from higher to lower doses. The three histogram approaches remain in close agreement up to 100% of the mPD but diverge at higher doses. Although urethral point doses are the most easily determined, they underestimate the amount of urethra at risk at higher doses compared to dose area analysis. Because dosimetric parameters detailing high-dose regions such as D 10 show only slight differences between calculation methods, they are recommended over the corresponding geometric entities G 150 or G 175 . The differences between the D gg entities are sufficiently small that they are unlikely to be of clinical significance or to confound analyses attempting to correlate urinary morbidity with urethral dosimetry.

  4. Histogram-based normalization technique on human brain magnetic resonance images from different acquisitions.

    Science.gov (United States)

    Sun, Xiaofei; Shi, Lin; Luo, Yishan; Yang, Wei; Li, Hongpeng; Liang, Peipeng; Li, Kuncheng; Mok, Vincent C T; Chu, Winnie C W; Wang, Defeng

    2015-07-28

    Intensity normalization is an important preprocessing step in brain magnetic resonance image (MRI) analysis. During MR image acquisition, different scanners or parameters would be used for scanning different subjects or the same subject at a different time, which may result in large intensity variations. This intensity variation will greatly undermine the performance of subsequent MRI processing and population analysis, such as image registration, segmentation, and tissue volume measurement. In this work, we proposed a new histogram normalization method to reduce the intensity variation between MRIs obtained from different acquisitions. In our experiment, we scanned each subject twice on two different scanners using different imaging parameters. With noise estimation, the image with lower noise level was determined and treated as the high-quality reference image. Then the histogram of the low-quality image was normalized to the histogram of the high-quality image. The normalization algorithm includes two main steps: (1) intensity scaling (IS), where, for the high-quality reference image, the intensities of the image are first rescaled to a range between the low intensity region (LIR) value and the high intensity region (HIR) value; and (2) histogram normalization (HN),where the histogram of low-quality image as input image is stretched to match the histogram of the reference image, so that the intensity range in the normalized image will also lie between LIR and HIR. We performed three sets of experiments to evaluate the proposed method, i.e., image registration, segmentation, and tissue volume measurement, and compared this with the existing intensity normalization method. It is then possible to validate that our histogram normalization framework can achieve better results in all the experiments. It is also demonstrated that the brain template with normalization preprocessing is of higher quality than the template with no normalization processing. We have proposed

  5. A New Method of Histogram Computation for Efficient Implementation of the HOG Algorithm

    Directory of Open Access Journals (Sweden)

    Mariana-Eugenia Ilas

    2018-03-01

    Full Text Available In this paper we introduce a new histogram computation method to be used within the histogram of oriented gradients (HOG algorithm. The new method replaces the arctangent with the slope computation and the classical magnitude allocation based on interpolation with a simpler algorithm. The new method allows a more efficient implementation of HOG in general, and particularly in field-programmable gate arrays (FPGAs, by considerably reducing the area (thus increasing the level of parallelism, while maintaining very close classification accuracy compared to the original algorithm. Thus, the new method is attractive for many applications, including car detection and classification.

  6. A 64 Mbyte VME histogramming memory card for the GA.SP gamma spectrometer

    International Nuclear Information System (INIS)

    Cavedini, Z.; DePoli, M.; Maron, G.; Vedovato, G.

    1990-01-01

    This paper reports on a 64 Mbyte VME histogramming memory card designed and built to cover the on-line and off-line data analysis needs of the GA.SP spectrometer (a 40 HpGe gamma detector array in development at LNL). The card combines the standard features of the VME/VSB bus with some special built-in functions: single cycle fast histogramming operations (typical channel increment time of 550 ns including the bus arbitration), fast clear of the whole memory (∼1 second to erase 64 Mbyte) and data broadcasting

  7. Hippocampal dose volume histogram predicts Hopkins Verbal Learning Test scores after brain irradiation

    Directory of Open Access Journals (Sweden)

    Catherine Okoukoni, PhD

    2017-10-01

    Full Text Available Purpose: Radiation-induced cognitive decline is relatively common after treatment for primary and metastatic brain tumors; however, identifying dosimetric parameters that are predictive of radiation-induced cognitive decline is difficult due to the heterogeneity of patient characteristics. The memory function is especially susceptible to radiation effects after treatment. The objective of this study is to correlate volumetric radiation doses received by critical neuroanatomic structures to post–radiation therapy (RT memory impairment. Methods and materials: Between 2008 and 2011, 53 patients with primary brain malignancies were treated with conventionally fractionated RT in prospectively accrued clinical trials performed at our institution. Dose-volume histogram analysis was performed for the hippocampus, parahippocampus, amygdala, and fusiform gyrus. Hopkins Verbal Learning Test-Revised scores were obtained at least 6 months after RT. Impairment was defined as an immediate recall score ≤15. For each anatomic region, serial regression was performed to correlate volume receiving a given dose (VD(Gy with memory impairment. Results: Hippocampal V53.4Gy to V60.9Gy significantly predicted post-RT memory impairment (P < .05. Within this range, the hippocampal V55Gy was the most significant predictor (P = .004. Hippocampal V55Gy of 0%, 25%, and 50% was associated with tumor-induced impairment rates of 14.9% (95% confidence interval [CI], 7.2%-28.7%, 45.9% (95% CI, 24.7%-68.6%, and 80.6% (95% CI, 39.2%-96.4%, respectively. Conclusions: The hippocampal V55Gy is a significant predictor for impairment, and a limiting dose below 55 Gy may minimize radiation-induced cognitive impairment.

  8. Apparent diffusion coefficient histogram analysis of neonatal hypoxic-ischemic encephalopathy

    International Nuclear Information System (INIS)

    Cauley, Keith A.; Filippi, Christopher G.

    2014-01-01

    Diffusion-weighted imaging is a valuable tool in the assessment of the neonatal brain, and changes in diffusion are seen in normal development as well as in pathological states such as hypoxic-ischemic encephalopathy (HIE). Various methods of quantitative assessment of diffusion values have been reported. Global ischemic injury occurring during the time of rapid developmental changes in brain myelination can complicate the imaging diagnosis of neonatal HIE. To compare a quantitative method of histographic analysis of brain apparent coefficient (ADC) maps to the qualitative interpretation of routine brain MR imaging studies. We correlate changes in diffusion values with gestational age in radiographically normal neonates, and we investigate the sensitivity of the method as a quantitative measure of hypoxic-ischemic encephalopathy. We reviewed all brain MRI studies from the neonatal intensive care unit (NICU) at our university medical center over a 4-year period to identify cases that were radiographically normal (23 cases) and those with diffuse, global hypoxic-ischemic encephalopathy (12 cases). We histographically displayed ADC values of a single brain slice at the level of the basal ganglia and correlated peak (s-sD av ) and lowest histogram values (s-sD lowest ) with gestational age. Normative s-sD av values correlated significantly with gestational age and declined linearly through the neonatal period (r 2 = 0.477, P av and s-sD lowest ADC values than were reflected in the normative distribution; several cases of HIE fell within a 95% confidence interval for normative studies, and one case demonstrated higher-than-normal s-sD av . Single-slice histographic display of ADC values is a rapid and clinically feasible method of quantitative analysis of diffusion. In this study normative values derived from consecutive neonates without radiographic evidence of ischemic injury are correlated with gestational age, declining linearly throughout the perinatal period. This

  9. Frequency and clinical correlates of elevated plasma Epstein-Barr virus DNA at diagnosis in peripheral T-cell lymphomas

    Science.gov (United States)

    Haverkos, Bradley M.; Huang, Ying; Gru, Alejandro; Pancholi, Preeti; Freud, Aharon G.; Mishra, Anjali; Ruppert, Amy S.; Baiocchi, Robert A.; Porcu, Pierluigi

    2016-01-01

    Epstein Barr virus (EBV)-encoded RNAs (EBER) in tumor tissue and cell-free plasma EBV-DNA (pEBVd) are detected in EBV-associated lymphomas. Studies have suggested that EBER+ peripheral T-cell lymphomas (PTCL) have worse prognosis, but the role of EBV in these neoplasms remains unclear. pEBVd is quantitative and more easily amenable to standardization than EBER, but frequency of pEBVd detection, clinical impact, and agreement with EBER status in PTCL are unknown. We retrospectively assessed frequency of detectable pre-treatment pEBVd, presence of EBER in tumor tissue, and outcomes in 61 of 135 EBV-assessable PTCL patients. Fifteen of 61 patients (24.5%, 95% CI: 14–37%) were pre-treatment pEBVd+, with no significant differences in baseline characteristics or treatment between pEBVd+ and pEBVd− patients. EBER-ISH was performed on 10 pEBVd+ and 35 pEBVd− tumors. All 10 pEBVd+ patients were EBER+, but 9 pEBVd− patients were also EBER+. With median follow up of 24 months (range 1–96), overall survival (OS) was shorter in pEBVd+ compared to pEBVd− patients (13 vs. 72 months; p=0.04). In this retrospective study, pre-treatment pEBVd was elevated in 25% of PTCL patients, was highly specific for EBER+ tumors, and was associated with shorter survival. pEBVd should be further explored as a prognostic variable and tumor biomarker in PTCL. PMID:27943278

  10. Terbinafine susceptibility and genotypic heterogeneity in clinical isolates of Trichophyton mentagrophytes by random amplified polymorphic DNA (RAPD).

    Science.gov (United States)

    Alipour, M; Mozafari, N A

    2015-03-01

    The four RAPD systems tested in the present study have aimed at investigating DNA fingerprinting of Trichophyton mentagrophytes strains and the correlation between genotyping and antifungal susceptibility to terbinafine. Twenty-nine clinical isolates of T. mentagrophytes were recovered from patients suspected of having active dermatophytosis who were referred to the laboratory of medical mycology department in Tehran university. Then, they were subjected to conventional examination by performing direct microscopic examination, culture on primary media, physiological tests. The in vitro antifungal susceptibility of twenty-nine T. mentagrophytes isolates against terbinafine was evaluated by modified agar dilution method to determine the minimum inhibitory concentration (MIC). Twenty-one sensitive and eight resistant to terbinafine, were submitted to RAPD using 4 decamer primers (A, B, C, D) with the purpose of encountering a genetic marker to terbinafine sensibility and resistance. The UPGMA-Jaccard's correlation coefficient was used to build up dendogram that could represent clusters of similarity. According to their correlation coefficient, the samples were classified as much related (100%), moderately related (80%) and unrelated (terbinafine. All susceptible samples were properly grouped, but a few numbers of resistant isolates were also included. Nevertheless, further biochemical and molecular biological studies will be required to fully elucidate the point that resistance might be the result of a mutation in the gene encoding squalene epoxidase in T. mentagrophytes. This study proved efficacy of applying RAPD molecular technique to complement traditional mycological culture and drug susceptibility tests for accurate and appropriate management of recurrent dermatophytosis and highlights the need for newer antifungals that can combat the emergence of terbinafine-resistant T. mentagrophytes strains. Copyright © 2015. Published by Elsevier Masson SAS.

  11. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  12. Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing

    OpenAIRE

    Wang, Huiping; Kong, Fanrong; Sorrell, Tania C; Wang, Bin; McNicholas, Paul; Pantarat, Namfon; Ellis, David; Xiao, Meng; Widmer, Fred; Chen, Sharon CA

    2009-01-01

    Abstract Background Amino acid substitutions in the target enzyme Erg11p of azole antifungals contribute to clinically-relevant azole resistance in Candida albicans. A simple molecular method for rapid detection of ERG11 gene mutations would be an advantage as a screening tool to identify potentially-resistant strains and to track their movement. To complement DNA sequencing, we developed a padlock probe and rolling circle amplification (RCA)-based method to detect a series of mutations in th...

  13. Tenofovir alafenamide (TAF) does not deplete mitochondrial DNA in human T-cell lines at intracellular concentrations exceeding clinically relevant drug exposures.

    Science.gov (United States)

    Stray, Kirsten M; Park, Yeojin; Babusis, Darius; Callebaut, Christian; Cihlar, Tomas; Ray, Adrian S; Perron, Michel

    2017-04-01

    HIV-infected patients treated with certain nucleoside reverse transcriptase inhibitors (NRTIs) have experienced adverse effects due to drug-related mitochondrial toxicity. Tenofovir alafenamide (TAF) is a novel prodrug of the NRTI tenofovir (TFV) with an improved safety profile compared to tenofovir disoproxil fumarate (TDF). Prior in vitro studies have demonstrated that the parent nucleotide TFV has no significant effects on mtDNA synthesis. This study investigated whether clinically relevant TAF and TDF exposures affect mtDNA content in human lymphocytes. First, activated or resting peripheral blood mononuclear cells (PBMCs), as well as MT-2 and Jurkat T-cell lines, were continuously treated with ddC for 10 days to establish their susceptibility to mtDNA depletion. PBMCs had low sensitivity to NRTI-mediated mtDNA depletion in vitro. In contrast, ddC treatment of rapidly dividing MT-2 and Jurkat cells resulted in a dose-dependent decrease in mtDNA. Therefore, these two T-cell lines were selected for evaluating TAF and TDF treatment effects. MT-2 and Jurkat cells were pulse-treated with TAF or TDF every 24 h for 10 days to mimic pharmacologically relevant drug exposures. Pulse treatment of cells with 3.3 μM TAF or 1.1 μM TDF for 10 days resulted in 2- to 7-fold greater steady-state intracellular TFV-diphosphate (TFV-DP) levels than those observed clinically in TAF- or TDF-treated patients. At these concentrations, no significant TAF- (106.7% and 84.1% of control; p = 0.77 and 0.12 for MT-2 and Jurkat, respectively) or TDF- (100.6% and 91.0% of control; p = 0.91 and 0.37, respectively) associated reduction in mtDNA content was observed compared with untreated control cells. This study demonstrates that, despite delivering higher intracellular levels of TFV-DP than TDF, TAF does not inhibit mtDNA synthesis in vitro at concentrations exceeding the clinically relevant intracellular drug exposures. Thus, TAF has a low potential for mitochondrial toxicity in

  14. Overexpression of Aldo-Keto-Reductase in Azole-resistant Clinical Isolates of Candida Glabrata Determined by cDNA-AFLP

    Directory of Open Access Journals (Sweden)

    Mansour Heidari

    2013-01-01

    Full Text Available Background: Candida glabrata causes significant medical problems in immunocompromised patients. Many strains of this yeast are intrinsically resistant to azole antifungal agents, and treatment is problematic, leading to high morbidity and mortality rates in immunosuppressed individuals. The primary goal of this study was to investigate the genes involved in the drug resistance of clinical isolates of C. glabrata.Methods: The clinical isolates of C. glabrata were collected in an epidemiological survey of candidal infection inimmunocompromised patients and consisted of four fluconazole and itraconazole resistant isolates, two fluconazoleand itraconazole sensitive isolates, and C. glabrata CBS 138 as reference strain. Antifungal susceptibility patterns ofthe organisms were determined beforehand by the Clinical and Laboratory Standards Institute (CLSI. The potentialgene(s implicated in antifungal resistance were investigated using complementary DNA- Amplified Fragment Length Polymorphism (cDNA-AFLP. Semi-quantitative RT-PCR was carried out to evaluate the expression of gene(s in resistant isolates as compared to sensitive and reference strains.Results and conclusions: The aldo-keto-reductase superfamily (AKR gene was upregulated in the resistant clinicalisolates as assessed by cDNA-AFLP. Semi-quantitative RT-PCR revealed AKR mRNA expression approximately twice that seen in the sensitive isolates. Overexpression of the AKR gene was associated with increased fluconazole and itraconazole resistance in C. glabrata. The data suggest that upregulation of the AKR gene might give a new insight into the mechanism of azole resistance.

  15. [On the use of FTA technology for collection, archieving, and molecular analysis of microsporidia dna from clinical stool samples].

    Science.gov (United States)

    Sokolova, O I; Dem'ianov, A V; Bovers, L S; Did'e, E S; Sokolova, Iu Ia

    2011-01-01

    The FTA technology was applied for sampling, archiving, and molecular analysis of the DNA isolated from stool samples to diagnose and identify microsporidia, the intracellular opportunistic parasites which induce malabsortion syndrome in immunosuppressed humans, particularly in patients with AIDS. Microsporidia DNA was successfully amplified in 6 of 50 stool samples of HIV-positive patients of the S. P. Botkin Memorial Infectious Disease Hospital (St. Petersburg) applied to FTA cards (FTA-Cars, Whatman Inc. Florham Park, NJ, USA). Amplicons (the fragments of rDNA) were directly sequenced, and microsporidia species--Encephalitozoon intestinalis, E. cuniculi, E. hellem, and Enterocytozoon bieneusi--were identified in Genbank by NCBI BLAST program. The FTA method of DNA immobilization is especially promising for epidemiological and field population studies which involve genotyping of microsporidia species and isolates.

  16. Robust Face Recognition by Computing Distances from Multiple Histograms of Oriented Gradients

    NARCIS (Netherlands)

    Karaaba, Mahir; Surinta, Olarik; Schomaker, Lambertus; Wiering, Marco

    2015-01-01

    The Single Sample per Person Problem is a challenging problem for face recognition algorithms. Patch-based methods have obtained some promising results for this problem. In this paper, we propose a new face recognition algorithm that is based on a combination of different histograms of oriented

  17. Using color histogram normalization for recovering chromatic illumination-changed images.

    Science.gov (United States)

    Pei, S C; Tseng, C L; Wu, C C

    2001-11-01

    We propose a novel image-recovery method using the covariance matrix of the red-green-blue (R-G-B) color histogram and tensor theories. The image-recovery method is called the color histogram normalization algorithm. It is known that the color histograms of an image taken under varied illuminations are related by a general affine transformation of the R-G-B coordinates when the illumination is changed. We propose a simplified affine model for application with illumination variation. This simplified affine model considers the effects of only three basic forms of distortion: translation, scaling, and rotation. According to this principle, we can estimate the affine transformation matrix necessary to recover images whose color distributions are varied as a result of illumination changes. We compare the normalized color histogram of the standard image with that of the tested image. By performing some operations of simple linear algebra, we can estimate the matrix of the affine transformation between two images under different illuminations. To demonstrate the performance of the proposed algorithm, we divide the experiments into two parts: computer-simulated images and real images corresponding to illumination changes. Simulation results show that the proposed algorithm is effective for both types of images. We also explain the noise-sensitive skew-rotation estimation that exists in the general affine model and demonstrate that the proposed simplified affine model without the use of skew rotation is better than the general affine model for such applications.

  18. Strain histograms are equal to strain ratios in predicting malignancy in breast tumours

    DEFF Research Database (Denmark)

    Carlsen, Jonathan Frederik; Ewertsen, Caroline; Sletting, Susanne

    2017-01-01

    Objectives: To assess whether strain histograms are equal to strain ratios in predicting breast tumour malignancy and to see if either could be used to upgrade Breast Imaging Reporting and Data System (BI-RADS) 3 tumours for immediate biopsy. Methods: Ninety-nine breast tumours were examined using...

  19. DIF Testing with an Empirical-Histogram Approximation of the Latent Density for Each Group

    Science.gov (United States)

    Woods, Carol M.

    2011-01-01

    This research introduces, illustrates, and tests a variation of IRT-LR-DIF, called EH-DIF-2, in which the latent density for each group is estimated simultaneously with the item parameters as an empirical histogram (EH). IRT-LR-DIF is used to evaluate the degree to which items have different measurement properties for one group of people versus…

  20. The application of the distance histogram in microdosimetry for evaluating heterogeneity

    International Nuclear Information System (INIS)

    Dieren, E.B. van; Lingen, A. van; Roos, J.C.; Teule, G.J.J.

    1992-01-01

    Heterogeneity of radionuclide distributions at a microscopic level is relevant for the dosimetry of short path-length emissions. The present study explores the methodological aspects and the limitations of source target histograms by using computer simulations of radionuclide distributions. Sources were formed by labeled cells, containing 50 decay sites each. Cell nuclei were considered as targets. Within a matrix of 2,500 cells, the authors investigated uniform distributions (MIRD assumption), various cluster sizes, the single labeled cell, and a random distribution. Furthermore, four different intracellular source localizations were studied in a matrix of one cell. The distance histograms for both matrices were combined. For both 125 I and 131 I , absorbed doses in the targets were calculated from multiplication of the distance histograms by the point source absorbed radiation dose distribution. The presented results indicate that the use of distance histograms might be a mathematically convenient approach to microdosimetrical studies. They provide a means to study combinations of source distributions at various levels of magnification for several radionuclides within a reasonable calculation time

  1. Histogram-based automatic thresholding for bruise detection of apples by structured-illumination reflectance imaging

    Science.gov (United States)

    Thresholding is an important step in the segmentation of image features, and the existing methods are not all effective when the image histogram exhibits a unimodal pattern, which is common in defect detection of fruit. This study was aimed at developing a general automatic thresholding methodology ...

  2. Quantitative Evaluation for Differentiating Malignant and Benign Thyroid Nodules Using Histogram Analysis of Grayscale Sonograms.

    Science.gov (United States)

    Nam, Se Jin; Yoo, Jaeheung; Lee, Hye Sun; Kim, Eun-Kyung; Moon, Hee Jung; Yoon, Jung Hyun; Kwak, Jin Young

    2016-04-01

    To evaluate the diagnostic value of histogram analysis using grayscale sonograms for differentiation of malignant and benign thyroid nodules. From July 2013 through October 2013, 579 nodules in 563 patients who had undergone ultrasound-guided fine-needle aspiration were included. For the grayscale histogram analysis, pixel echogenicity values in regions of interest were measured as 0 to 255 (0, black; 255, white) with in-house software. Five parameters (mean, skewness, kurtosis, standard deviation, and entropy) were obtained for each thyroid nodule. With principal component analysis, an index was derived. Diagnostic performance rates for the 5 histogram parameters and the principal component analysis index were calculated. A total of 563 patients were included in the study (mean age ± SD, 50.3 ± 12.3 years;range, 15-79 years). Of the 579 nodules, 431 were benign, and 148 were malignant. Among the 5 parameters and the principal component analysis index, the standard deviation (75.546 ± 14.153 versus 62.761 ± 16.01; P histogram analysis was feasible for differentiating malignant and benign thyroid nodules but did not show better diagnostic performance than subjective analysis performed by radiologists. Further technical advances will be needed to objectify interpretations of thyroid grayscale sonograms. © 2016 by the American Institute of Ultrasound in Medicine.

  3. Reducing variability in the output of pattern classifiers using histogram shaping

    International Nuclear Information System (INIS)

    Gupta, Shalini; Kan, Chih-Wen; Markey, Mia K.

    2010-01-01

    Purpose: The authors present a novel technique based on histogram shaping to reduce the variability in the output and (sensitivity, specificity) pairs of pattern classifiers with identical ROC curves, but differently distributed outputs. Methods: The authors identify different sources of variability in the output of linear pattern classifiers with identical ROC curves, which also result in classifiers with differently distributed outputs. They theoretically develop a novel technique based on the matching of the histograms of these differently distributed pattern classifier outputs to reduce the variability in their (sensitivity, specificity) pairs at fixed decision thresholds, and to reduce the variability in their actual output values. They empirically demonstrate the efficacy of the proposed technique by means of analyses on the simulated data and real world mammography data. Results: For the simulated data, with three different known sources of variability, and for the real world mammography data with unknown sources of variability, the proposed classifier output calibration technique significantly reduced the variability in the classifiers' (sensitivity, specificity) pairs at fixed decision thresholds. Furthermore, for classifiers with monotonically or approximately monotonically related output variables, the histogram shaping technique also significantly reduced the variability in their actual output values. Conclusions: Classifier output calibration based on histogram shaping can be successfully employed to reduce the variability in the output values and (sensitivity, specificity) pairs of pattern classifiers with identical ROC curves, but differently distributed outputs.

  4. Whole-tumor MRI histogram analyses of hepatocellular carcinoma: Correlations with Ki-67 labeling index.

    Science.gov (United States)

    Hu, Xin-Xing; Yang, Zhao-Xia; Liang, He-Yue; Ding, Ying; Grimm, Robert; Fu, Cai-Xia; Liu, Hui; Yan, Xu; Ji, Yuan; Zeng, Meng-Su; Rao, Sheng-Xiang

    2017-08-01

    To evaluate whether whole-tumor histogram-derived parameters for an apparent diffusion coefficient (ADC) map and contrast-enhanced magnetic resonance imaging (MRI) could aid in assessing Ki-67 labeling index (LI) of hepatocellular carcinoma (HCC). In all, 57 patients with HCC who underwent pretreatment MRI with a 3T MR scanner were included retrospectively. Histogram parameters including mean, median, standard deviation, skewness, kurtosis, and percentiles (5 th , 25 th , 75 th , 95 th ) were derived from the ADC map and MR enhancement. Correlations between histogram parameters and Ki-67 LI were evaluated and differences between low Ki-67 (≤10%) and high Ki-67 (>10%) groups were assessed. Mean, median, 5 th , 25 th , 75 th percentiles of ADC, and mean, median, 25 th , 75 th , 95 th percentiles of enhancement of arterial phase (AP) demonstrated significant inverse correlations with Ki-67 LI (rho up to -0.48 for ADC, -0.43 for AP) and showed significant differences between low and high Ki-67 groups (P Histogram-derived parameters of ADC and AP were potentially helpful for predicting Ki-67 LI of HCC. 3 Technical Efficacy: Stage 3 J. MAGN. RESON. IMAGING 2017;46:383-392. © 2016 International Society for Magnetic Resonance in Medicine.

  5. Flat-histogram methods in quantum Monte Carlo simulations: Application to the t-J model

    International Nuclear Information System (INIS)

    Diamantis, Nikolaos G.; Manousakis, Efstratios

    2016-01-01

    We discuss that flat-histogram techniques can be appropriately applied in the sampling of quantum Monte Carlo simulation in order to improve the statistical quality of the results at long imaginary time or low excitation energy. Typical imaginary-time correlation functions calculated in quantum Monte Carlo are subject to exponentially growing errors as the range of imaginary time grows and this smears the information on the low energy excitations. We show that we can extract the low energy physics by modifying the Monte Carlo sampling technique to one in which configurations which contribute to making the histogram of certain quantities flat are promoted. We apply the diagrammatic Monte Carlo (diag-MC) method to the motion of a single hole in the t-J model and we show that the implementation of flat-histogram techniques allows us to calculate the Green's function in a wide range of imaginary-time. In addition, we show that applying the flat-histogram technique alleviates the “sign”-problem associated with the simulation of the single-hole Green's function at long imaginary time. (paper)

  6. Whole-lesion apparent diffusion coefficient histogram analysis: significance in T and N staging of gastric cancers.

    Science.gov (United States)

    Liu, Song; Zhang, Yujuan; Chen, Ling; Guan, Wenxian; Guan, Yue; Ge, Yun; He, Jian; Zhou, Zhengyang

    2017-10-02

    Whole-lesion apparent diffusion coefficient (ADC) histogram analysis has been introduced and proved effective in assessment of multiple tumors. However, the application of whole-volume ADC histogram analysis in gastrointestinal tumors has just started and never been reported in T and N staging of gastric cancers. Eighty patients with pathologically confirmed gastric carcinomas underwent diffusion weighted (DW) magnetic resonance imaging before surgery prospectively. Whole-lesion ADC histogram analysis was performed by two radiologists independently. The differences of ADC histogram parameters among different T and N stages were compared with independent-samples Kruskal-Wallis test. Receiver operating characteristic (ROC) analysis was performed to evaluate the performance of ADC histogram parameters in differentiating particular T or N stages of gastric cancers. There were significant differences of all the ADC histogram parameters for gastric cancers at different T (except ADC min and ADC max ) and N (except ADC max ) stages. Most ADC histogram parameters differed significantly between T1 vs T3, T1 vs T4, T2 vs T4, N0 vs N1, N0 vs N3, and some parameters (ADC 5% , ADC 10% , ADC min ) differed significantly between N0 vs N2, N2 vs N3 (all P histogram parameters held great potential in differentiating different T and N stages of gastric cancers preoperatively.

  7. Stochastic learning of multi-instance dictionary for earth mover’s distance-based histogram comparison

    KAUST Repository

    Fan, Jihong

    2016-09-17

    Dictionary plays an important role in multi-instance data representation. It maps bags of instances to histograms. Earth mover’s distance (EMD) is the most effective histogram distance metric for the application of multi-instance retrieval. However, up to now, there is no existing multi-instance dictionary learning methods designed for EMD-based histogram comparison. To fill this gap, we develop the first EMD-optimal dictionary learning method using stochastic optimization method. In the stochastic learning framework, we have one triplet of bags, including one basic bag, one positive bag, and one negative bag. These bags are mapped to histograms using a multi-instance dictionary. We argue that the EMD between the basic histogram and the positive histogram should be smaller than that between the basic histogram and the negative histogram. Base on this condition, we design a hinge loss. By minimizing this hinge loss and some regularization terms of the dictionary, we update the dictionary instances. The experiments over multi-instance retrieval applications shows its effectiveness when compared to other dictionary learning methods over the problems of medical image retrieval and natural language relation classification. © 2016 The Natural Computing Applications Forum

  8. Efficient visibility-driven medical image visualisation via adaptive binned visibility histogram.

    Science.gov (United States)

    Jung, Younhyun; Kim, Jinman; Kumar, Ashnil; Feng, David Dagan; Fulham, Michael

    2016-07-01

    'Visibility' is a fundamental optical property that represents the observable, by users, proportion of the voxels in a volume during interactive volume rendering. The manipulation of this 'visibility' improves the volume rendering processes; for instance by ensuring the visibility of regions of interest (ROIs) or by guiding the identification of an optimal rendering view-point. The construction of visibility histograms (VHs), which represent the distribution of all the visibility of all voxels in the rendered volume, enables users to explore the volume with real-time feedback about occlusion patterns among spatially related structures during volume rendering manipulations. Volume rendered medical images have been a primary beneficiary of VH given the need to ensure that specific ROIs are visible relative to the surrounding structures, e.g. the visualisation of tumours that may otherwise be occluded by neighbouring structures. VH construction and its subsequent manipulations, however, are computationally expensive due to the histogram binning of the visibilities. This limits the real-time application of VH to medical images that have large intensity ranges and volume dimensions and require a large number of histogram bins. In this study, we introduce an efficient adaptive binned visibility histogram (AB-VH) in which a smaller number of histogram bins are used to represent the visibility distribution of the full VH. We adaptively bin medical images by using a cluster analysis algorithm that groups the voxels according to their intensity similarities into a smaller subset of bins while preserving the distribution of the intensity range of the original images. We increase efficiency by exploiting the parallel computation and multiple render targets (MRT) extension of the modern graphical processing units (GPUs) and this enables efficient computation of the histogram. We show the application of our method to single-modality computed tomography (CT), magnetic resonance

  9. ADC Histogram Analysis of Cervical Cancer Aids Detecting Lymphatic Metastases-a Preliminary Study.

    Science.gov (United States)

    Schob, Stefan; Meyer, Hans Jonas; Pazaitis, Nikolaos; Schramm, Dominik; Bremicker, Kristina; Exner, Marc; Höhn, Anne Kathrin; Garnov, Nikita; Surov, Alexey

    2017-12-01

    Apparent diffusion coefficient (ADC) histogram analysis has been used to some extent in cervical cancer (CC) to distinguish between low-grade and high-grade tumors. Although this differentiation is undoubtedly helpful, it would be even more crucial in the presurgical setting to determine whether a tumor already gained the potential to metastasize via the lymphatic system. So far, no studies investigated the potential of 3T ADC histogram analysis in CC to differentiate between nodal-positive and nodal-negative entities. Therefore, the principal aim of our study was to investigate the potential of 3T ADC histogram analysis to differentiate between CC with and without lymph node metastasis. The second aim was to elucidate possible differences in ADC histogram parameters between CC with limited vs. advanced tumor stages and well-differentiated vs. undifferentiated lesions. Finally, correlations of p53 expression and Ki-67 index with ADC parameters were analyzed. Eighteen female patients (mean age 55.4 years, range 32-79 years) with histopathologically confirmed cervical squamous cell carcinoma of the uterine cervix were prospectively enrolled. Tumor stages, tumor grading, status of metastatic dissemination, Ki67-index, and p53 expression were assessed in these patients. Diffusion weighted imaging (DWI) was obtained in a 3T scanner using the following b values: b0 and b1000 s/mm 2 . Group comparisons using Mann-Whitney U test revealed the following findings: nodal-positive CC had statistically significant lower ADC parameters (ADCmin, ADCmean, median ADC, Mode, p10, p25, p75, and p90) in comparison to nodal-negative CC (all p histogram analysis in 3T DWI. This information is crucial for the gynecological surgeon to identify the optimal treatment strategy for patients suffering from CC. Furthermore, ADCentropy was identified as a potential imaging biomarker for tumor heterogeneity and might be able to indicate further molecular changes like loss of p53 expression

  10. Apparent diffusion coefficient histogram analysis can evaluate radiation-induced parotid damage and predict late xerostomia degree in nasopharyngeal carcinoma.

    Science.gov (United States)

    Zhou, Nan; Guo, Tingting; Zheng, Huanhuan; Pan, Xia; Chu, Chen; Dou, Xin; Li, Ming; Liu, Song; Zhu, Lijing; Liu, Baorui; Chen, Weibo; He, Jian; Yan, Jing; Zhou, Zhengyang; Yang, Xiaofeng

    2017-09-19

    We investigated apparent diffusion coefficient (ADC) histogram analysis to evaluate radiation-induced parotid damage and predict xerostomia degrees in nasopharyngeal carcinoma (NPC) patients receiving radiotherapy. The imaging of bilateral parotid glands in NPC patients was conducted 2 weeks before radiotherapy (time point 1), one month after radiotherapy (time point 2), and four months after radiotherapy (time point 3). From time point 1 to 2, parotid volume, skewness, and kurtosis decreased ( P histogram parameters increased (all P histogram parameters. Early mean change rates for bilateral parotid SD and ADC max could predict late xerostomia degrees at seven months after radiotherapy (three months after time point 3) with AUC of 0.781 and 0.818 ( P = 0.014, 0.005, respectively). ADC histogram parameters were reproducible (intraclass correlation coefficient, 0.830 - 0.999). ADC histogram analysis could be used to evaluate radiation-induced parotid damage noninvasively, and predict late xerostomia degrees of NPC patients treated with radiotherapy.

  11. Histogram and gray level co-occurrence matrix on gray-scale ultrasound images for diagnosing lymphocytic thyroiditis.

    Science.gov (United States)

    Shin, Young Gyung; Yoo, Jaeheung; Kwon, Hyeong Ju; Hong, Jung Hwa; Lee, Hye Sun; Yoon, Jung Hyun; Kim, Eun-Kyung; Moon, Hee Jung; Han, Kyunghwa; Kwak, Jin Young

    2016-08-01

    The objective of the study was to evaluate whether texture analysis using histogram and gray level co-occurrence matrix (GLCM) parameters can help clinicians diagnose lymphocytic thyroiditis (LT) and differentiate LT according to pathologic grade. The background thyroid pathology of 441 patients was classified into no evidence of LT, chronic LT (CLT), and Hashimoto's thyroiditis (HT). Histogram and GLCM parameters were extracted from the regions of interest on ultrasound. The diagnostic performances of the parameters for diagnosing and differentiating LT were calculated. Of the histogram and GLCM parameters, the mean on histogram had the highest Az (0.63) and VUS (0.303). As the degrees of LT increased, the mean decreased and the standard deviation and entropy increased. The mean on histogram from gray-scale ultrasound showed the best diagnostic performance as a single parameter in differentiating LT according to pathologic grade as well as in diagnosing LT. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Clinical value of polymerase chain reaction in the diagnosis of joint tuberculosis by detecting the DNA of Mycobacterium tuberculosis.

    Science.gov (United States)

    Sun, Yong-sheng; Lou, Si-quan; Wen, Jian-min; Lv, Wei-xin; Jiao, Chang-geng; Yang, Su-min; Xu, Hai-bin

    2011-02-01

    To assess the clinical value of polymerase chain reaction (PCR) in the diagnosis and differential diagnosis of joint tuberculosis (TB). PCR was used blindly to detect the DNA of Mycobacterium tuberculosis (M.TB) in five specimens of M.TB, 5 of BCG, and 10 of other bacteria. Then, M. TB in 98 samples from patients with joint TB and 100 samples from patients with non-tubercular joint disorders were detected by PCR, acid-fast staining and culture,. The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of PCR were calculated. The χ2 test was used for statistical analysis of the frequency of various factors. At the same time, some problems with PCR were also systematically analyzed. (1) In the "standard samples", both M. TB and BCG showed positive while other bacteria were negative. (2) In 98 cases from patients with joint TB, 81 were positive by PCR, 6 by acid-fast staining, and 17 by culture. In 100 cases from patients with non-tuberculous joint disorders, 9 were positive by PCR, and none by either acid-fast staining or culture. Sensitivity, specificity, accuracy, positive and negative predictive value of PCR were 82.65% (81/98), 91.00% (91/100), 86.87% (172/198), 90.00% (81/90) and 84.26% (91/108), respectively. (3) The positive rates for PCR, acid-fast staining and culture in detection of M. TB were 82.65% (81/98), 6.12% (6/98), and 17.34% (17/98), respectively. There were statistically significant differences between the three methods (P < 0.001). (4) The process of PCR is automatic, and can be completed within 3 to 6 hours, whereas 4 to 8 weeks are required for the conventional culture of M. TB. PCR is a sensitive, specific, rapid, simple and minimally invasive method for detection of M. TB in samples from joint TB, and can play an important role in early and rapid diagnosis and differential diagnosis of joint TB. But it also has some limitations, such as false positivity and false negativity. © 2011 Tianjin Hospital

  13. Correlation of histogram analysis of apparent diffusion coefficient with uterine cervical pathologic finding.

    Science.gov (United States)

    Lin, Yuning; Li, Hui; Chen, Ziqian; Ni, Ping; Zhong, Qun; Huang, Huijuan; Sandrasegaran, Kumar

    2015-05-01

    The purpose of this study was to investigate the application of histogram analysis of apparent diffusion coefficient (ADC) in characterizing pathologic features of cervical cancer and benign cervical lesions. This prospective study was approved by the institutional review board, and written informed consent was obtained. Seventy-three patients with cervical cancer (33-69 years old; 35 patients with International Federation of Gynecology and Obstetrics stage IB cervical cancer) and 38 patients (38-61 years old) with normal cervix or cervical benign lesions (control group) were enrolled. All patients underwent 3-T diffusion-weighted imaging (DWI) with b values of 0 and 800 s/mm(2). ADC values of the entire tumor in the patient group and the whole cervix volume in the control group were assessed. Mean ADC, median ADC, 25th and 75th percentiles of ADC, skewness, and kurtosis were calculated. Histogram parameters were compared between different pathologic features, as well as between stage IB cervical cancer and control groups. Mean ADC, median ADC, and 25th percentile of ADC were significantly higher for adenocarcinoma (p = 0.021, 0.006, and 0.004, respectively), and skewness was significantly higher for squamous cell carcinoma (p = 0.011). Median ADC was statistically significantly higher for well or moderately differentiated tumors (p = 0.044), and skewness was statistically significantly higher for poorly differentiated tumors (p = 0.004). No statistically significant difference of ADC histogram was observed between lymphovascular space invasion subgroups. All histogram parameters differed significantly between stage IB cervical cancer and control groups (p histogram analysis may help to distinguish early-stage cervical cancer from normal cervix or cervical benign lesions and may be useful for evaluating the different pathologic features of cervical cancer.

  14. Estimation of pneumonitis risk in three-dimensional treatment planning using dose-volume histogram analysis

    International Nuclear Information System (INIS)

    Oetzel, Dieter; Schraube, Peter; Hensley, Frank; Sroka-Perez, Gabriele; Menke, Markus; Flentje, Michael

    1995-01-01

    Purpose: Investigations to study correlations between the estimations of biophysical models in three dimensional (3D) treatment planning and clinical observations are scarce. The development of clinically symptomatic pneumonitis in the radiotherapy of thoracic malignomas was chosen to test the predictive power of Lyman's normal tissue complication probability (NTCP) model for the assessment of side effects for nonuniform irradiation. Methods and Materials: In a retrospective analysis individual computed-tomography-based 3D dose distributions of a random sample of (46(20)) patients with lung/esophageal cancer were reconstructed. All patients received tumor doses between 50 and 60 Gy in a conventional treatment schedule. Biological isoeffective dose-volume histograms (DVHs) were used for the calculation of complication probabilities after applying Lyman's and Kutcher's DVH-reduction algorithm. Lung dose statistics were performed for single lung (involved ipsilateral and contralateral) and for the lung as a paired organ. Results: In the lung cancer group, about 20% of the patients (9 out of 46) developed pneumonitis 3-12 (median 7.5) weeks after completion of radiotherapy. For the majority of these lung cancer patients, the involved ipsilateral lung received a much higher dose than the contralateral lung, and the pneumonitis patients had on average a higher lung exposure with a doubling of the predicted complication risk (38% vs. 20%). The lower lung exposure for the esophagus patients resulted in a mean lung dose of 13.2 Gy (lung cancer: 20.5 Gy) averaged over all patients in correlation with an almost zero complication risk and only one observed case of pneumonitis (1 out of 20). To compare the pneumonitis risk estimations with observed complication rates, the patients were ranked into bins of mean ipsilateral lung dose. Particularly, in the bins with the highest patient numbers, a good correlation was achieved. Agreement was not reached for the lung functioning as

  15. Preliminary studies on DNA retardation by MutS applied to the detection of point mutations in clinical samples

    International Nuclear Information System (INIS)

    Stanislawska-Sachadyn, Anna; Paszko, Zygmunt; Kluska, Anna; Skasko, Elzibieta; Sromek, Maria; Balabas, Aneta; Janiec-Jankowska, Aneta; Wisniewska, Alicja; Kur, Jozef; Sachadyn, Pawel

    2005-01-01

    MutS ability to bind DNA mismatches was applied to the detection of point mutations in PCR products. MutS recognized mismatches from single up to five nucleotides and retarded the electrophoretic migration of mismatched DNA. The electrophoretic detection of insertions/deletions above three nucleotides is also possible without MutS, thanks to the DNA mobility shift caused by the presence of large insertion/deletion loops in the heteroduplex DNA. Thus, the method enables the search for a broad range of mutations: from single up to several nucleotides. The mobility shift assays were carried out in polyacrylamide gels stained with SYBR-Gold. One assay required 50-200 ng of PCR product and 1-3 μg of Thermus thermophilus his 6 -MutS protein. The advantages of this approach are: the small amounts of DNA required for the examination, simple and fast staining, no demand for PCR product purification, no labelling and radioisotopes required. The method was tested in the detection of cancer predisposing mutations in RET, hMSH2, hMLH1, BRCA1, BRCA2 and NBS1 genes. The approach appears to be promising in screening for unknown point mutations

  16. SU-G-BRC-08: Evaluation of Dose Mass Histogram as a More Representative Dose Description Method Than Dose Volume Histogram in Lung Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J; Eldib, A; Ma, C [Fox Chase Cancer Center, Philadelphia, PA (United States); Lin, M [The University of Texas Southwestern Medical Ctr, Dallas, TX (United States); Li, J [Cyber Medical Inc, Xian, Shaanxi (China); Mora, G [Universidade de Lisboa, Codex, Lisboa (Portugal)

    2016-06-15

    Purpose: Dose-volume-histogram (DVH) is widely used for plan evaluation in radiation treatment. The concept of dose-mass-histogram (DMH) is expected to provide a more representative description as it accounts for heterogeneity in tissue density. This study is intended to assess the difference between DVH and DMH for evaluating treatment planning quality. Methods: 12 lung cancer treatment plans were exported from the treatment planning system. DVHs for the planning target volume (PTV), the normal lung and other structures of interest were calculated. DMHs were calculated in a similar way as DVHs expect that the voxel density converted from the CT number was used in tallying the dose histogram bins. The equivalent uniform dose (EUD) was calculated based on voxel volume and mass, respectively. The normal tissue complication probability (NTCP) in relation to the EUD was calculated for the normal lung to provide quantitative comparison of DVHs and DMHs for evaluating the radiobiological effect. Results: Large differences were observed between DVHs and DMHs for lungs and PTVs. For PTVs with dense tumor cores, DMHs are higher than DVHs due to larger mass weighing in the high dose conformal core regions. For the normal lungs, DMHs can either be higher or lower than DVHs depending on the target location within the lung. When the target is close to the lower lung, DMHs show higher values than DVHs because the lower lung has higher density than the central portion or the upper lung. DMHs are lower than DVHs for targets in the upper lung. The calculated NTCPs showed a large range of difference between DVHs and DMHs. Conclusion: The heterogeneity of lung can be well considered using DMH for evaluating target coverage and normal lung pneumonitis. Further studies are warranted to quantify the benefits of DMH over DVH for plan quality evaluation.

  17. Clinical and molecular features of an infant patient affected by Leigh Disease associated to m.14459G > A mitochondrial DNA mutation: a case report

    Directory of Open Access Journals (Sweden)

    Moggio Maurizio

    2011-07-01

    Full Text Available Abstract Background Leigh Syndrome (LS is a severe neurodegenerative disorder characterized by bilateral symmetrical necrotic lesions in the basal ganglia and brainstem. Onset is in early infancy and prognosis is poor. Causative mutations have been disclosed in mitochondrial DNA and nuclear genes affecting respiratory chain subunits and assembly factors. Case presentation Here we report the clinical and molecular features of a 15-month-old female LS patient. Direct sequencing of her muscle-derived mtDNA revealed the presence of two apparently homoplasmic variants: the novel m.14792C > G and the already known m.14459G > A resulting in p.His16Asp change in cytochrome b (MT-CYB and p.Ala72Val substitution in ND6 subunit, respectively. The m.14459G > A was heteroplasmic in the mother's blood-derived DNA. Conclusions The m.14459G > A might lead to LS, complicated LS or Leber Optic Hereditary Neuropathy. A comprehensive re-evaluation of previously described 14459G > A-mutated patients does not explain this large clinical heterogeneity.

  18. Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae.

    LENUS (Irish Health Repository)

    Walsh, Fiona

    2010-06-01

    A DNA microarray was developed to detect plasmid-mediated antimicrobial resistance (AR) and virulence factor (VF) genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae. The array was validated with the following bacterial species: Escherichiacoli (n=17); Klebsiellapneumoniae (n=3); Enterobacter spp. (n=6); Acinetobacter genospecies 3 (n=1); Acinetobacterbaumannii (n=1); Pseudomonasaeruginosa (n=2); and Stenotrophomonasmaltophilia (n=2). The AR gene profiles of these isolates were identified by polymerase chain reaction (PCR). The DNA microarray consisted of 155 and 133 AR and VF gene probes, respectively. Results were compared with the commercially available Identibac AMR-ve Array Tube. Hybridisation results indicated that there was excellent correlation between PCR and array results for AR and VF genes. Genes conferring resistance to each antibiotic class were identified by the DNA array. Unusual resistance genes were also identified, such as bla(SHV-5) in a bla(OXA-23)-positive carbapenem-resistant A. baumannii. The phylogenetic group of each E. coli isolate was verified by the array. These data demonstrate that it is possible to screen simultaneously for all important classes of mobile AR and VF genes in Enterobacteriaceae and non-Enterobacteriaceae whilst also assigning a correct phylogenetic group to E. coli isolates. Therefore, it is feasible to test clinical Gram-negative bacteria for all known AR genes and to provide important information regarding pathogenicity simultaneously.

  19. Sistem Verifikasi Tanda Tangan Off-Line Berdasar Ciri Histogram Of Oriented Gradient (HOG Dan Histogram Of Curvature (HoC

    Directory of Open Access Journals (Sweden)

    Agus Wahyu Widodo

    2015-08-01

    Full Text Available Abstrak Tanda tangan dengan sifat uniknya merupakan salah satu dari sekian banyak atribut personal yang diterima secara luas untuk verifikasi indentitas seseorang, alat pembuktian kepemilikan berbagai transaksi atau dokumen di dalam masyarakat. Keberhasilan penggunaan ciri gradien dan curvature dalam bidang-bidang penelitian pengenalan pola dan bahwa tanda tangan dapat dikatakan merupakan hasil tulisan tangan yang tersusun atas beragam garis dan lengkungan (curve yang memiliki arah atau orientasi merupakan alasan bahwa kedua ciri tersebut digunakan sebagai metoda verifikasi tanda tangan offline di penelitian ini. Berbagai implementasi dari pre-processing, ekstraksi dan representasi ciri, dan pembelajaran SVM serta usaha perbaikan yang telah dilakukan dalam penelitian ini menunjukkan hasil bahwa ciri HOG dan HoC mampu dimanfaatkan dalam proses verifikasi tanda tangan secara offline.  Pada basis data GPDS960Signature, HOG dan HoC yang dihitung pada ukuran sel 30 x 30 piksel memberikan dengan nilai %FRR terbaik 26,90 dan %FAR 37,56.  Sedangkan pada basis data FUM-PHSDB, HOG dn HoC yang dihitung pada ukuran 60 x 60 piksel memberikan nilai %FRR terbaik 4 dan %FAR 57. Kata kunci: verifikasi tanda tangan, curvature, orientation, gradient, histogram of curvature (HoC, histogram of oriented gradient (HOG Abstract Signature with unique properties is one of the many personal attributes that are widely accepted to verify a person's identity, proof of ownership transactions instrument or document in the community. The successful use of gradient and curvature feature in the research fields of pattern recognition is the reason that both of these features are used as an offline signature verification method in this study. Various implementations of preprocessing, feature extraction and representation, and SVM learning has been done in the study showed results that HOG and HoC feature can be utilized in the process of offline signature verification.  HOG and

  20. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

    Science.gov (United States)

    Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

    2016-11-01

    Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  1. Clinical Relevance of CDH1 and CDH13 DNA-Methylation in Serum of Cervical Cancer Patients

    Directory of Open Access Journals (Sweden)

    Günther K. Bonn

    2012-07-01

    Full Text Available This study was designed to investigate the DNA-methylation status of E-cadherin (CDH1 and H-cadherin (CDH13 in serum samples of cervical cancer patients and control patients with no malignant diseases and to evaluate the clinical utility of these markers. DNA-methylation status of CDH1 and CDH13 was analyzed by means of MethyLight-technology in serum samples from 49 cervical cancer patients and 40 patients with diseases other than cancer. To compare this methylation analysis with another technique, we analyzed the samples with a denaturing high performance liquid chromatography (DHPLC PCR-method. The specificity and sensitivity of CDH1 DNA-methylation measured by MethyLight was 75% and 55%, and for CDH13 DNA-methylation 95% and 10%. We identified a specificity of 92.5% and a sensitivity of only 27% for the CDH1 DHPLC-PCR analysis. Multivariate analysis showed that serum CDH1 methylation-positive patients had a 7.8-fold risk for death (95% CI: 2.2–27.7; p = 0.001 and a 92.8-fold risk for relapse (95% CI: 3.9–2207.1; p = 0.005. We concluded that the serological detection of CDH1 and CDH13 DNA-hypermethylation is not an ideal diagnostic tool due to low diagnostic specificity and sensitivity. However, it was validated that CDH1 methylation analysis in serum samples may be of potential use as a prognostic marker for cervical cancer patients.

  2. Rapid diagnosis of virulent Pasteurella multocida isolated from farm animals with clinical manifestation of pneumonia respiratory infection using 16S rDNA and KMT1 gene

    Directory of Open Access Journals (Sweden)

    Gamal Mohamedin Hassan

    2016-01-01

    Full Text Available Objective: To characterize intra-isolates variation between clinical isolates of Pasteurella multocida (P. multocida isolated from sheep, cattle and buffalo at molecular level to check the distribution of pneumonia and hemorrhagic septicemia in some regions of Fayoum, Egypt. Methods: These isolates were obtained from various locations in the Fayoum Governorate, Egypt and they were identified by amplifying 16S rDNA and KMT1 genes using their DNA as a template in PCR reaction. Results: The results demonstrated that the five selective isolates of P. multocida had similar size of PCR products that generated one band of 16S rDNA having 1 471 bp and KMT1 gene having 460 bp. The phylogenetic tree and similarity of the five selective isolates of P. multocida which were collected from GenBank database were calculated and analyzed for the nucleotide sequence of 16S rDNA and KMT1 genes. The sequencing result of 16S rRNA gene product (1 471 bp for the five selective isolates of P. multocida showed that the isolates of sheep (FUP2 shared 94.08%, 88.10% homology with the buffalo isolate (FUP8 and cattle isolate (FUP9 respectively, whereas, the buffalo isolate (FUP5 shared 98.18% and 94.40% homology with the cattle isolates (FUP12 and FUP9. Conclusions: The results indicated the relationships of P. multocida isolated from buffalo and cattle rather than the close relationships between P. multocida isolated from cattle and sheep. Diagnosis of P. multocida by 16S rDNA and KMT1 gene sequences was important to determine the antigen that is responsible for protective cover within the same group of animals and to help for the production of new vaccines for the control of microbial infection for domestic animals.

  3. Anti-double stranded DNA antibodies in systemic lupus erythematosus : Detection and clinical relevance of IgM-class antibodies

    NARCIS (Netherlands)

    Bootsma, H; Spronk, PE; Hummel, EJ; deBoer, G; terBorg, EJ; Limburg, PC; Kallenberg, CGM

    1996-01-01

    We determined the discriminative value of the Farr assay in comparison to ELISA and Crithidia luciliae immunofluorescence assay (IFT) for detecting anti-dsDNA antibodies as a diagnostic tool for systemic lupus erythematosus (SLE). Special attention was paid to the diagnostic significance of

  4. Subtype differentiation of renal tumors using voxel-based histogram analysis of intravoxel incoherent motion parameters.

    Science.gov (United States)

    Gaing, Byron; Sigmund, Eric E; Huang, William C; Babb, James S; Parikh, Nainesh S; Stoffel, David; Chandarana, Hersh

    2015-03-01

    The aim of this study was to determine if voxel-based histogram analysis of intravoxel incoherent motion imaging (IVIM) parameters can differentiate various subtypes of renal tumors, including benign and malignant lesions. A total of 44 patients with renal tumors who underwent surgery and had histopathology available were included in this Health Insurance Portability and Accountability Act-compliant, institutional review board-approved, single-institution prospective study. In addition to routine renal magnetic resonance imaging examination performed on a 1.5-T system, all patients were imaged with axial diffusion-weighted imaging using 8 b values (range, 0-800 s/mm). A biexponential model was fitted to the diffusion signal data using a segmented algorithm to extract the IVIM parameters perfusion fraction (fp), tissue diffusivity (Dt), and pseudodiffusivity (Dp) for each voxel. Mean and histogram measures of heterogeneity (standard deviation, skewness, and kurtosis) of IVIM parameters were correlated with pathology results of tumor subtype using unequal variance t tests to compare subtypes in terms of each measure. Correction for multiple comparisons was accomplished using the Tukey honestly significant difference procedure. A total of 44 renal tumors including 23 clear cell (ccRCC), 4 papillary (pRCC), 5 chromophobe, and 5 cystic renal cell carcinomas, as well as benign lesions, 4 oncocytomas (Onc) and 3 angiomyolipomas (AMLs), were included in our analysis. Mean IVIM parameters fp and Dt differentiated 8 of 15 pairs of renal tumors. Histogram analysis of IVIM parameters differentiated 9 of 15 subtype pairs. One subtype pair (ccRCC vs pRCC) was differentiated by mean analysis but not by histogram analysis. However, 2 other subtype pairs (AML vs Onc and ccRCC vs Onc) were differentiated by histogram distribution parameters exclusively. The standard deviation of Dt [σ(Dt)] differentiated ccRCC (0.362 ± 0.136 × 10 mm/s) from AML (0.199 ± 0.043 × 10 mm/s) (P = 0

  5. Evidence for different mechanisms of ‘unhooking’ for melphalan and cisplatin-induced DNA interstrand cross-links in vitro and in clinical acquired resistant tumour samples

    Directory of Open Access Journals (Sweden)

    Spanswick Victoria J

    2012-09-01

    Full Text Available Abstract Background DNA interstrand cross-links (ICLs are critical lesions produced by several cancer chemotherapy agents including platinum drugs and nitrogen mustards. We have previously shown in haematological (multiple myeloma and solid tumours (ovarian cancer that clinical sensitivity to such agents can result from a defect in DNA ICL processing leading to their persistence. Conversely, enhanced repair can result in clinical acquired resistance following chemotherapy. The repair of ICLs is complex but it is assumed that the ‘unhooking’ step is common to all ICLs. Methods Using a modification of the single cell gel electrophoresis (Comet assay we measured the formation and unhooking of melphalan and cisplatin-induced ICLs in cell lines and clinical samples. DNA damage response in the form of γ-H2AX foci formation and the formation of RAD51 foci as a marker of homologous recombination were also determined. Real-time PCR of 84 genes involved in DNA damage signalling pathways was also examined pre- and post-treatment. Results Plasma cells from multiple myeloma patients known to be clinically resistant to melphalan showed significant unhooking of melphalan-induced ICLs at 48 hours, but did not unhook cisplatin-induced ICLs. In ovarian cancer cells obtained from patients following platinum-based chemotherapy, unhooking of cisplatin-induced ICLs was observed at 48 hours, but no unhooking of melphalan-induced ICLs. In vitro, A549 cells were proficient at unhooking both melphalan and cisplatin-induced ICLs. γ-H2AX foci formation closely followed the formation of ICLs for both drugs, and rapidly declined following the peak of formation. RPMI8226 cells unhooked melphalan, but not cisplatin-induced ICLs. In these cells, although cross-links form with cisplatin, the γ-H2AX response is weak. In A549 cells, addition of 3nM gemcitabine resulted in complete inhibition of cisplatin-induced ICL unhooking but no effect on repair of melphalan ICLs. The

  6. Evidence for different mechanisms of ‘unhooking’ for melphalan and cisplatin-induced DNA interstrand cross-links in vitro and in clinical acquired resistant tumour samples

    International Nuclear Information System (INIS)

    Spanswick, Victoria J; Hartley, John A; Lowe, Helen L; Newton, Claire; Bingham, John P; Bagnobianchi, Alessia; Kiakos, Konstantinos; Craddock, Charles; Ledermann, Jonathan A; Hochhauser, Daniel

    2012-01-01

    DNA interstrand cross-links (ICLs) are critical lesions produced by several cancer chemotherapy agents including platinum drugs and nitrogen mustards. We have previously shown in haematological (multiple myeloma) and solid tumours (ovarian cancer) that clinical sensitivity to such agents can result from a defect in DNA ICL processing leading to their persistence. Conversely, enhanced repair can result in clinical acquired resistance following chemotherapy. The repair of ICLs is complex but it is assumed that the ‘unhooking’ step is common to all ICLs. Using a modification of the single cell gel electrophoresis (Comet) assay we measured the formation and unhooking of melphalan and cisplatin-induced ICLs in cell lines and clinical samples. DNA damage response in the form of γ-H2AX foci formation and the formation of RAD51 foci as a marker of homologous recombination were also determined. Real-time PCR of 84 genes involved in DNA damage signalling pathways was also examined pre- and post-treatment. Plasma cells from multiple myeloma patients known to be clinically resistant to melphalan showed significant unhooking of melphalan-induced ICLs at 48 hours, but did not unhook cisplatin-induced ICLs. In ovarian cancer cells obtained from patients following platinum-based chemotherapy, unhooking of cisplatin-induced ICLs was observed at 48 hours, but no unhooking of melphalan-induced ICLs. In vitro, A549 cells were proficient at unhooking both melphalan and cisplatin-induced ICLs. γ-H2AX foci formation closely followed the formation of ICLs for both drugs, and rapidly declined following the peak of formation. RPMI8226 cells unhooked melphalan, but not cisplatin-induced ICLs. In these cells, although cross-links form with cisplatin, the γ-H2AX response is weak. In A549 cells, addition of 3nM gemcitabine resulted in complete inhibition of cisplatin-induced ICL unhooking but no effect on repair of melphalan ICLs. The RAD51 foci response was both drug and cell line

  7. Apparent diffusion coefficient histogram analysis of neonatal hypoxic-ischemic encephalopathy

    Energy Technology Data Exchange (ETDEWEB)

    Cauley, Keith A. [University of Massachusetts Medical School, Department of Radiology, Worcester, MA (United States); New York Presbyterian Hospital, Columbia University Medical Center, Department of Radiology, New York, NY (United States); Filippi, Christopher G. [New York Presbyterian Hospital, Columbia University Medical Center, Department of Radiology, New York, NY (United States)

    2014-06-15

    Diffusion-weighted imaging is a valuable tool in the assessment of the neonatal brain, and changes in diffusion are seen in normal development as well as in pathological states such as hypoxic-ischemic encephalopathy (HIE). Various methods of quantitative assessment of diffusion values have been reported. Global ischemic injury occurring during the time of rapid developmental changes in brain myelination can complicate the imaging diagnosis of neonatal HIE. To compare a quantitative method of histographic analysis of brain apparent coefficient (ADC) maps to the qualitative interpretation of routine brain MR imaging studies. We correlate changes in diffusion values with gestational age in radiographically normal neonates, and we investigate the sensitivity of the method as a quantitative measure of hypoxic-ischemic encephalopathy. We reviewed all brain MRI studies from the neonatal intensive care unit (NICU) at our university medical center over a 4-year period to identify cases that were radiographically normal (23 cases) and those with diffuse, global hypoxic-ischemic encephalopathy (12 cases). We histographically displayed ADC values of a single brain slice at the level of the basal ganglia and correlated peak (s-sD{sub av}) and lowest histogram values (s-sD{sub lowest}) with gestational age. Normative s-sD{sub av} values correlated significantly with gestational age and declined linearly through the neonatal period (r {sup 2} = 0.477, P < 0.01). Six of 12 cases of known HIE demonstrated significantly lower s-sD{sub av} and s-sD{sub lowest} ADC values than were reflected in the normative distribution; several cases of HIE fell within a 95% confidence interval for normative studies, and one case demonstrated higher-than-normal s-sD{sub av}. Single-slice histographic display of ADC values is a rapid and clinically feasible method of quantitative analysis of diffusion. In this study normative values derived from consecutive neonates without radiographic evidence of

  8. A Strengths-Weaknesses-Opportunities-Threats (SWOT) analysis on the clinical utility of sperm DNA fragmentation testing in specific male infertility scenarios.

    Science.gov (United States)

    Esteves, Sandro C; Agarwal, Ashok; Cho, Chak-Lam; Majzoub, Ahmad

    2017-09-01

    Sperm DNA fragmentation (SDF) is recognized as a leading cause of male infertility because it can impair the paternal genome through distinct pathophysiological mechanisms. Current evidence supports SDF as a major factor in the pathophysiology of several conditions, including varicocele, unexplained infertility, assisted reproductive technology failure, and environmental lifestyle factors, although the mechanisms involved have not been fully described yet. Measurement of the levels of DNA fragmentation in semen provides valuable information on the integrity of paternal chromatin and may guide therapeutic strategies. A recently published clinical practice guideline (CPG) highlighted how to use the information provided by SDF testing in daily practice, which triggered a series of commentaries by leading infertility experts. These commentaries contained an abundance of information and conflicting views about the clinical utility of SDF testing, which underline the complex nature of SDF. A search of papers published in response to the CPG entitled "Clinical utility of sperm DNA fragmentation testing: practice recommendations based on clinical scenarios" was performed within the Translational Andrology and Urology ( TAU ) website (http://tau.amegroups.com/). The start and end dates for the search were May 2017 and August 2017, respectively. Each commentary meeting our inclusion criteria was rated as "supportive without reservation", "supportive with reservation", "not supportive" or "neutral". We recorded whether articles discussed either SDF characteristics as a laboratory test method or clinical scenarios, or both. Subsequently, we extracted the particulars from each commentary and utilized the 'Strengths-Weaknesses-Opportunities-Threats' (SWOT) analysis to understand the perceived advantages and drawbacks of SDF as a specialized sperm function method in clinical practice. Fifty-eight fertility experts from six continents and twenty-two countries contributed

  9. Contrast Enhancement Using Brightness Preserving Histogram Equalization Technique for Classification of Date Varieties

    Directory of Open Access Journals (Sweden)

    G Thomas

    2014-06-01

    Full Text Available Computer vision technique is becoming popular for quality assessment of many products in food industries. Image enhancement is the first step in analyzing the images in order to obtain detailed information for the determination of quality. In this study, Brightness preserving histogram equalization technique was used to enhance the features of gray scale images to classify three date varieties (Khalas, Fard and Madina. Mean, entropy, kurtosis and skewness features were extracted from the original and enhanced images. Mean and entropy from original images and kurtosis from the enhanced images were selected based on Lukka's feature selection approach. An overall classification efficiency of 93.72% was achieved with just three features. Brightness preserving histogram equalization technique has great potential to improve the classification in various quality attributes of food and agricultural products with minimum features.

  10. Real time object localization based on histogram of s-RGB

    Science.gov (United States)

    Mudjirahardjo, Panca; Suyono, Hadi; Setyawan, Raden Arief

    2017-09-01

    Object localization is the first task in pattern detection and recognition. This task is very important due to it reduces the searching time to the interest object. In this paper we introduce our novel method of object localization based on color feature. Our novel method is a histogram of s-RGB. This histogram is used in the training phase to determine the color dominant in the initial Region of Interest (ROI). Then this information is used to label the interest object. To reduce noise and localize the interest object, we apply the row and column density function of pixels. The comparison result with some processes, our system gives a best result and takes a short computation time of 26.56 ms, in the video rate of 15 frames per second (fps).

  11. 3D facial expression recognition based on histograms of surface differential quantities

    KAUST Repository

    Li, Huibin

    2011-01-01

    3D face models accurately capture facial surfaces, making it possible for precise description of facial activities. In this paper, we present a novel mesh-based method for 3D facial expression recognition using two local shape descriptors. To characterize shape information of the local neighborhood of facial landmarks, we calculate the weighted statistical distributions of surface differential quantities, including histogram of mesh gradient (HoG) and histogram of shape index (HoS). Normal cycle theory based curvature estimation method is employed on 3D face models along with the common cubic fitting curvature estimation method for the purpose of comparison. Based on the basic fact that different expressions involve different local shape deformations, the SVM classifier with both linear and RBF kernels outperforms the state of the art results on the subset of the BU-3DFE database with the same experimental setting. © 2011 Springer-Verlag.

  12. Clarification of the use of chi-square and likelihood functions in fits to histograms

    International Nuclear Information System (INIS)

    Baker, S.; Cousins, R.D.

    1984-01-01

    We consider the problem of fitting curves to histograms in which the data obey multinomial or Poisson statistics. Techniques commonly used by physicists are examined in light of standard results found in the statistics literature. We review the relationship between multinomial and Poisson distributions, and clarify a sufficient condition for equality of the area under the fitted curve and the number of events on the histogram. Following the statisticians, we use the likelihood ratio test to construct a general Z 2 statistic, Zsub(lambda) 2 , which yields parameter and error estimates identical to those of the method of maximum likelihood. The Zsub(lambda) 2 statistic is further useful for testing goodness-of-fit since the value of its minimum asymptotically obeys a classical chi-square distribution. One should be aware, however, of the potential for statistical bias, especially when the number of events is small. (orig.)

  13. Kernel Learning of Histogram of Local Gabor Phase Patterns for Face Recognition

    Directory of Open Access Journals (Sweden)

    Bineng Zhong

    2008-06-01

    Full Text Available This paper proposes a new face recognition method, named kernel learning of histogram of local Gabor phase pattern (K-HLGPP, which is based on Daugman’s method for iris recognition and the local XOR pattern (LXP operator. Unlike traditional Gabor usage exploiting the magnitude part in face recognition, we encode the Gabor phase information for face classification by the quadrant bit coding (QBC method. Two schemes are proposed for face recognition. One is based on the nearest-neighbor classifier with chi-square as the similarity measurement, and the other makes kernel discriminant analysis for HLGPP (K-HLGPP using histogram intersection and Gaussian-weighted chi-square kernels. The comparative experiments show that K-HLGPP achieves a higher recognition rate than other well-known face recognition systems on the large-scale standard FERET, FERET200, and CAS-PEAL-R1 databases.

  14. Adaptive local backlight dimming algorithm based on local histogram and image characteristics

    DEFF Research Database (Denmark)

    Nadernejad, Ehsan; Burini, Nino; Korhonen, Jari

    2013-01-01

    -off between power consumption and image quality preservation than the other algorithms representing the state of the art among feature based backlight algorithms. © (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.......Liquid Crystal Display (LCDs) with Light Emitting Diode (LED) backlight is a very popular display technology, used for instance in television sets, monitors and mobile phones. This paper presents a new backlight dimming algorithm that exploits the characteristics of the target image......, such as the local histograms and the average pixel intensity of each backlight segment, to reduce the power consumption of the backlight and enhance image quality. The local histogram of the pixels within each backlight segment is calculated and, based on this average, an adaptive quantile value is extracted...

  15. An improved contrast enhancement algorithm for infrared images based on adaptive double plateaus histogram equalization

    Science.gov (United States)

    Li, Shuo; Jin, Weiqi; Li, Li; Li, Yiyang

    2018-05-01

    Infrared thermal images can reflect the thermal-radiation distribution of a particular scene. However, the contrast of the infrared images is usually low. Hence, it is generally necessary to enhance the contrast of infrared images in advance to facilitate subsequent recognition and analysis. Based on the adaptive double plateaus histogram equalization, this paper presents an improved contrast enhancement algorithm for infrared thermal images. In the proposed algorithm, the normalized coefficient of variation of the histogram, which characterizes the level of contrast enhancement, is introduced as feedback information to adjust the upper and lower plateau thresholds. The experiments on actual infrared images show that compared to the three typical contrast-enhancement algorithms, the proposed algorithm has better scene adaptability and yields better contrast-enhancement results for infrared images with more dark areas or a higher dynamic range. Hence, it has high application value in contrast enhancement, dynamic range compression, and digital detail enhancement for infrared thermal images.

  16. Multi-stream LSTM-HMM decoding and histogram equalization for noise robust keyword spotting.

    Science.gov (United States)

    Wöllmer, Martin; Marchi, Erik; Squartini, Stefano; Schuller, Björn

    2011-09-01

    Highly spontaneous, conversational, and potentially emotional and noisy speech is known to be a challenge for today's automatic speech recognition (ASR) systems, which highlights the need for advanced algorithms that improve speech features and models. Histogram Equalization is an efficient method to reduce the mismatch between clean and noisy conditions by normalizing all moments of the probability distribution of the feature vector components. In this article, we propose to combine histogram equalization and multi-condition training for robust keyword detection in noisy speech. To better cope with conversational speaking styles, we show how contextual information can be effectively exploited in a multi-stream ASR framework that dynamically models context-sensitive phoneme estimates generated by a long short-term memory neural network. The proposed techniques are evaluated on the SEMAINE database-a corpus containing emotionally colored conversations with a cognitive system for "Sensitive Artificial Listening".

  17. Locally advanced rectal cancer: post-chemoradiotherapy ADC histogram analysis for predicting a complete response.

    Science.gov (United States)

    Cho, Seung Hyun; Kim, Gab Chul; Jang, Yun-Jin; Ryeom, Hunkyu; Kim, Hye Jung; Shin, Kyung-Min; Park, Jun Seok; Choi, Gyu-Seog; Kim, See Hyung

    2015-09-01

    The value of diffusion-weighted imaging (DWI) for reliable differentiation between pathologic complete response (pCR) and residual tumor is still unclear. Recently, a few studies reported that histogram analysis can be helpful to monitor the therapeutic response in various cancer research. To investigate whether post-chemoradiotherapy (CRT) apparent diffusion coefficient (ADC) histogram analysis can be helpful to predict a pCR in locally advanced rectal cancer (LARC). Fifty patients who underwent preoperative CRT followed by surgery were enrolled in this retrospective study, non-pCR (n = 41) and pCR (n = 9), respectively. ADC histogram analysis encompassing the whole tumor was performed on two post-CRT ADC600 and ADC1000 (b factors 0, 600 vs. 0, 1000 s/mm(2)) maps. Mean, minimum, maximum, SD, mode, 10th, 25th, 50th, 75th, 90th percentile ADCs, skewness, and kurtosis were derived. Diagnostic performance for predicting pCR was evaluated and compared. On both maps, 10th and 25th ADCs showed better diagnostic performance than that using mean ADC. Tenth percentile ADCs revealed the best diagnostic performance on both ADC600 (AZ 0.841, sensitivity 100%, specificity 70.7%) and ADC1000 (AZ 0.821, sensitivity 77.8%, specificity 87.8%) maps. In comparison between 10th percentile and mean ADC, the specificity was significantly improved on both ADC600 (70.7% vs. 53.7%; P = 0.031) and ADC1000 (87.8% vs. 73.2%; P = 0.039) maps. Post-CRT ADC histogram analysis is helpful for predicting pCR in LARC, especially, in improving the specificity, compared with mean ADC. © The Foundation Acta Radiologica 2014.

  18. Treatment and Combination of Data Quality Monitoring Histograms to Perform Data vs. Monte Carlo Validation

    CERN Document Server

    Colin, Nolan

    2013-01-01

    In CMS's automated data quality validation infrastructure, it is not currently possible to assess how well Monte Carlo simulations describe data from collisions, if at all. In order to guarantee high quality data, a novel work flow was devised to perform `data vs. Monte Carlo' validation. Support for this comparison was added by allowing distributions from several Monte Carlo samples to be combined, matched to the data and then displayed in a histogram stack, overlaid with the experimental data.

  19. Differentiation of orbital lymphoma and idiopathic orbital inflammatory pseudotumor: combined diagnostic value of conventional MRI and histogram analysis of ADC maps.

    Science.gov (United States)

    Ren, Jiliang; Yuan, Ying; Wu, Yingwei; Tao, Xiaofeng

    2018-05-02

    The overlap of morphological feature and mean ADC value restricted clinical application of MRI in the differential diagnosis of orbital lymphoma and idiopathic orbital inflammatory pseudotumor (IOIP). In this paper, we aimed to retrospectively evaluate the combined diagnostic value of conventional magnetic resonance imaging (MRI) and whole-tumor histogram analysis of apparent diffusion coefficient (ADC) maps in the differentiation of the two lesions. In total, 18 patients with orbital lymphoma and 22 patients with IOIP were included, who underwent both conventional MRI and diffusion weighted imaging before treatment. Conventional MRI features and histogram parameters derived from ADC maps, including mean ADC (ADC mean ), median ADC (ADC median ), skewness, kurtosis, 10th, 25th, 75th and 90th percentiles of ADC (ADC 10 , ADC 25 , ADC 75 , ADC 90 ) were evaluated and compared between orbital lymphoma and IOIP. Multivariate logistic regression analysis was used to identify the most valuable variables for discriminating. Differential model was built upon the selected variables and receiver operating characteristic (ROC) analysis was also performed to determine the differential ability of the model. Multivariate logistic regression showed ADC 10 (P = 0.023) and involvement of orbit preseptal space (P = 0.029) were the most promising indexes in the discrimination of orbital lymphoma and IOIP. The logistic model defined by ADC 10 and involvement of orbit preseptal space was built, which achieved an AUC of 0.939, with sensitivity of 77.30% and specificity of 94.40%. Conventional MRI feature of involvement of orbit preseptal space and ADC histogram parameter of ADC 10 are valuable in differential diagnosis of orbital lymphoma and IOIP.

  20. Comparison of dose-volume histograms for Tomo therapy, linear accelerator-based 3D conformal radiation therapy, and intensity-modulated radiation therapy

    International Nuclear Information System (INIS)

    Ji, Youn-Sang; Dong, Kyung-Rae; Kim, Chang-Bok; Choi, Seong-Kwan; Chung, Woon-Kwan; Lee, Jong-Woong

    2011-01-01

    Highlights: → Evaluation of DVH from 3D CRT, IMRT and Tomo therapy was conducted for tumor therapy. → The doses of GTV and CTV were compared using DVHs from 3D CRT, IMRT and Tomo therapy. → The GTV was higher when Tomo therapy was used, while the doses of critical organ were low. → They said that Tomo therapy satisfied the goal of radiation therapy more than the others. - Abstract: Evaluation of dose-volume histograms from three-dimensional conformal radiation therapy (3D CRT), intensity-modulated radiation therapy (IMRT), and Tomo therapy was conducted. These three modalities are among the diverse treatment systems available for tumor therapy. Three patients who received tumor therapy for a malignant oligodendroglioma in the cranium, nasopharyngeal carcinoma in the cervical neck, and prostate cancer in the pelvis were selected as study subjects. Therapy plans were made for the three patients before dose-volume histograms were obtained. The doses of the gross tumor volume (GTV) and the clinical target volume (CTV) were compared using the dose-volume histograms obtained from the LINAC-based 3D CRT, IMRT planning station (Varian Eclipse-Varian, version 8.1), and Tomo therapy planning station. In addition, the doses of critical organs in the cranium, cervix, and pelvis that should be protected were compared. The GTV was higher when Tomo therapy was used compared to 3D CRT and the LINAC-based IMRT, while the doses of critical organ tissues that required protection were low. These results demonstrated that Tomo therapy satisfied the ultimate goal of radiation therapy more than the other therapies.

  1. A novel method for the evaluation of uncertainty in dose-volume histogram computation.

    Science.gov (United States)

    Henríquez, Francisco Cutanda; Castrillón, Silvia Vargas

    2008-03-15

    Dose-volume histograms (DVHs) are a useful tool in state-of-the-art radiotherapy treatment planning, and it is essential to recognize their limitations. Even after a specific dose-calculation model is optimized, dose distributions computed by using treatment-planning systems are affected by several sources of uncertainty, such as algorithm limitations, measurement uncertainty in the data used to model the beam, and residual differences between measured and computed dose. This report presents a novel method to take them into account. To take into account the effect of associated uncertainties, a probabilistic approach using a new kind of histogram, a dose-expected volume histogram, is introduced. The expected value of the volume in the region of interest receiving an absorbed dose equal to or greater than a certain value is found by using the probability distribution of the dose at each point. A rectangular probability distribution is assumed for this point dose, and a formulation that accounts for uncertainties associated with point dose is presented for practical computations. This method is applied to a set of DVHs for different regions of interest, including 6 brain patients, 8 lung patients, 8 pelvis patients, and 6 prostate patients planned for intensity-modulated radiation therapy. Results show a greater effect on planning target volume coverage than in organs at risk. In cases of steep DVH gradients, such as planning target volumes, this new method shows the largest differences with the corresponding DVH; thus, the effect of the uncertainty is larger.

  2. Neutrosophic Similarity Score Based Weighted Histogram for Robust Mean-Shift Tracking

    Directory of Open Access Journals (Sweden)

    Keli Hu

    2017-10-01

    Full Text Available Visual object tracking is a critical task in computer vision. Challenging things always exist when an object needs to be tracked. For instance, background clutter is one of the most challenging problems. The mean-shift tracker is quite popular because of its efficiency and performance in a range of conditions. However, the challenge of background clutter also disturbs its performance. In this article, we propose a novel weighted histogram based on neutrosophic similarity score to help the mean-shift tracker discriminate the target from the background. Neutrosophic set (NS is a new branch of philosophy for dealing with incomplete, indeterminate, and inconsistent information. In this paper, we utilize the single valued neutrosophic set (SVNS, which is a subclass of NS to improve the mean-shift tracker. First, two kinds of criteria are considered as the object feature similarity and the background feature similarity, and each bin of the weight histogram is represented in the SVNS domain via three membership functions T(Truth, I(indeterminacy, and F(Falsity. Second, the neutrosophic similarity score function is introduced to fuse those two criteria and to build the final weight histogram. Finally, a novel neutrosophic weighted mean-shift tracker is proposed. The proposed tracker is compared with several mean-shift based trackers on a dataset of 61 public sequences. The results revealed that our method outperforms other trackers, especially when confronting background clutter.

  3. Control system of hexacopter using color histogram footprint and convolutional neural network

    Science.gov (United States)

    Ruliputra, R. N.; Darma, S.

    2017-07-01

    The development of unmanned aerial vehicles (UAV) has been growing rapidly in recent years. The use of logic thinking which is implemented into the program algorithms is needed to make a smart system. By using visual input from a camera, UAV is able to fly autonomously by detecting a target. However, some weaknesses arose as usage in the outdoor environment might change the target's color intensity. Color histogram footprint overcomes the problem because it divides color intensity into separate bins that make the detection tolerant to the slight change of color intensity. Template matching compare its detection result with a template of the reference image to determine the target position and use it to position the vehicle in the middle of the target with visual feedback control based on Proportional-Integral-Derivative (PID) controller. Color histogram footprint method localizes the target by calculating the back projection of its histogram. It has an average success rate of 77 % from a distance of 1 meter. It can position itself in the middle of the target by using visual feedback control with an average positioning time of 73 seconds. After the hexacopter is in the middle of the target, Convolutional Neural Networks (CNN) classifies a number contained in the target image to determine a task depending on the classified number, either landing, yawing, or return to launch. The recognition result shows an optimum success rate of 99.2 %.

  4. Sistem Pendeteksi Kualitas Daging Dengan Ekualisasi Histogram Dan Thresholding Berbasis Android

    Directory of Open Access Journals (Sweden)

    Anggit Sri Herlambang

    2016-04-01

    Full Text Available Kebutuhan daging sapi yang meningkat sering dimanfaatkan oleh penjual daging sapi untuk melakukan kecurangan. Kecurangan yang sering dimanfaatkan biasanya dalam hal kualitas daging sapi. Kualitas daging ditentukan oleh beberapa parameter, termasuk parameter ukuran, tekstur, karakteristik warna, bau daging dan lain - lain. Parameter adalah salah satu faktor penting untuk menentukan kualitas daging. Umumnya dalam menentukan kualitas daging dilakukan dengan menggunakan indra penglihatan. Sehingga cara manual masih bersifat subjektif dalam menilai kualitas daging. Penelitian ini bertujuan untuk merancang aplikasi sistem pendeteksi kualitas daging dengan sampel 20 citra daging data uji. Sistem pendeteksi kualitas daging dengan ekualisasi histogram dan thresholding berbasis android ini dibangun dengan menggunakan bahasa pemrograman berbasis Android yang terintegrasi dengan SDK Android, Eclipse dan library OpenCV. Metode yang digunakan menggunakan metode pra-pengolahan ekualisasi histogram dan segmentasi thresholding pengolahan citra. Deteksi kualitas daging dilakukan dengan mencari nilai statistik ekstraksi ciri citra berdasarkan data citra daging dari penelitian. Hasil penelitian ini adalah dapat menentukan nilai statistik mean dan standar deviasi dari hasil citra olahan ekualisasi histogram dan thresholding disertai analisis kualitas citra daging sapi. Pengujian black box dari aplikasi sistem pendeteksi kualitas daging ini menunjukkan bahwa semua fungsi yang terdapat pada aplikasi ini telah berhasil berjalan sesuai fungsinya. Penelitian ini harapannya bisa digunakan untuk membantu penelitian tahap selanjutnya.

  5. RGB Color Cube-Based Histogram Specification for Hue-Preserving Color Image Enhancement

    Directory of Open Access Journals (Sweden)

    Kohei Inoue

    2017-07-01

    Full Text Available A large number of color image enhancement methods are based on the methods for grayscale image enhancement in which the main interest is contrast enhancement. However, since colors usually have three attributes, including hue, saturation and intensity of more than only one attribute of grayscale values, the naive application of the methods for grayscale images to color images often results in unsatisfactory consequences. Conventional hue-preserving color image enhancement methods utilize histogram equalization (HE for enhancing the contrast. However, they cannot always enhance the saturation simultaneously. In this paper, we propose a histogram specification (HS method for enhancing the saturation in hue-preserving color image enhancement. The proposed method computes the target histogram for HS on the basis of the geometry of RGB (rad, green and blue color space, whose shape is a cube with a unit side length. Therefore, the proposed method includes no parameters to be set by users. Experimental results show that the proposed method achieves higher color saturation than recent parameter-free methods for hue-preserving color image enhancement. As a result, the proposed method can be used for an alternative method of HE in hue-preserving color image enhancement.

  6. Introducing the Jacobian-volume-histogram of deforming organs: application to parotid shrinkage evaluation

    International Nuclear Information System (INIS)

    Fiorino, Claudio; Maggiulli, Eleonora; Broggi, Sara; Cattaneo, Giovanni Mauro; Calandrino, Riccardo; Liberini, Simone; Faggiano, Elena; Rizzo, Giovanna; Dell'Oca, Italo; Di Muzio, Nadia

    2011-01-01

    The Jacobian of the deformation field of elastic registration between images taken during radiotherapy is a measure of inter-fraction local deformation. The histogram of the Jacobian values (Jac) within an organ was introduced (JVH-Jacobian-volume-histogram) and first applied in quantifying parotid shrinkage. MVCTs of 32 patients previously treated with helical tomotherapy for head-neck cancers were collected. Parotid deformation was evaluated through elastic registration between MVCTs taken at the first and last fractions. Jac was calculated for each voxel of all parotids, and integral JVHs were calculated for each parotid; the correlation between the JVH and the planning dose-volume histogram (DVH) was investigated. On average, 82% (±17%) of the voxels shrinks (Jac 50% (Jac < 0.5). The best correlation between the DVH and the JVH was found between V10 and V15, and Jac < 0.4-0.6 (p < 0.01). The best constraint predicting a higher number of largely compressing voxels (Jac0.5<7.5%, median value) was V15 ≥ 75% (OR: 7.6, p = 0.002). Jac and the JVH are promising tools for scoring/modelling toxicity and for evaluating organ/contour variations with potential applications in adaptive radiotherapy.

  7. Whole brain magnetization transfer histogram analysis of pediatric acute lymphoblastic leukemia patients receiving intrathecal methotrexate therapy

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, Akira [Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto-shi Kyoto 606-8507 (Japan)]. E-mail: yakira@kuhp.kyoto-u.ac.jp; Miki, Yukio [Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto-shi Kyoto 606-8507 (Japan)]. E-mail: mikiy@kuhp.kyoto-u.ac.jp; Adachi, Souichi [Department of Pediatrics, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto-shi Kyoto 606-8507 (Japan)]. E-mail: sadachi@kuhp.kyoto-u.ac.jp (and others)

    2006-03-15

    Background and purpose: The purpose of this prospective study was to evaluate the hypothesis that magnetization transfer ratio (MTR) histogram analysis of the whole brain could detect early and subtle brain changes nonapparent on conventional magnetic resonance imaging (MRI) in children with acute lymphoblastic leukemia (ALL) receiving methotrexate (MTX) therapy. Materials and methods: Subjects in this prospective study comprised 10 children with ALL (mean age, 6 years; range, 0-16 years). In addition to conventional MRI, magnetization transfer images were obtained before and after intrathecal and intravenous MTX therapy. MTR values were calculated and plotted as a histogram, and peak height and location were calculated. Differences in peak height and location between pre- and post-MTX therapy scans were statistically analyzed. Conventional MRI was evaluated for abnormal signal area in white matter. Results: MTR peak height was significantly lower on post-MTX therapy scans than on pre-MTX therapy scans (p = 0.002). No significant differences in peak location were identified between pre- and post-chemotherapy imaging. No abnormal signals were noted in white matter on either pre- or post-MTX therapy conventional MRI. Conclusions: This study demonstrates that MTR histogram analysis allows better detection of early and subtle brain changes in ALL patients who receive MTX therapy than conventional MRI.

  8. LOR-OSEM: statistical PET reconstruction from raw line-of-response histograms

    International Nuclear Information System (INIS)

    Kadrmas, Dan J

    2004-01-01

    Iterative statistical reconstruction methods are becoming the standard in positron emission tomography (PET). Conventional maximum-likelihood expectation-maximization (MLEM) and ordered-subsets (OSEM) algorithms act on data which have been pre-processed into corrected, evenly-spaced histograms; however, such pre-processing corrupts the Poisson statistics. Recent advances have incorporated attenuation, scatter and randoms compensation into the iterative reconstruction. The objective of this work was to incorporate the remaining pre-processing steps, including arc correction, to reconstruct directly from raw unevenly-spaced line-of-response (LOR) histograms. This exactly preserves Poisson statistics and full spatial information in a manner closely related to listmode ML, making full use of the ML statistical model. The LOR-OSEM algorithm was implemented using a rotation-based projector which maps directly to the unevenly-spaced LOR grid. Simulation and phantom experiments were performed to characterize resolution, contrast and noise properties for 2D PET. LOR-OSEM provided a beneficial noise-resolution tradeoff, outperforming AW-OSEM by about the same margin that AW-OSEM outperformed pre-corrected OSEM. The relationship between LOR-ML and listmode ML algorithms was explored, and implementation differences are discussed. LOR-OSEM is a viable alternative to AW-OSEM for histogram-based reconstruction with improved spatial resolution and noise properties

  9. Digital image classification with the help of artificial neural network by simple histogram.

    Science.gov (United States)

    Dey, Pranab; Banerjee, Nirmalya; Kaur, Rajwant

    2016-01-01

    Visual image classification is a great challenge to the cytopathologist in routine day-to-day work. Artificial neural network (ANN) may be helpful in this matter. In this study, we have tried to classify digital images of malignant and benign cells in effusion cytology smear with the help of simple histogram data and ANN. A total of 404 digital images consisting of 168 benign cells and 236 malignant cells were selected for this study. The simple histogram data was extracted from these digital images and an ANN was constructed with the help of Neurointelligence software [Alyuda Neurointelligence 2.2 (577), Cupertino, California, USA]. The network architecture was 6-3-1. The images were classified as training set (281), validation set (63), and test set (60). The on-line backpropagation training algorithm was used for this study. A total of 10,000 iterations were done to train the ANN system with the speed of 609.81/s. After the adequate training of this ANN model, the system was able to identify all 34 malignant cell images and 24 out of 26 benign cells. The ANN model can be used for the identification of the individual malignant cells with the help of simple histogram data. This study will be helpful in the future to identify malignant cells in unknown situations.

  10. Multipeak Mean Based Optimized Histogram Modification Framework Using Swarm Intelligence for Image Contrast Enhancement

    Directory of Open Access Journals (Sweden)

    P. Babu

    2015-01-01

    Full Text Available A novel approach, Multipeak mean based optimized histogram modification framework (MMOHM is introduced for the purpose of enhancing the contrast as well as preserving essential details for any given gray scale and colour images. The basic idea of this technique is the calculation of multiple peaks (local maxima from the original histogram. The mean value of multiple peaks is computed and the input image’s histogram is segmented into two subhistograms based on this multipeak mean (mmean value. Then, a bicriteria optimization problem is formulated and the subhistograms are modified by selecting optimal contrast enhancement parameters. While formulating the enhancement parameters, particle swarm optimization is employed to find optimal values of them. Finally, the union of the modified subhistograms produces a contrast enhanced and details preserved output image. This mechanism enhances the contrast of the input image better than the existing contemporary HE methods. The performance of the proposed method is well supported by the contrast enhancement quantitative metrics such as discrete entropy, natural image quality evaluator, and absolute mean brightness error.

  11. Infrared Small Moving Target Detection via Saliency Histogram and Geometrical Invariability

    Directory of Open Access Journals (Sweden)

    Minjie Wan

    2017-06-01

    Full Text Available In order to detect both bright and dark small moving targets effectively in infrared (IR video sequences, a saliency histogram and geometrical invariability based method is presented in this paper. First, a saliency map that roughly highlights the salient regions of the original image is obtained by tuning its amplitude spectrum in the frequency domain. Then, a saliency histogram is constructed by means of averaging the accumulated saliency value of each gray level in the map, through which bins corresponding to bright target and dark target are assigned with large values in the histogram. Next, single-frame detection of candidate targets is accomplished by a binarized segmentation using an adaptive threshold, and their centroid coordinates with sub-pixel accuracy are calculated through a connected components labeling method as well as a gray-weighted criterion. Finally, considering the motion characteristics in consecutive frames, an inter-frame false alarm suppression method based on geometrical invariability is developed to improve the precision rate further. Quantitative analyses demonstrate the detecting precision of this proposed approach can be up to 97% and Receiver Operating Characteristic (ROC curves further verify our method outperforms other state-of-the-arts methods in both detection rate and false alarm rate.

  12. Conductance histogram evolution of an EC-MCBJ fabricated Au atomic point contact

    Energy Technology Data Exchange (ETDEWEB)

    Yang Yang; Liu Junyang; Chen Zhaobin; Tian Jinghua; Jin Xi; Liu Bo; Yang Fangzu; Tian Zhongqun [State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China); Li Xiulan; Tao Nongjian [Center for Bioelectronics and Biosensors, Biodesign Institute, Department of Electrical Engineering, Arizona State University, Tempe, AZ 85287-6206 (United States); Luo Zhongzi; Lu Miao, E-mail: zqtian@xmu.edu.cn [Micro-Electro-Mechanical Systems Research Center, Pen-Tung Sah Micro-Nano Technology Institute, Xiamen University, Xiamen 361005 (China)

    2011-07-08

    This work presents a study of Au conductance quantization based on a combined electrochemical deposition and mechanically controllable break junction (MCBJ) method. We describe the microfabrication process and discuss improved features of our microchip structure compared to the previous one. The improved structure prolongs the available life of the microchip and also increases the success rate of the MCBJ experiment. Stepwise changes in the current were observed at the last stage of atomic point contact breakdown and conductance histograms were constructed. The evolution of 1G{sub 0} peak height in conductance histograms was used to investigate the probability of formation of an atomic point contact. It has been shown that the success rate in forming an atomic point contact can be improved by decreasing the stretching speed and the degree that the two electrodes are brought into contact. The repeated breakdown and formation over thousands of cycles led to a distinctive increase of 1G{sub 0} peak height in the conductance histograms, and this increased probability of forming a single atomic point contact is discussed.

  13. Conductance histogram evolution of an EC-MCBJ fabricated Au atomic point contact

    International Nuclear Information System (INIS)

    Yang Yang; Liu Junyang; Chen Zhaobin; Tian Jinghua; Jin Xi; Liu Bo; Yang Fangzu; Tian Zhongqun; Li Xiulan; Tao Nongjian; Luo Zhongzi; Lu Miao

    2011-01-01

    This work presents a study of Au conductance quantization based on a combined electrochemical deposition and mechanically controllable break junction (MCBJ) method. We describe the microfabrication process and discuss improved features of our microchip structure compared to the previous one. The improved structure prolongs the available life of the microchip and also increases the success rate of the MCBJ experiment. Stepwise changes in the current were observed at the last stage of atomic point contact breakdown and conductance histograms were constructed. The evolution of 1G 0 peak height in conductance histograms was used to investigate the probability of formation of an atomic point contact. It has been shown that the success rate in forming an atomic point contact can be improved by decreasing the stretching speed and the degree that the two electrodes are brought into contact. The repeated breakdown and formation over thousands of cycles led to a distinctive increase of 1G 0 peak height in the conductance histograms, and this increased probability of forming a single atomic point contact is discussed.

  14. Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing

    Directory of Open Access Journals (Sweden)

    Ellis David

    2009-08-01

    Full Text Available Abstract Background Amino acid substitutions in the target enzyme Erg11p of azole antifungals contribute to clinically-relevant azole resistance in Candida albicans. A simple molecular method for rapid detection of ERG11 gene mutations would be an advantage as a screening tool to identify potentially-resistant strains and to track their movement. To complement DNA sequencing, we developed a padlock probe and rolling circle amplification (RCA-based method to detect a series of mutations in the C. albicans ERG11 gene using "reference" azole-resistant isolates with known mutations. The method was then used to estimate the frequency of ERG11 mutations and their type in 25 Australian clinical C. albicans isolates with reduced susceptibility to fluconazole and in 23 fluconazole-susceptible isolates. RCA results were compared DNA sequencing. Results The RCA assay correctly identified all ERG11 mutations in eight "reference" C. albicans isolates. When applied to 48 test strains, the RCA method showed 100% agreement with DNA sequencing where an ERG11 mutation-specific probe was used. Of 20 different missense mutations detected by sequencing in 24 of 25 (96% isolates with reduced fluconazole susceptibility, 16 were detected by RCA. Five missense mutations were detected by both methods in 18 of 23 (78% fluconazole-susceptible strains. DNA sequencing revealed that mutations in non-susceptible isolates were all due to homozygous nucleotide changes. With the exception of the mutations leading to amino acid substitution E266D, those in fluconazole-susceptible strains were heterozygous. Amino acid substitutions common to both sets of isolates were D116E, E266D, K128T, V437I and V488I. Substitutions unique to isolates with reduced fluconazole susceptibility were G464 S (n = 4 isolates, G448E (n = 3, G307S (n = 3, K143R (n = 3 and Y123H, S405F and R467K (each n = 1. DNA sequencing revealed a novel substitution, G450V, in one isolate. Conclusion The sensitive RCA

  15. Evaluation of kDNA PCR hybridization and ITS1 nPCR methods in different clinical samples for visceral leishmaniasis diagnosis in dogs with and without clinical signs

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, Aline Leandra C.; Carregal, Virginia M.; Leite, Rodrigo S.; Ferreira, Sidney A.; Andrade, Antero Silva R., E-mail: alineleandra@hotmail.com, E-mail: streptos@hotmail.com, E-mail: rleite2005@gmail.com, E-mail: vidasnino@yahoo.com.br, E-mail: antero@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil). Lab. de Radiobiologia; Melo, Maria N., E-mail: melo@icb.ufmg.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Parasitologia

    2013-07-01

    Visceral leishmaniasis (VL) in Brazil is caused by Leishmania infantum and dogs are considered the main domestic reservoirs of this parasite. The VL control program in Brazil emphasizes the use of serological surveys, followed by elimination of seropositive dogs. However, serologic tests have limitations in terms of sensitivity and specificity. Molecular methods such as PCR (Polymerase Chain Reaction) associated with hybridization using {sup 32}P radiolabeled DNA probes (kDNA PCR hybridization) are useful tools in this scenario, since they are more specific and sensitive than conventional methods. A variety of samples can be employed with PCR; however non-invasive procedures are the most adequate. One of main obstacles for implementation of PCR in the canine visceral leishmaniasis (CVL) diagnosis is the lack of standardization. Few studies up to the moment compared the effectiveness of the different PCR methods and clinical samples available. The objective of this study was to compare the kDNA PCR hybridization and the Internal Transcribed Spacer 1 nested PCR (ITS1 nPCR) methods and four types of clinical samples for the diagnosis of CVL in dogs with and without clinical signs of the disease. The methods were compared using samples of conjunctival swab (SC), bone marrow (BM), skin (S) and peripheral blood (PB). A group of 60 mongrel dogs, all positive in serological and parasitological tests, were equally divided in two groups: S (with clinical signs) and A (without clinical signs). The frequencies of positive results for the kDNA PCR hybridization in the S group were: CS 97% (29/30), BM 83 % (25/30), S 63% (19/30) and PB 4 7% (14/30). By the same method the following results were obtained in the A group: CS 70% (21/30), BM 63% (19/30), S 57% (17/30) and PB 17% (5/30). The ITS1 nPCR allowed the following positivities for the S group: CS 83% (25/30), BM 97% (29/30), S 83% (25/30) and PB 70% (21/30). For the A group the following results were obtained: CS and BM 83

  16. Evaluation of kDNA PCR hybridization and ITS1 nPCR methods in different clinical samples for visceral leishmaniasis diagnosis in dogs with and without clinical signs

    International Nuclear Information System (INIS)

    Ferreira, Aline Leandra C.; Carregal, Virginia M.; Leite, Rodrigo S.; Ferreira, Sidney A.; Andrade, Antero Silva R.; Melo, Maria N.

    2013-01-01

    Visceral leishmaniasis (VL) in Brazil is caused by Leishmania infantum and dogs are considered the main domestic reservoirs of this parasite. The VL control program in Brazil emphasizes the use of serological surveys, followed by elimination of seropositive dogs. However, serologic tests have limitations in terms of sensitivity and specificity. Molecular methods such as PCR (Polymerase Chain Reaction) associated with hybridization using 32 P radiolabeled DNA probes (kDNA PCR hybridization) are useful tools in this scenario, since they are more specific and sensitive than conventional methods. A variety of samples can be employed with PCR; however non-invasive procedures are the most adequate. One of main obstacles for implementation of PCR in the canine visceral leishmaniasis (CVL) diagnosis is the lack of standardization. Few studies up to the moment compared the effectiveness of the different PCR methods and clinical samples available. The objective of this study was to compare the kDNA PCR hybridization and the Internal Transcribed Spacer 1 nested PCR (ITS1 nPCR) methods and four types of clinical samples for the diagnosis of CVL in dogs with and without clinical signs of the disease. The methods were compared using samples of conjunctival swab (SC), bone marrow (BM), skin (S) and peripheral blood (PB). A group of 60 mongrel dogs, all positive in serological and parasitological tests, were equally divided in two groups: S (with clinical signs) and A (without clinical signs). The frequencies of positive results for the kDNA PCR hybridization in the S group were: CS 97% (29/30), BM 83 % (25/30), S 63% (19/30) and PB 4 7% (14/30). By the same method the following results were obtained in the A group: CS 70% (21/30), BM 63% (19/30), S 57% (17/30) and PB 17% (5/30). The ITS1 nPCR allowed the following positivities for the S group: CS 83% (25/30), BM 97% (29/30), S 83% (25/30) and PB 70% (21/30). For the A group the following results were obtained: CS and BM 83% (25

  17. Breast lesion characterization using whole-lesion histogram analysis with stretched-exponential diffusion model.

    Science.gov (United States)

    Liu, Chunling; Wang, Kun; Li, Xiaodan; Zhang, Jine; Ding, Jie; Spuhler, Karl; Duong, Timothy; Liang, Changhong; Huang, Chuan

    2018-06-01

    Diffusion-weighted imaging (DWI) has been studied in breast imaging and can provide more information about diffusion, perfusion and other physiological interests than standard pulse sequences. The stretched-exponential model has previously been shown to be more reliable than conventional DWI techniques, but different diagnostic sensitivities were found from study to study. This work investigated the characteristics of whole-lesion histogram parameters derived from the stretched-exponential diffusion model for benign and malignant breast lesions, compared them with conventional apparent diffusion coefficient (ADC), and further determined which histogram metrics can be best used to differentiate malignant from benign lesions. This was a prospective study. Seventy females were included in the study. Multi-b value DWI was performed on a 1.5T scanner. Histogram parameters of whole lesions for distributed diffusion coefficient (DDC), heterogeneity index (α), and ADC were calculated by two radiologists and compared among benign lesions, ductal carcinoma in situ (DCIS), and invasive carcinoma confirmed by pathology. Nonparametric tests were performed for comparisons among invasive carcinoma, DCIS, and benign lesions. Comparisons of receiver operating characteristic (ROC) curves were performed to show the ability to discriminate malignant from benign lesions. The majority of histogram parameters (mean/min/max, skewness/kurtosis, 10-90 th percentile values) from DDC, α, and ADC were significantly different among invasive carcinoma, DCIS, and benign lesions. DDC 10% (area under curve [AUC] = 0.931), ADC 10% (AUC = 0.893), and α mean (AUC = 0.787) were found to be the best metrics in differentiating benign from malignant tumors among all histogram parameters derived from ADC and α, respectively. The combination of DDC 10% and α mean , using logistic regression, yielded the highest sensitivity (90.2%) and specificity (95.5%). DDC 10% and α mean derived from

  18. Measuring kinetics of complex single ion channel data using mean-variance histograms.

    Science.gov (United States)

    Patlak, J B

    1993-07-01

    The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean

  19. Centroid and full-width at half maximum uncertainties of histogrammed data with an underlying Gaussian distribution -- The moments method

    International Nuclear Information System (INIS)

    Valentine, J.D.; Rana, A.E.

    1996-01-01

    The effect of approximating a continuous Gaussian distribution with histogrammed data are studied. The expressions for theoretical uncertainties in centroid and full-width at half maximum (FWHM), as determined by calculation of moments, are derived using the error propagation method for a histogrammed Gaussian distribution. The results are compared with the corresponding pseudo-experimental uncertainties for computer-generated histogrammed Gaussian peaks to demonstrate the effect of binning the data. It is shown that increasing the number of bins in the histogram improves the continuous distribution approximation. For example, a FWHM ≥ 9 and FWHM ≥ 12 bins are needed to reduce the pseudo-experimental standard deviation of FWHM to within ≥5% and ≥1%, respectively, of the theoretical value for a peak containing 10,000 counts. In addition, the uncertainties in the centroid and FWHM as a function of peak area are studied. Finally, Sheppard's correction is applied to partially correct for the binning effect

  20. Whole-tumor apparent diffusion coefficient (ADC) histogram analysis to differentiate benign peripheral neurogenic tumors from soft tissue sarcomas.

    Science.gov (United States)

    Nakajo, Masanori; Fukukura, Yoshihiko; Hakamada, Hiroto; Yoneyama, Tomohide; Kamimura, Kiyohisa; Nagano, Satoshi; Nakajo, Masayuki; Yoshiura, Takashi

    2018-02-22

    Apparent diffusion coefficient (ADC) histogram analyses have been used to differentiate tumor grades and predict therapeutic responses in various anatomic sites with moderate success. To determine the ability of diffusion-weighted imaging (DWI) with a whole-tumor ADC histogram analysis to differentiate benign peripheral neurogenic tumors (BPNTs) from soft tissue sarcomas (STSs). Retrospective study, single institution. In all, 25 BPNTs and 31 STSs. Two-b value DWI (b-values = 0, 1000s/mm 2 ) was at 3.0T. The histogram parameters of whole-tumor for ADC were calculated by two radiologists and compared between BPNTs and STSs. Nonparametric tests were performed for comparisons between BPNTs and STSs. P histogram parameters except kurtosis and entropy differed significantly between BPNTs and STSs. 3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

  1. Aerial radiometric and magnetic reconnaissance survey of the Delta Quadrangle, Utah. Volume 2. Maps, profiles, and histograms. Final report

    International Nuclear Information System (INIS)

    1978-11-01

    Results of the interpretation of the gamma-ray spectrometric data in the form of a preferred anomaly map, along with significance-factor profile maps, stacked profiles, and histograms are presented in Volume 2

  2. Genital herpes evaluation by quantitative TaqMan PCR: correlating single detection and quantity of HSV-2 DNA in cervicovaginal lavage fluids with cross-sectional and longitudinal clinical data

    Directory of Open Access Journals (Sweden)

    Cox Christopher

    2010-11-01

    Full Text Available Abstract Objective To evaluate the utility of a single quantitative PCR (qPCR measurement of HSV (HSV-1&2 DNA in cervicovaginal lavage (CVL specimens collected from women with predominantly chronic HSV-2 infection in assessing genital HSV shedding and the clinical course of genital herpes (GH within a cohort with semiannual schedule of follow up and collection of specimens. Methods Two previously described methods used for detection of HSV DNA in mucocutaneous swab samples were adapted for quantification of HSV DNA in CVLs. Single CVL specimens from 509 women were tested. Presence and quantity of CVL HSV DNA were explored in relation to observed cross-sectional and longitudinal clinical data. Results The PCR assay was sensitive and reproducible with a limit of quantification of ~50 copies per milliliter of CVL. Overall, 7% of the samples were positive for HSV-2 DNA with median log10 HSV-2 DNA copy number of 3.9 (IQR: 2.6-5.7. No HSV-1 was detected. Presence and quantity of HSV-2 DNA in CVL directly correlated with the clinical signs and symptoms of presence of active symptomatic disease with frequent recurrences. Conclusion Single qPCR measurement of HSV DNA in CVL fluids of women with chronic HSV-2 infection provided useful information for assessing GH in the setting of infrequent sampling of specimens. Observed positive correlation of the presence and quantity of HSV-2 DNA with the presence of active and more severe course of HSV-2 infection may have clinical significance in the evaluation and management of HSV-2 infected patients.

  3. Different Recognition of DNA Modified by Antitumor Cisplatin and Its Clinically Ineffective trans Isomer by Tumor Suppressor Protein p53

    Czech Academy of Sciences Publication Activity Database

    Kašpárková, Jana; Pospíšilová, Š.; Brabec, Viktor

    2001-01-01

    Roč. 276, č. 19 (2001), s. 16064-16069 ISSN 0021-9258 R&D Projects: GA ČR GA305/99/0695; GA ČR GA305/01/0418; GA ČR GA301/00/P094; GA AV ČR IAA5004101; GA MZd NL6058 Grant - others:HHMI(US) 55000313; Wellcome Trust(GB) 062366/Z/00/Z Institutional research plan: CEZ:AV0Z5004920 Keywords : Interstrand cross-links * platinum complexes * supercoiled DNA Subject RIV: BO - Biophysics Impact factor: 7.258, year: 2001

  4. Potential of MR histogram analyses for prediction of response to chemotherapy in patients with colorectal hepatic metastases.

    Science.gov (United States)

    Liang, He-Yue; Huang, Ya-Qin; Yang, Zhao-Xia; Ying-Ding; Zeng, Meng-Su; Rao, Sheng-Xiang

    2016-07-01

    To determine if magnetic resonance imaging (MRI) histogram analyses can help predict response to chemotherapy in patients with colorectal hepatic metastases by using response evaluation criteria in solid tumours (RECIST1.1) as the reference standard. Standard MRI including diffusion-weighted imaging (b=0, 500 s/mm(2)) was performed before chemotherapy in 53 patients with colorectal hepatic metastases. Histograms were performed for apparent diffusion coefficient (ADC) maps, arterial, and portal venous phase images; thereafter, mean, percentiles (1st, 10th, 50th, 90th, 99th), skewness, kurtosis, and variance were generated. Quantitative histogram parameters were compared between responders (partial and complete response, n=15) and non-responders (progressive and stable disease, n=38). Receiver operator characteristics (ROC) analyses were further analyzed for the significant parameters. The mean, 1st percentile, 10th percentile, 50th percentile, 90th percentile, 99th percentile of the ADC maps were significantly lower in responding group than that in non-responding group (p=0.000-0.002) with area under the ROC curve (AUCs) of 0.76-0.82. The histogram parameters of arterial and portal venous phase showed no significant difference (p>0.05) between the two groups. Histogram-derived parameters for ADC maps seem to be a promising tool for predicting response to chemotherapy in patients with colorectal hepatic metastases. • ADC histogram analyses can potentially predict chemotherapy response in colorectal liver metastases. • Lower histogram-derived parameters (mean, percentiles) for ADC tend to have good response. • MR enhancement histogram analyses are not reliable to predict response.

  5. Subtype Differentiation of Small (≤ 4 cm) Solid Renal Mass Using Volumetric Histogram Analysis of DWI at 3-T MRI.

    Science.gov (United States)

    Li, Anqin; Xing, Wei; Li, Haojie; Hu, Yao; Hu, Daoyu; Li, Zhen; Kamel, Ihab R

    2018-05-29

    The purpose of this article is to evaluate the utility of volumetric histogram analysis of apparent diffusion coefficient (ADC) derived from reduced-FOV DWI for small (≤ 4 cm) solid renal mass subtypes at 3-T MRI. This retrospective study included 38 clear cell renal cell carcinomas (RCCs), 16 papillary RCCs, 18 chromophobe RCCs, 13 minimal fat angiomyolipomas (AMLs), and seven oncocytomas evaluated with preoperative MRI. Volumetric ADC maps were generated using all slices of the reduced-FOV DW images to obtain histogram parameters, including mean, median, 10th percentile, 25th percentile, 75th percentile, 90th percentile, and SD ADC values, as well as skewness, kurtosis, and entropy. Comparisons of these parameters were made by one-way ANOVA, t test, and ROC curves analysis. ADC histogram parameters differentiated eight of 10 pairs of renal tumors. Three subtype pairs (clear cell RCC vs papillary RCC, clear cell RCC vs chromophobe RCC, and clear cell RCC vs minimal fat AML) were differentiated by mean ADC. However, five other subtype pairs (clear cell RCC vs oncocytoma, papillary RCC vs minimal fat AML, papillary RCC vs oncocytoma, chromophobe RCC vs minimal fat AML, and chromophobe RCC vs oncocytoma) were differentiated by histogram distribution parameters exclusively (all p histogram parameters yielded the highest AUC (0.851; sensitivity, 80.0%; specificity, 86.1%). Quantitative volumetric ADC histogram analysis may help differentiate various subtypes of small solid renal tumors, including benign and malignant lesions.

  6. Gliomas: Application of Cumulative Histogram Analysis of Normalized Cerebral Blood Volume on 3 T MRI to Tumor Grading

    Science.gov (United States)

    Kim, Hyungjin; Choi, Seung Hong; Kim, Ji-Hoon; Ryoo, Inseon; Kim, Soo Chin; Yeom, Jeong A.; Shin, Hwaseon; Jung, Seung Chai; Lee, A. Leum; Yun, Tae Jin; Park, Chul-Kee; Sohn, Chul-Ho; Park, Sung-Hye

    2013-01-01

    Background Glioma grading assumes significant importance in that low- and high-grade gliomas display different prognoses and are treated with dissimilar therapeutic strategies. The objective of our study was to retrospectively assess the usefulness of a cumulative normalized cerebral blood volume (nCBV) histogram for glioma grading based on 3 T MRI. Methods From February 2010 to April 2012, 63 patients with astrocytic tumors underwent 3 T MRI with dynamic susceptibility contrast perfusion-weighted imaging. Regions of interest containing the entire tumor volume were drawn on every section of the co-registered relative CBV (rCBV) maps and T2-weighted images. The percentile values from the cumulative nCBV histograms and the other histogram parameters were correlated with tumor grades. Cochran’s Q test and the McNemar test were used to compare the diagnostic accuracies of the histogram parameters after the receiver operating characteristic curve analysis. Using the parameter offering the highest diagnostic accuracy, a validation process was performed with an independent test set of nine patients. Results The 99th percentile of the cumulative nCBV histogram (nCBV C99), mean and peak height differed significantly between low- and high-grade gliomas (P = histogram analysis of nCBV using 3 T MRI can be a useful method for preoperative glioma grading. The nCBV C99 value is helpful in distinguishing high- from low-grade gliomas and grade IV from III gliomas. PMID:23704910

  7. Enhancing tumor apparent diffusion coefficient histogram skewness stratifies the postoperative survival in recurrent glioblastoma multiforme patients undergoing salvage surgery.

    Science.gov (United States)

    Zolal, Amir; Juratli, Tareq A; Linn, Jennifer; Podlesek, Dino; Sitoci Ficici, Kerim Hakan; Kitzler, Hagen H; Schackert, Gabriele; Sobottka, Stephan B; Rieger, Bernhard; Krex, Dietmar

    2016-05-01

    Objective To determine the value of apparent diffusion coefficient (ADC) histogram parameters for the prediction of individual survival in patients undergoing surgery for recurrent glioblastoma (GBM) in a retrospective cohort study. Methods Thirty-one patients who underwent surgery for first recurrence of a known GBM between 2008 and 2012 were included. The following parameters were collected: age, sex, enhancing tumor size, mean ADC, median ADC, ADC skewness, ADC kurtosis and fifth percentile of the ADC histogram, initial progression free survival (PFS), extent of second resection and further adjuvant treatment. The association of these parameters with survival and PFS after second surgery was analyzed using log-rank test and Cox regression. Results Using log-rank test, ADC histogram skewness of the enhancing tumor was significantly associated with both survival (p = 0.001) and PFS after second surgery (p = 0.005). Further parameters associated with prolonged survival after second surgery were: gross total resection at second surgery (p = 0.026), tumor size (0.040) and third surgery (p = 0.003). In the multivariate Cox analysis, ADC histogram skewness was shown to be an independent prognostic factor for survival after second surgery. Conclusion ADC histogram skewness of the enhancing lesion, enhancing lesion size, third surgery, as well as gross total resection have been shown to be associated with survival following the second surgery. ADC histogram skewness was an independent prognostic factor for survival in the multivariate analysis.

  8. Contingent first-trimester screening for aneuploidies with cell-free DNA in a Danish clinical setting

    DEFF Research Database (Denmark)

    Miltoft, Caroline Borregaard; Rode, Line; Ekelund, Charlotte Kvist

    2017-01-01

    OBJECTIVES: The primary aim was to compare the screening performance for Trisomy 21, of standard combined first trimester screening with referral to invasive testing at a cut-off at 1 in 300, with a contingent testing, consisting of referral to invasive testing at a 1 in 100 cut-off and referral...... to cell-free DNA (cfDNA) testing for a risk between 1 in 100 and 1 in 1000. METHODS: Singleton pregnant women with a combined first trimester risk ≥ 1 in 1000 were consecutively recruited from two Danish hospitals between August 2014 and May 2015. First trimester combined screening was based on maternal...... these there were 15 cases of Trisomy 21, one case of Trisomy 18 and two cases of Trisomy 13. The sensitivity for Trisomy 21 was 100% using both screening scenarios, while specificity increased significantly from 97.0% to 98.8% (p contingent approach. The sensitivity for Trisomy 21, 18 and 13...

  9. Temporal Evolution and Dose-Volume Histogram Predictors of Visual Acuity After Proton Beam Radiation Therapy of Uveal Melanoma

    Energy Technology Data Exchange (ETDEWEB)

    Polishchuk, Alexei L. [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California (United States); Mishra, Kavita K., E-mail: Kavita.Mishra@ucsf.edu [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California (United States); Weinberg, Vivian; Daftari, Inder K. [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California (United States); Nguyen, Jacqueline M.; Cole, Tia B. [Tumori Foundation, San Francisco, California (United States); Quivey, Jeanne M.; Phillips, Theodore L. [Department of Radiation Oncology, University of California, San Francisco, San Francisco, California (United States); Char, Devron H. [Tumori Foundation, San Francisco, California (United States)

    2017-01-01

    Purpose: To perform an in-depth temporal analysis of visual acuity (VA) outcomes after proton beam radiation therapy (PBRT) in a large, uniformly treated cohort of uveal melanoma (UM) patients, to determine trends in VA evolution depending on pretreatment and temporally defined posttreatment VA measurements; and to investigate the relevance of specific patient, tumor and dose-volume parameters to posttreatment vision loss. Methods and Materials: Uveal melanoma patients receiving PBRT were identified from a prospectively maintained database. Included patients (n=645) received 56 GyE in 4 fractions, had pretreatment best corrected VA (BCVA) in the affected eye of count fingers (CF) or better, with posttreatment VA assessment at specified post-PBRT time point(s). Patients were grouped according to the pretreatment BCVA into favorable (≥20/40) or unfavorable (20/50-20/400) and poor (CF) strata. Temporal analysis of BCVA changes was described, and univariate and forward stepwise multivariate logistic regression analyses were performed to identify predictors for VA loss. Results: Median VA follow-up was 53 months (range, 3-213 months). At 60-month follow up, among evaluable treated eyes with favorable pretreatment BCVA, 45% retained BCVA ≥20/40, whereas among evaluable treated eyes with initially unfavorable/poor BCVA, 21% had vision ≥20/100. Among those with a favorable initial BCVA, attaining BCVA of ≥20/40 at any posttreatment time point was associated with subsequent maintenance of excellent BCVA. Multivariate analysis identified volume of the macula receiving 28GyE (P<.0001) and optic nerve (P=.0004) as independent dose-volume histogram predictors of 48-month post-PBRT vision loss among initially favorable treated eyes. Conclusions: Approximately half of PBRT-treated UM eyes with excellent pretreatment BCVA assessed at 5 years after treatment will retain excellent long-term vision. 28GyE macula and optic nerve dose-volume histogram parameters allow for

  10. Normal tissue complication probabilities: dependence on choice of biological model and dose-volume histogram reduction scheme

    International Nuclear Information System (INIS)

    Moiseenko, Vitali; Battista, Jerry; Van Dyk, Jake

    2000-01-01

    Purpose: To evaluate the impact of dose-volume histogram (DVH) reduction schemes and models of normal tissue complication probability (NTCP) on ranking of radiation treatment plans. Methods and Materials: Data for liver complications in humans and for spinal cord in rats were used to derive input parameters of four different NTCP models. DVH reduction was performed using two schemes: 'effective volume' and 'preferred Lyman'. DVHs for competing treatment plans were derived from a sample DVH by varying dose uniformity in a high dose region so that the obtained cumulative DVHs intersected. Treatment plans were ranked according to the calculated NTCP values. Results: Whenever the preferred Lyman scheme was used to reduce the DVH, competing plans were indistinguishable as long as the mean dose was constant. The effective volume DVH reduction scheme did allow us to distinguish between these competing treatment plans. However, plan ranking depended on the radiobiological model used and its input parameters. Conclusions: Dose escalation will be a significant part of radiation treatment planning using new technologies, such as 3-D conformal radiotherapy and tomotherapy. Such dose escalation will depend on how the dose distributions in organs at risk are interpreted in terms of expected complication probabilities. The present study indicates considerable variability in predicted NTCP values because of the methods used for DVH reduction and radiobiological models and their input parameters. Animal studies and collection of standardized clinical data are needed to ascertain the effects of non-uniform dose distributions and to test the validity of the models currently in use

  11. CLINICAL

    African Journals Online (AJOL)

    laborative Study (HPMCS), representing the combined data of 3 941 HIV-infected infants and children ... antibody-positive infants with severe disease before confirmation by HIV DNA polymerase chain .... human immunodeficiency virus infection in children less than 13 years of age. MMWR Morb Mortal Wkly Rep 1994; 43: ...

  12. CHOBS: Color Histogram of Block Statistics for Automatic Bleeding Detection in Wireless Capsule Endoscopy Video.

    Science.gov (United States)

    Ghosh, Tonmoy; Fattah, Shaikh Anowarul; Wahid, Khan A

    2018-01-01

    Wireless capsule endoscopy (WCE) is the most advanced technology to visualize whole gastrointestinal (GI) tract in a non-invasive way. But the major disadvantage here, it takes long reviewing time, which is very laborious as continuous manual intervention is necessary. In order to reduce the burden of the clinician, in this paper, an automatic bleeding detection method for WCE video is proposed based on the color histogram of block statistics, namely CHOBS. A single pixel in WCE image may be distorted due to the capsule motion in the GI tract. Instead of considering individual pixel values, a block surrounding to that individual pixel is chosen for extracting local statistical features. By combining local block features of three different color planes of RGB color space, an index value is defined. A color histogram, which is extracted from those index values, provides distinguishable color texture feature. A feature reduction technique utilizing color histogram pattern and principal component analysis is proposed, which can drastically reduce the feature dimension. For bleeding zone detection, blocks are classified using extracted local features that do not incorporate any computational burden for feature extraction. From extensive experimentation on several WCE videos and 2300 images, which are collected from a publicly available database, a very satisfactory bleeding frame and zone detection performance is achieved in comparison to that obtained by some of the existing methods. In the case of bleeding frame detection, the accuracy, sensitivity, and specificity obtained from proposed method are 97.85%, 99.47%, and 99.15%, respectively, and in the case of bleeding zone detection, 95.75% of precision is achieved. The proposed method offers not only low feature dimension but also highly satisfactory bleeding detection performance, which even can effectively detect bleeding frame and zone in a continuous WCE video data.

  13. Yet Another Method for Image Segmentation based on Histograms and Heuristics

    Directory of Open Access Journals (Sweden)

    Horia-Nicolai L. Teodorescu

    2012-07-01

    Full Text Available We introduce a method for image segmentation that requires little computations, yet providing comparable results to other methods. While the proposed method resembles to the known ones based on histograms, it is still different in the use of the gray level distribution. When to the basic procedure we add several heuristic rules, the method produces results that, in some cases, may outperform the results produced by the known methods. The paper reports preliminary results. More details on the method, improvements, and results will be presented in a future paper.

  14. Content Based Radiographic Images Indexing and Retrieval Using Pattern Orientation Histogram

    Directory of Open Access Journals (Sweden)

    Abolfazl Lakdashti

    2008-06-01

    Full Text Available Introduction: Content Based Image Retrieval (CBIR is a method of image searching and retrieval in a  database. In medical applications, CBIR is a tool used by physicians to compare the previous and current  medical images associated with patients pathological conditions. As the volume of pictorial information  stored in medical image databases is in progress, efficient image indexing and retrieval is increasingly  becoming a necessity.  Materials and Methods: This paper presents a new content based radiographic image retrieval approach  based on histogram of pattern orientations, namely pattern orientation histogram (POH. POH represents  the  spatial  distribution  of  five  different  pattern  orientations:  vertical,  horizontal,  diagonal  down/left,  diagonal down/right and non-orientation. In this method, a given image is first divided into image-blocks  and  the  frequency  of  each  type  of  pattern  is  determined  in  each  image-block.  Then,  local  pattern  histograms for each of these image-blocks are computed.   Results: The method was compared to two well known texture-based image retrieval methods: Tamura  and  Edge  Histogram  Descriptors  (EHD  in  MPEG-7  standard.  Experimental  results  based  on  10000  IRMA  radiography  image  dataset,  demonstrate  that  POH  provides  better  precision  and  recall  rates  compared to Tamura and EHD. For some images, the recall and precision rates obtained by POH are,  respectively, 48% and 18% better than the best of the two above mentioned methods.    Discussion and Conclusion: Since we exploit the absolute location of the pattern in the image as well as  its global composition, the proposed matching method can retrieve semantically similar medical images.

  15. SUPERVISED AUTOMATIC HISTOGRAM CLUSTERING AND WATERSHED SEGMENTATION. APPLICATION TO MICROSCOPIC MEDICAL COLOR IMAGES

    Directory of Open Access Journals (Sweden)

    Olivier Lezoray

    2011-05-01

    Full Text Available In this paper, an approach to the segmentation of microscopic color images is addressed, and applied to medical images. The approach combines a clustering method and a region growing method. Each color plane is segmented independently relying on a watershed based clustering of the plane histogram. The marginal segmentation maps intersect in a label concordance map. The latter map is simplified based on the assumption that the color planes are correlated. This produces a simplified label concordance map containing labeled and unlabeled pixels. The formers are used as an image of seeds for a color watershed. This fast and robust segmentation scheme is applied to several types of medical images.

  16. Mobile Visual Search Based on Histogram Matching and Zone Weight Learning

    Science.gov (United States)

    Zhu, Chuang; Tao, Li; Yang, Fan; Lu, Tao; Jia, Huizhu; Xie, Xiaodong

    2018-01-01

    In this paper, we propose a novel image retrieval algorithm for mobile visual search. At first, a short visual codebook is generated based on the descriptor database to represent the statistical information of the dataset. Then, an accurate local descriptor similarity score is computed by merging the tf-idf weighted histogram matching and the weighting strategy in compact descriptors for visual search (CDVS). At last, both the global descriptor matching score and the local descriptor similarity score are summed up to rerank the retrieval results according to the learned zone weights. The results show that the proposed approach outperforms the state-of-the-art image retrieval method in CDVS.

  17. Frontal Face Detection using Haar Wavelet Coefficients and Local Histogram Correlation

    Directory of Open Access Journals (Sweden)

    Iwan Setyawan

    2011-12-01

    Full Text Available Face detection is the main building block on which all automatic systems dealing with human faces is built. For example, a face recognition system must rely on face detection to process an input image and determine which areas contain human faces. These areas then become the input for the face recognition system for further processing. This paper presents a face detection system designed to detect frontal faces. The system uses Haar wavelet coefficients and local histogram correlation as differentiating features. Our proposed system is trained using 100 training images. Our experiments show that the proposed system performed well during testing, achieving a detection rate of 91.5%.

  18. Three-dimensional volumetric gray-scale uterine cervix histogram prediction of days to delivery in full term pregnancy.

    Science.gov (United States)

    Kim, Ji Youn; Kim, Hai-Joong; Hahn, Meong Hi; Jeon, Hye Jin; Cho, Geum Joon; Hong, Sun Chul; Oh, Min Jeong

    2013-09-01

    Our aim was to figure out whether volumetric gray-scale histogram difference between anterior and posterior cervix can indicate the extent of cervical consistency. We collected data of 95 patients who were appropriate for vaginal delivery with 36th to 37th weeks of gestational age from September 2010 to October 2011 in the Department of Obstetrics and Gynecology, Korea University Ansan Hospital. Patients were excluded who had one of the followings: Cesarean section, labor induction, premature rupture of membrane. Thirty-four patients were finally enrolled. The patients underwent evaluation of the cervix through Bishop score, cervical length, cervical volume, three-dimensional (3D) cervical volumetric gray-scale histogram. The interval days from the cervix evaluation to the delivery day were counted. We compared to 3D cervical volumetric gray-scale histogram, Bishop score, cervical length, cervical volume with interval days from the evaluation of the cervix to the delivery. Gray-scale histogram difference between anterior and posterior cervix was significantly correlated to days to delivery. Its correlation coefficient (R) was 0.500 (P = 0.003). The cervical length was significantly related to the days to delivery. The correlation coefficient (R) and P-value between them were 0.421 and 0.013. However, anterior lip histogram, posterior lip histogram, total cervical volume, Bishop score were not associated with days to delivery (P >0.05). By using gray-scale histogram difference between anterior and posterior cervix and cervical length correlated with the days to delivery. These methods can be utilized to better help predict a cervical consistency.

  19. Clinical and Molecular Characteristics in 100 Chinese Pediatric Patients with m.3243A>G Mutation in Mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Chang-Yu Xia

    2016-01-01

    Conclusions: Our study showed that half of Chinese pediatric patients with m.3243A>G mutation presented seizures, short stature, abnormal MRI/CT changes, elevated plasma lactate, vomiting, and headache. Pediatric patients with these recurrent symptoms should be considered for screening m.3243A>G mutation. Clinical manifestations and laboratory abnormalities should be carefully monitored in patients with this point mutation.

  20. Human papilloma virus DNA and p53 mutation analysis on bladder washes in relation to clinical outcome of bladder cancer.

    NARCIS (Netherlands)

    Moonen, P.M.J.; Bakkers, J.M.J.E.; Kiemeney, L.A.L.M.; Schalken, J.A.; Melchers, W.J.G.; Witjes, J.A.

    2007-01-01

    OBJECTIVES: High-risk human papilloma virus (HPV) types stimulate degradation and deactivation of protein associated with the p53 tumour suppressor gene via the ubiquitin-dependent pathway. For a long time, changes of the p53 tumour suppressor gene have been correlated with poor clinical outcome in

  1. Effect of specific or random c-DNA priming on sensitivity of tyrosinase nested RT-PCR : Potential clinical relevance

    NARCIS (Netherlands)

    Calogero, A; Hospers, GAP; Timmer-Bosscha, H; Mulder, NH; Schraffordt Koops, H.

    2000-01-01

    The reverse transcriptase polymerase chain reaction (RT-PCR) can be of clinical relevance in identifying malignant melanoma cells in blood or tissues of patients at risk for disseminated melanoma. The diagnostic value of this marker however, is still controversial. The objective of this study was to

  2. Illustrative cases for monitoring by quantitative analysis of BRAF/NRAS ctDNA mutations in liquid biopsies of metastatic melanoma patients who gained clinical benefits from anti-PD1 antibody therapy.

    Science.gov (United States)

    Seremet, Teofila; Planken, Simon; Schreuer, Max; Jansen, Yanina; Delaunoy, Mélanie; El Housni, Hakim; Lienard, Danielle; Del Marmol, Véronique; Heimann, Pierre; Neyns, Bart

    2018-02-01

    Anti-programmed death 1 (PD-1) monoclonal antibodies improve the survival of metastatic melanoma patients. Predictive or monitoring biomarkers for response to this therapy could improve the clinical management of these patients. To date, no established biomarkers are available for monitoring the response to immunotherapy. Tumor- specific mutations in circulating tumor DNA (ctDNA) such as BRAF and NRAS mutations for melanoma patients have been proposed for monitoring of immunotherapy response. We present seven illustrative cases for the use of ctDNA BRAF and NRAS mutations' monitoring in plasma. The cases described exemplify four distinct clinical benefit patterns: rapid and durable complete response (CR), early progression, followed by CR, CR followed by early progression after interrupting treatment and long-term disease stabilization. These representative cases suggest that comprehensive BRAF/NRAS ctDNA monitoring during anti-PD1 therapy is informative and can be of added value for the monitoring of melanoma patients gaining clinical benefit on anti-PD1 treatment. An important advantage of our approach is that using the cartridge system on the Idylla platform for mutation analysis, the results become available the same day 2 h after plasma collection. Therefore, in the future, the ctDNA level can be an element in the clinical management of the patients.

  3. Use of a repetitive DNA probe to type clinical and environmental isolates of Aspergillus flavus from a cluster of cutaneous infections in a neonatal intensive care unit.

    Science.gov (United States)

    James, M J; Lasker, B A; McNeil, M M; Shelton, M; Warnock, D W; Reiss, E

    2000-10-01

    Aspergillus flavus is second to A. fumigatus as a cause of invasive aspergillosis, but no standard method exists for molecular typing of strains from human sources. A repetitive DNA sequence cloned from A. flavus and subcloned into a pUC19 vector, pAF28, was used to type 18 isolates from diverse clinical, environmental, and geographic sources. The restriction fragment length polymorphisms generated with EcoRI- or PstI-digested genomic DNA and probed with digoxigenin-labeled pAF28 revealed complete concordance between patterns. Eighteen distinct fingerprints were observed. The probe was used to investigate two cases of cutaneous A. flavus infection in low-birth-weight infants in a neonatal intensive care unit (NICU). Both infants were transported by the same ambulance and crew to the NICU on the same day. A. flavus strains of the same genotype were isolated from both infants, from a roll of tape used to fasten their umbilical catheters, from a canvas bag used to store the tape in the ambulance, and from the tape tray in the ambulance isolette. These cases highlight the need to consider exposures in critically ill neonates that might occur during their transport to the NICU and for stringent infection control practices. The hybridization profiles of strains from a second cluster of invasive A. flavus infections in two pediatric hematology-oncology patients revealed a genotype common to strains from a definite case patient and a health care worker. A probable case patient was infected with a strain with a genotype different from that of the strain from the definite case patient but highly related to that of an environmental isolate. The high degree of discrimination and reproducibility obtained with the pAF28 probe underscores its utility for typing clinical and environmental isolates of A. flavus.

  4. Detection of Bartonella henselae DNA in clinical samples including peripheral blood of immune competent and immune compromised patients by three nested amplifications

    Directory of Open Access Journals (Sweden)

    Karina Hatamoto Kawasato

    2013-02-01

    Full Text Available Bacteria of the genus Bartonella are emerging pathogens detected in lymph node biopsies and aspirates probably caused by increased concentration of bacteria. Twenty-three samples of 18 patients with clinical, laboratory and/or epidemiological data suggesting bartonellosis were subjected to three nested amplifications targeting a fragment of the 60-kDa heat shock protein (HSP, the internal transcribed spacer 16S-23S rRNA (ITS and the cell division (FtsZ of Bartonella henselae, in order to improve detection in clinical samples. In the first amplification 01, 04 and 05 samples, were positive by HSP (4.3%, FtsZ (17.4% and ITS (21.7%, respectively. After the second round six positive samples were identified by nested-HSP (26%, eight by nested-ITS (34.8% and 18 by nested-FtsZ (78.2%, corresponding to 10 peripheral blood samples, five lymph node biopsies, two skin biopsies and one lymph node aspirate. The nested-FtsZ was more sensitive than nested-HSP and nested-ITS (p < 0.0001, enabling the detection of Bartonella henselae DNA in 15 of 18 patients (83.3%. In this study, three nested-PCR that should be specific for Bartonella henselae amplification were developed, but only the nested-FtsZ did not amplify DNA from Bartonella quintana. We conclude that nested amplifications increased detection of B. henselae DNA, and that the nested-FtsZ was the most sensitive and the only specific to B. henselae in different biological samples. As all samples detected by nested-HSP and nested-ITS, were also by nested-FtsZ, we infer that in our series infections were caused by Bartonella henselae. The high number of positive blood samples draws attention to the use of this biological material in the investigation of bartonellosis, regardless of the immune status of patients. This fact is important in the case of critically ill patients and young children to avoid more invasive procedures such as lymph nodes biopsies and aspirates.

  5. Online Data Monitoring Framework Based on Histogram Packaging in Network Distributed Data Acquisition Systems

    International Nuclear Information System (INIS)

    Konno, T; Ishitsuka, M; Kuze, M; Cabarera, A; Sakamoto, Y

    2011-01-01

    O nline monitor frameworkis a new general software framework for online data monitoring, which provides a way to collect information from online systems, including data acquisition, and displays them to shifters far from experimental sites. 'Monitor Server', a core system in this framework gathers the monitoring information from the online subsystems and the information is handled as collections of histograms named H istogram Package . Monitor Server broadcasts the histogram packages to 'Monitor Viewers', graphical user interfaces in the framework. We developed two types of the viewers with different technologies: Java and web browser. We adapted XML based file for the configuration of GUI components on the windows and graphical objects on the canvases. Monitor Viewer creates its GUIs automatically with the configuration files.This monitoring framework has been developed for the Double Chooz reactor neutrino oscillation experiment in France, but can be extended for general application to be used in other experiments. This document reports the structure of the online monitor framework with some examples from the adaption to the Double Chooz experiment.

  6. Radial polar histogram: obstacle avoidance and path planning for robotic cognition and motion control

    Science.gov (United States)

    Wang, Po-Jen; Keyawa, Nicholas R.; Euler, Craig

    2012-01-01

    In order to achieve highly accurate motion control and path planning for a mobile robot, an obstacle avoidance algorithm that provided a desired instantaneous turning radius and velocity was generated. This type of obstacle avoidance algorithm, which has been implemented in California State University Northridge's Intelligent Ground Vehicle (IGV), is known as Radial Polar Histogram (RPH). The RPH algorithm utilizes raw data in the form of a polar histogram that is read from a Laser Range Finder (LRF) and a camera. A desired open block is determined from the raw data utilizing a navigational heading and an elliptical approximation. The left and right most radii are determined from the calculated edges of the open block and provide the range of possible radial paths the IGV can travel through. In addition, the calculated obstacle edge positions allow the IGV to recognize complex obstacle arrangements and to slow down accordingly. A radial path optimization function calculates the best radial path between the left and right most radii and is sent to motion control for speed determination. Overall, the RPH algorithm allows the IGV to autonomously travel at average speeds of 3mph while avoiding all obstacles, with a processing time of approximately 10ms.

  7. AN ILLUMINATION INVARIANT FACE RECOGNITION BY ENHANCED CONTRAST LIMITED ADAPTIVE HISTOGRAM EQUALIZATION

    Directory of Open Access Journals (Sweden)

    A. Thamizharasi

    2016-05-01

    Full Text Available Face recognition system is gaining more importance in social networks and surveillance. The face recognition task is complex due to the variations in illumination, expression, occlusion, aging and pose. The illumination variations in image are due to changes in lighting conditions, poor illumination, low contrast or increased brightness. The variations in illumination adversely affect the quality of image and recognition accuracy. The illumination variations in face image have to be pre-processed prior to face recognition. The Contrast Limited Adaptive Histogram Equalization (CLAHE is an image enhancement technique popular in enhancing medical images. The proposed work is to create illumination invariant face recognition system by enhancing Contrast Limited Adaptive Histogram Equalization technique. This method is termed as “Enhanced CLAHE”. The efficiency of Enhanced CLAHE is tested using Fuzzy K Nearest Neighbour classifier and fisher face subspace projection method. The face recognition accuracy percentage rate, Equal Error Rate and False Acceptance Rate at 1% are calculated. The performance of CLAHE and Enhanced CLAHE methods is compared. The efficiency of the Enhanced CLAHE method is tested with three public face databases AR, Yale and ORL. The Enhanced CLAHE has very high recognition accuracy percentage rate when compared to CLAHE.

  8. Predicting the nodal status in gastric cancers: The role of apparent diffusion coefficient histogram characteristic analysis.

    Science.gov (United States)

    Liu, Song; Zhang, Yujuan; Xia, Jie; Chen, Ling; Guan, Wenxian; Guan, Yue; Ge, Yun; He, Jian; Zhou, Zhengyang

    2017-10-01

    To explore the application of histogram analysis in preoperative T and N staging of gastric cancers, with a focus on characteristic parameters of apparent diffusion coefficient (ADC) maps. Eighty-seven patients with gastric cancers underwent diffusion weighted magnetic resonance imaging (b=0, 1000s/mm 2 ), which generated ADC maps. Whole-volume histogram analysis was performed on ADC maps and 7 characteristic parameters were obtained. All those patients underwent surgery and postoperative pathologic T and N stages were determined. Four parameters, including skew, kurtosis, s-sD av and sample number, showed significant differences among gastric cancers at different T and N stages. Most parameters correlated with T and N stages significantly and worked in differentiating gastric cancers at different T or N stages. Especially skew yielded a sensitivity of 0.758, a specificity of 0.810, and an area under the curve (AUC) of 0.802 for differentiating gastric cancers with and without lymph node metastasis (Phistogram analysis could help assessing preoperative T and N stages of gastric cancers. Copyright © 2017. Published by Elsevier Inc.

  9. Conductance of single-atom platinum contacts: Voltage dependence of the conductance histogram

    DEFF Research Database (Denmark)

    Nielsen, S.K.; Noat, Y.; Brandbyge, Mads

    2003-01-01

    The conductance of a single-atom contact is sensitive to the coupling of this contact atom to the atoms in the leads. Notably for the transition metals this gives rise to a considerable spread in the observed conductance values. The mean conductance value and spread can be obtained from the first...... peak in conductance histograms recorded from a large set of contact-breaking cycles. In contrast to the monovalent metals, this mean value for Pt depends strongly on the applied voltage bias and other experimental conditions and values ranging from about 1 G(0) to 2.5 G(0) (G(0)=2e(2)/h) have been...... reported. We find that at low bias the first peak in the conductance histogram is centered around 1.5 G(0). However, as the bias increases past 300 mV the peak shifts to 1.8 G(0). Here we show that this bias dependence is due to a geometric effect where monatomic chains are replaced by single-atom contacts...

  10. Tools for the analysis of dose optimization: I. Effect-volume histogram

    International Nuclear Information System (INIS)

    Alber, M.; Nuesslin, F.

    2002-01-01

    With the advent of dose optimization algorithms, predominantly for intensity-modulated radiotherapy (IMRT), computer software has progressed beyond the point of being merely a tool at the hands of an expert and has become an active, independent mediator of the dosimetric conflicts between treatment goals and risks. To understand and control the internal decision finding as well as to provide means to influence it, a tool for the analysis of the dose distribution is presented which reveals the decision-making process performed by the algorithm. The internal trade-offs between partial volumes receiving high or low doses are driven by functions which attribute a weight to each volume element. The statistics of the distribution of these weights is cast into an effect-volume histogram (EVH) in analogy to dose-volume histograms. The analysis of the EVH reveals which traits of the optimum dose distribution result from the defined objectives, and which are a random consequence of under- or misspecification of treatment goals. The EVH can further assist in the process of finding suitable objectives and balancing conflicting objectives. If biologically inspired objectives are used, the EVH shows the distribution of local dose effect relative to the prescribed level. (author)

  11. Two non-parametric methods for derivation of constraints from radiotherapy dose–histogram data

    International Nuclear Information System (INIS)

    Ebert, M A; Kennedy, A; Joseph, D J; Gulliford, S L; Buettner, F; Foo, K; Haworth, A; Denham, J W

    2014-01-01

    Dose constraints based on histograms provide a convenient and widely-used method for informing and guiding radiotherapy treatment planning. Methods of derivation of such constraints are often poorly described. Two non-parametric methods for derivation of constraints are described and investigated in the context of determination of dose-specific cut-points—values of the free parameter (e.g., percentage volume of the irradiated organ) which best reflect resulting changes in complication incidence. A method based on receiver operating characteristic (ROC) analysis and one based on a maximally-selected standardized rank sum are described and compared using rectal toxicity data from a prostate radiotherapy trial. Multiple test corrections are applied using a free step-down resampling algorithm, which accounts for the large number of tests undertaken to search for optimal cut-points and the inherent correlation between dose–histogram points. Both methods provide consistent significant cut-point values, with the rank sum method displaying some sensitivity to the underlying data. The ROC method is simple to implement and can utilize a complication atlas, though an advantage of the rank sum method is the ability to incorporate all complication grades without the need for grade dichotomization. (note)

  12. Histogram analysis of greyscale sonograms to differentiate between the subtypes of follicular variant of papillary thyroid cancer.

    Science.gov (United States)

    Kwon, M-R; Shin, J H; Hahn, S Y; Oh, Y L; Kwak, J Y; Lee, E; Lim, Y

    2018-06-01

    To evaluate the diagnostic value of histogram analysis using ultrasound (US) to differentiate between the subtypes of follicular variant of papillary thyroid carcinoma (FVPTC). The present study included 151 patients with surgically confirmed FVPTC diagnosed between January 2014 and May 2016. Their preoperative US features were reviewed retrospectively. Histogram parameters (mean, maximum, minimum, range, root mean square, skewness, kurtosis, energy, entropy, and correlation) were obtained for each nodule. The 152 nodules in 151 patients comprised 48 non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTPs; 31.6%), 60 invasive encapsulated FVPTCs (EFVPTCs; 39.5%), and 44 infiltrative FVPTCs (28.9%). The US features differed significantly between the subtypes of FVPTC. Discrimination was achieved between NIFTPs and infiltrative FVPTC, and between invasive EFVPTC and infiltrative FVPTC using histogram parameters; however, the parameters were not significantly different between NIFTP and invasive EFVPTC. It is feasible to use greyscale histogram analysis to differentiate between NIFTP and infiltrative FVPTC, but not between NIFTP and invasive EFVPTC. Histograms can be used as a supplementary tool to differentiate the subtypes of FVPTC. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  13. Histogram analysis of apparent diffusion coefficient for monitoring early response in patients with advanced cervical cancers undergoing concurrent chemo-radiotherapy.

    Science.gov (United States)

    Meng, Jie; Zhu, Lijing; Zhu, Li; Ge, Yun; He, Jian; Zhou, Zhengyang; Yang, Xiaofeng

    2017-11-01

    Background Apparent diffusion coefficient (ADC) histogram analysis has been widely used in determining tumor prognosis. Purpose To investigate the dynamic changes of ADC histogram parameters during concurrent chemo-radiotherapy (CCRT) in patients with advanced cervical cancers. Material and Methods This prospective study enrolled 32 patients with advanced cervical cancers undergoing CCRT who received diffusion-weighted (DW) magnetic resonance imaging (MRI) before CCRT, at the end of the second and fourth week during CCRT and one month after CCRT completion. The ADC histogram for the entire tumor volume was generated, and a series of histogram parameters was obtained. Dynamic changes of those parameters in cervical cancers were investigated as early biomarkers for treatment response. Results All histogram parameters except AUC low showed significant changes during CCRT (all P histogram parameters of cervical cancers changed significantly at the early stage of CCRT, indicating their potential in monitoring early tumor response to therapy.

  14. The influence of ginger (Zingiber officinale on human sperm quality and DNA fragmentation: A double-blind randomized clinical trial

    Directory of Open Access Journals (Sweden)

    Jalil Hosseini

    2016-08-01

    Full Text Available Background: Although the effectiveness of ginger as an antioxidant agent has been exploited, little human research has been conducted on its activity on male reproductive functions. Objective: This study was designed to investigate the effects of ginger (Zingiber officinale on sperm DNA fragmentation (SDF in infertile men. Materials and Methods: This randomized double-blind, placebo-controlled trial with a 1:1 allocation was performed on 100 infertility treatment candidates who were admitted to Royan Institute for Reproductive Biomedicine, Tehran, Iran. Patients were randomly assigned to receive one of two treatments: ginger and placebo. Patients were given a 3-month oral treatment (members received capsules containing 250 mg of ginger powder twice a day in ginger and a placebo in other group. Before and after treatment, standardized semen samples were obtained to determine sperm concentration, motility, and SDF according to World Health Organization. Results: There was no significant difference between two groups regarding SDF at baseline (53.48. 95%CI: 37.95-69.02 in cases and (56.75, 95%CI: 40.01-73.5 in controls. The average positive percentage of SDF in patients receiving ginger (17.77, 95%CI: 6.16-29.39 was lower compared with placebo (40.54, 95%CI: 23.94-57.13 after three month of treatment (p=0.02. In multivariate analysis, SDF was significantly lower in patients receiving ginger compared with placebo (mean difference: 3.21, 95%CI: 0.78-5.63, p=0.009. There were no significant differences between two groups regarding to semen parameters. Conclusion: The present study has demonstrated that ginger in a controlled study of efficacy was effective in decreasing SDF in infertile men.

  15. Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers.

    Directory of Open Access Journals (Sweden)

    Xinzhong Li

    Full Text Available Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations.We evaluated two next-generation sequencing (NGS platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm, and sequenced on the MiSeq (Illumina and Ion Torrent PGM (Life Technologies. Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%. At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs, with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS.MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias

  16. Correlation between surrogates of bladder dosimetry and dose–volume histograms of the bladder wall defined on MRI in prostate cancer radiotherapy

    International Nuclear Information System (INIS)

    Carillo, Viviana; Cozzarini, Cesare; Chietera, Andreina; Perna, Lucia; Gianolini, Stefano; Maggio, Angelo; Botti, Andrea; Rancati, Tiziana; Valdagni, Riccardo; Fiorino, Claudio

    2012-01-01

    The correlation between bladder dose–wall-histogram (DWH) and dose–volume-histogram (DVH), dose–surface-histogram (DSH), and DVH-5/10 was investigated in a group of 28 patients; bladder walls were drawn on T2-MRI. DVH showed the poorest correlation with DWH; DSH or DVH-5/10 should be preferred in planning; absolute DVH may be used for radical patients, although less robust.

  17. Spot detection and image segmentation in DNA microarray data.

    Science.gov (United States)

    Qin, Li; Rueda, Luis; Ali, Adnan; Ngom, Alioune

    2005-01-01

    Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

  18. Condition monitoring of face milling tool using K-star algorithm and histogram features of vibration signal

    Directory of Open Access Journals (Sweden)

    C.K. Madhusudana

    2016-09-01

    Full Text Available This paper deals with the fault diagnosis of the face milling tool based on machine learning approach using histogram features and K-star algorithm technique. Vibration signals of the milling tool under healthy and different fault conditions are acquired during machining of steel alloy 42CrMo4. Histogram features are extracted from the acquired signals. The decision tree is used to select the salient features out of all the extracted features and these selected features are used as an input to the classifier. K-star algorithm is used as a classifier and the output of the model is utilised to study and classify the different conditions of the face milling tool. Based on the experimental results, K-star algorithm is provided a better classification accuracy in the range from 94% to 96% with histogram features and is acceptable for fault diagnosis.

  19. Expression robust 3D face recognition via mesh-based histograms of multiple order surface differential quantities

    KAUST Repository

    Li, Huibin

    2011-09-01

    This paper presents a mesh-based approach for 3D face recognition using a novel local shape descriptor and a SIFT-like matching process. Both maximum and minimum curvatures estimated in the 3D Gaussian scale space are employed to detect salient points. To comprehensively characterize 3D facial surfaces and their variations, we calculate weighted statistical distributions of multiple order surface differential quantities, including histogram of mesh gradient (HoG), histogram of shape index (HoS) and histogram of gradient of shape index (HoGS) within a local neighborhood of each salient point. The subsequent matching step then robustly associates corresponding points of two facial surfaces, leading to much more matched points between different scans of a same person than the ones of different persons. Experimental results on the Bosphorus dataset highlight the effectiveness of the proposed method and its robustness to facial expression variations. © 2011 IEEE.

  20. Histogram analysis of diffusion kurtosis imaging derived maps may distinguish between low and high grade gliomas before surgery.

    Science.gov (United States)

    Qi, Xi-Xun; Shi, Da-Fa; Ren, Si-Xie; Zhang, Su-Ya; Li, Long; Li, Qing-Chang; Guan, Li-Ming

    2018-04-01

    To investigate the value of histogram analysis of diffusion kurtosis imaging (DKI) maps in the evaluation of glioma grading. A total of 39 glioma patients who underwent preoperative magnetic resonance imaging (MRI) were classified into low-grade (13 cases) and high-grade (26 cases) glioma groups. Parametric DKI maps were derived, and histogram metrics between low- and high-grade gliomas were analysed. The optimum diagnostic thresholds of the parameters, area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were achieved using a receiver operating characteristic (ROC). Significant differences were observed not only in 12 metrics of histogram DKI parameters (PHistogram analysis of DKI may be more effective in glioma grading.

  1. Clinical evaluation and mitochondrial DNA sequence analysis in two Chinese families with aminoglycoside-induced and non-syndromic hearing loss

    International Nuclear Information System (INIS)

    Zhao Lidong; Wang Qiuju; Qian Yaping; Li Ronghua; Cao Juayng; Hart, Laura Christine; Zhai Suoqiang; Han Dongyi; Young Wieyen; Guan Minxin

    2005-01-01

    We report here the clinical, genetic, and molecular characterization of two Chinese pedigrees with aminoglycoside-induced and non-syndromic hearing impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects. Penetrances of hearing loss in BJ105 and BJ106 pedigrees are 67% and 33%, respectively. In particular, three of 10 affected matrilineal relatives of BJ105 pedigree had aminoglycoside-induced hearing loss, while seven affected matrilineal relatives in BJ105 pedigree and six affected matrilineal relatives in BJ106 pedigree did not have a history of exposure to aminoglycosides. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the identical homoplasmic A1555G mutation and distinct sets of mtDNA variants belonging to haplogroups F3 and M7b. These variants showed no evolutionary conservation, implying that mitochondrial haplotype may not play a significant role in the phenotypic expression of the A1555G mutation in these Chinese pedigrees. However, aminoglycosides and nuclear backgrounds appear to be major modifier factors for the phenotypic manifestation of the A1555G mutation in these Chinese families

  2. Assessment of histological differentiation in gastric cancers using whole-volume histogram analysis of apparent diffusion coefficient maps.

    Science.gov (United States)

    Zhang, Yujuan; Chen, Jun; Liu, Song; Shi, Hua; Guan, Wenxian; Ji, Changfeng; Guo, Tingting; Zheng, Huanhuan; Guan, Yue; Ge, Yun; He, Jian; Zhou, Zhengyang; Yang, Xiaofeng; Liu, Tian

    2017-02-01

    To investigate the efficacy of histogram analysis of the entire tumor volume in apparent diffusion coefficient (ADC) maps for differentiating between histological grades in gastric cancer. Seventy-eight patients with gastric cancer were enrolled in a retrospective 3.0T magnetic resonance imaging (MRI) study. ADC maps were obtained at two different b values (0 and 1000 sec/mm 2 ) for each patient. Tumors were delineated on each slice of the ADC maps, and a histogram for the entire tumor volume was subsequently generated. A series of histogram parameters (eg, skew and kurtosis) were calculated and correlated with the histological grade of the surgical specimen. The diagnostic performance of each parameter for distinguishing poorly from moderately well-differentiated gastric cancers was assessed by using the area under the receiver operating characteristic curve (AUC). There were significant differences in the 5 th , 10 th , 25 th , and 50 th percentiles, skew, and kurtosis between poorly and well-differentiated gastric cancers (P histogram parameters, including the 10 th percentile, skew, kurtosis, and max frequency; the correlation coefficients were 0.273, -0.361, -0.339, and -0.370, respectively. Among all the histogram parameters, the max frequency had the largest AUC value, which was 0.675. Histogram analysis of the ADC maps on the basis of the entire tumor volume can be useful in differentiating between histological grades for gastric cancer. 4 J. Magn. Reson. Imaging 2017;45:440-449. © 2016 International Society for Magnetic Resonance in Medicine.

  3. Histogram Analysis of CT Perfusion of Hepatocellular Carcinoma for Predicting Response to Transarterial Radioembolization: Value of Tumor Heterogeneity Assessment.

    Science.gov (United States)

    Reiner, Caecilia S; Gordic, Sonja; Puippe, Gilbert; Morsbach, Fabian; Wurnig, Moritz; Schaefer, Niklaus; Veit-Haibach, Patrick; Pfammatter, Thomas; Alkadhi, Hatem

    2016-03-01

    To evaluate in patients with hepatocellular carcinoma (HCC), whether assessment of tumor heterogeneity by histogram analysis of computed tomography (CT) perfusion helps predicting response to transarterial radioembolization (TARE). Sixteen patients (15 male; mean age 65 years; age range 47-80 years) with HCC underwent CT liver perfusion for treatment planning prior to TARE with Yttrium-90 microspheres. Arterial perfusion (AP) derived from CT perfusion was measured in the entire tumor volume, and heterogeneity was analyzed voxel-wise by histogram analysis. Response to TARE was evaluated on follow-up imaging (median follow-up, 129 days) based on modified Response Evaluation Criteria in Solid Tumors (mRECIST). Results of histogram analysis and mean AP values of the tumor were compared between responders and non-responders. Receiver operating characteristics were calculated to determine the parameters' ability to discriminate responders from non-responders. According to mRECIST, 8 patients (50%) were responders and 8 (50%) non-responders. Comparing responders and non-responders, the 50th and 75th percentile of AP derived from histogram analysis was significantly different [AP 43.8/54.3 vs. 27.6/34.3 mL min(-1) 100 mL(-1)); p 0.05) was not. Further heterogeneity parameters from histogram analysis (skewness, coefficient of variation, and 25th percentile) did not differ between responders and non-responders (p > 0.05). If the cut-off for the 75th percentile was set to an AP of 37.5 mL min(-1) 100 mL(-1), therapy response could be predicted with a sensitivity of 88% (7/8) and specificity of 75% (6/8). Voxel-wise histogram analysis of pretreatment CT perfusion indicating tumor heterogeneity of HCC improves the pretreatment prediction of response to TARE.

  4. Support vector machine for breast cancer classification using diffusion-weighted MRI histogram features: Preliminary study.

    Science.gov (United States)

    Vidić, Igor; Egnell, Liv; Jerome, Neil P; Teruel, Jose R; Sjøbakk, Torill E; Østlie, Agnes; Fjøsne, Hans E; Bathen, Tone F; Goa, Pål Erik

    2018-05-01

    Diffusion-weighted MRI (DWI) is currently one of the fastest developing MRI-based techniques in oncology. Histogram properties from model fitting of DWI are useful features for differentiation of lesions, and classification can potentially be improved by machine learning. To evaluate classification of malignant and benign tumors and breast cancer subtypes using support vector machine (SVM). Prospective. Fifty-one patients with benign (n = 23) and malignant (n = 28) breast tumors (26 ER+, whereof six were HER2+). Patients were imaged with DW-MRI (3T) using twice refocused spin-echo echo-planar imaging with echo time / repetition time (TR/TE) = 9000/86 msec, 90 × 90 matrix size, 2 × 2 mm in-plane resolution, 2.5 mm slice thickness, and 13 b-values. Apparent diffusion coefficient (ADC), relative enhanced diffusivity (RED), and the intravoxel incoherent motion (IVIM) parameters diffusivity (D), pseudo-diffusivity (D*), and perfusion fraction (f) were calculated. The histogram properties (median, mean, standard deviation, skewness, kurtosis) were used as features in SVM (10-fold cross-validation) for differentiation of lesions and subtyping. Accuracies of the SVM classifications were calculated to find the combination of features with highest prediction accuracy. Mann-Whitney tests were performed for univariate comparisons. For benign versus malignant tumors, univariate analysis found 11 histogram properties to be significant differentiators. Using SVM, the highest accuracy (0.96) was achieved from a single feature (mean of RED), or from three feature combinations of IVIM or ADC. Combining features from all models gave perfect classification. No single feature predicted HER2 status of ER + tumors (univariate or SVM), although high accuracy (0.90) was achieved with SVM combining several features. Importantly, these features had to include higher-order statistics (kurtosis and skewness), indicating the importance to account for heterogeneity. Our

  5. PROCESS PERFORMANCE EVALUATION USING HISTOGRAM AND TAGUCHI TECHNIQUE IN LOCK MANUFACTURING COMPANY

    Directory of Open Access Journals (Sweden)

    Hagos Berhane

    2013-12-01

    Full Text Available Process capability analysis is a vital part of an overall quality improvement program. It is a technique that has application in many segments of the product cycle, including product and process design, vendor sourcing, production or manufacturing planning, and manufacturing. Frequently, a process capability study involves observing a quality characteristic of the product. Since this information usually pertains to the product rather than the process, this analysis should strictly speaking be called a product analysis study. A true process capability study in this context would involve collecting data that relates to process parameters so that remedial actions can be identified on a timely basis. The present study attempts to analyze performance of drilling, pressing, and reaming operations carried out for the manufacturing of two major lock components viz. handle and lever plate, at Gaurav International, Aligarh (India. The data collected for depth of hole on handle, central hole diameter, and key hole diameter are used to construct histogram. Next, the information available in frequency distribution table, the process mean, process capability from calculations and specification limits provided by the manufacturing concern are used with Taguchi technique. The data obtained from histogram and Taguchi technique combined are used to evaluate the performance of the manufacturing process. Results of this study indicated that the performance of all the processes used to produce depth of hole on handle, key hole diameter, and central hole diameter are potentially incapable as the process capability indices are found to be 0.54, 0.54 and 0.76 respectively. The number of nonconforming parts expressed in terms of parts per million (ppm that have fallen out of the specification limits are found to be 140000, 26666.66, and 146666.66 for depth of hole on handle, central hole diameter, and key hole diameter respectively. As a result, the total loss incurred

  6. Modular routing interface for simoultaneous list mode and histogramming mode storage of coincident data

    International Nuclear Information System (INIS)

    D'Achard van Eschut, J.F.M.; Nationaal Inst. voor Kernfysica en Hoge-Energiefysica

    1985-01-01

    A routing interface has been developed and built for successive storage of the digital output of four 13-bit ADCs, within 6 μs, into selected parts of two 16K CAMAC histogramming modules and, if an event trigger is applied, simultaneously into four 64-words deep (16-bit) first-in first-out (FIFO) CAMAC modules. In this way it is possible to accumulate on-line single spectra and, at the same time, write coincident data in list mode to magnetic tape under control of a computer. Additional routing interfaces can be used in parallel so that extensive data-collecting systems can be set up to store multi-parameter events. (orig.)

  7. Wavelength-Adaptive Dehazing Using Histogram Merging-Based Classification for UAV Images

    Directory of Open Access Journals (Sweden)

    Inhye Yoon

    2015-03-01

    Full Text Available Since incoming light to an unmanned aerial vehicle (UAV platform can be scattered by haze and dust in the atmosphere, the acquired image loses the original color and brightness of the subject. Enhancement of hazy images is an important task in improving the visibility of various UAV images. This paper presents a spatially-adaptive dehazing algorithm that merges color histograms with consideration of the wavelength-dependent atmospheric turbidity. Based on the wavelength-adaptive hazy image acquisition model, the proposed dehazing algorithm consists of three steps: (i image segmentation based on geometric classes; (ii generation of the context-adaptive transmission map; and (iii intensity transformation for enhancing a hazy UAV image. The major contribution of the research is a novel hazy UAV image degradation model by considering the wavelength of light sources. In addition, the proposed transmission map provides a theoretical basis to differentiate visually important regions from others based on the turbidity and merged classification results.

  8. REAL-TIME FACE RECOGNITION BASED ON OPTICAL FLOW AND HISTOGRAM EQUALIZATION

    Directory of Open Access Journals (Sweden)

    D. Sathish Kumar

    2013-05-01

    Full Text Available Face recognition is one of the intensive areas of research in computer vision and pattern recognition but many of which are focused on recognition of faces under varying facial expressions and pose variation. A constrained optical flow algorithm discussed in this paper, recognizes facial images involving various expressions based on motion vector computation. In this paper, an optical flow computation algorithm which computes the frames of varying facial gestures, and integrating with synthesized image in a probabilistic environment has been proposed. Also Histogram Equalization technique has been used to overcome the effect of illuminations while capturing the input data using camera devices. It also enhances the contrast of the image for better processing. The experimental results confirm that the proposed face recognition system is more robust and recognizes the facial images under varying expressions and pose variations more accurately.

  9. Underwater Image Enhancement by Adaptive Gray World and Differential Gray-Levels Histogram Equalization

    Directory of Open Access Journals (Sweden)

    WONG, S.-L.

    2018-05-01

    Full Text Available Most underwater images tend to be dominated by a single color cast. This paper presents a solution to remove the color cast and improve the contrast in underwater images. However, after the removal of the color cast using Gray World (GW method, the resultant image is not visually pleasing. Hence, we propose an integrated approach using Adaptive GW (AGW and Differential Gray-Levels Histogram Equalization (DHE that operate in parallel. The AGW is applied to remove the color cast while DHE is used to improve the contrast of the underwater image. The outputs of both chromaticity components of AGW and intensity components of DHE are combined to form the enhanced image. The results of the proposed method are compared with three existing methods using qualitative and quantitative measures. The proposed method increased the visibility of underwater images and in most cases produces better quantitative scores when compared to the three existing methods.

  10. Histogram analysis for age change of human lung with computed tomography

    International Nuclear Information System (INIS)

    Shirabe, Ichiju

    1990-01-01

    In order to evaluate physiological changes of normal lung with aging by computed tomography (CT), the peak position (PP) and full width half maximum (FWHM) of CT-histogram were studied in 77 normal human lung. Above 30 years old, PP tended to be seen in the lower attenuation value with advancing ages, with the result that the follow equation was obtained. CT attenuation value of PP=-0.87 x age -815. The peak position shifted to the range of higher CT attenuation in 30's. FWHM did not change with advancing ages. There were no differences of peak value and FWHM among the upper, middle and lower lung field. In this study, physiological changes of lung were evaluated quantitatively. Furthermore, this study was considered to be useful for diagnosis and treatment in lung diseases. (author)

  11. Wavelength-adaptive dehazing using histogram merging-based classification for UAV images.

    Science.gov (United States)

    Yoon, Inhye; Jeong, Seokhwa; Jeong, Jaeheon; Seo, Doochun; Paik, Joonki

    2015-03-19

    Since incoming light to an unmanned aerial vehicle (UAV) platform can be scattered by haze and dust in the atmosphere, the acquired image loses the original color and brightness of the subject. Enhancement of hazy images is an important task in improving the visibility of various UAV images. This paper presents a spatially-adaptive dehazing algorithm that merges color histograms with consideration of the wavelength-dependent atmospheric turbidity. Based on the wavelength-adaptive hazy image acquisition model, the proposed dehazing algorithm consists of three steps: (i) image segmentation based on geometric classes; (ii) generation of the context-adaptive transmission map; and (iii) intensity transformation for enhancing a hazy UAV image. The major contribution of the research is a novel hazy UAV image degradation model by considering the wavelength of light sources. In addition, the proposed transmission map provides a theoretical basis to differentiate visually important regions from others based on the turbidity and merged classification results.

  12. A Novel Histogram Region Merging Based Multithreshold Segmentation Algorithm for MR Brain Images

    Directory of Open Access Journals (Sweden)

    Siyan Liu

    2017-01-01

    Full Text Available Multithreshold segmentation algorithm is time-consuming, and the time complexity will increase exponentially with the increase of thresholds. In order to reduce the time complexity, a novel multithreshold segmentation algorithm is proposed in this paper. First, all gray levels are used as thresholds, so the histogram of the original image is divided into 256 small regions, and each region corresponds to one gray level. Then, two adjacent regions are merged in each iteration by a new designed scheme, and a threshold is removed each time. To improve the accuracy of the merger operation, variance and probability are used as energy. No matter how many the thresholds are, the time complexity of the algorithm is stable at O(L. Finally, the experiment is conducted on many MR brain images to verify the performance of the proposed algorithm. Experiment results show that our method can reduce the running time effectively and obtain segmentation results with high accuracy.

  13. Detection of License Plate using Sliding Window, Histogram of Oriented Gradient, and Support Vector Machines Method

    Science.gov (United States)

    Astawa, INGA; Gusti Ngurah Bagus Caturbawa, I.; Made Sajayasa, I.; Dwi Suta Atmaja, I. Made Ari

    2018-01-01

    The license plate recognition usually used as part of system such as parking system. License plate detection considered as the most important step in the license plate recognition system. We propose methods that can be used to detect the vehicle plate on mobile phone. In this paper, we used Sliding Window, Histogram of Oriented Gradient (HOG), and Support Vector Machines (SVM) method to license plate detection so it will increase the detection level even though the image is not in a good quality. The image proceed by Sliding Window method in order to find plate position. Feature extraction in every window movement had been done by HOG and SVM method. Good result had shown in this research, which is 96% of accuracy.

  14. Using Relational Histogram Features and Action Labelled Data to Learn Preconditions for Means-End Actions

    DEFF Research Database (Denmark)

    Fichtl, Severin; Kraft, Dirk; Krüger, Norbert

    2015-01-01

    The outcome of many complex manipulation ac- tions is contingent on the spatial relationships among pairs of objects, e.g. if an object is “inside” or “on top” of another. Recognising these spatial relationships requires a vision system which can extract appropriate features from the vision input...... that capture and represent the spatial relationships in an easily accessible way. We are interested in learning to predict the success of “means end” actions that manipulate two objects at once, from exploratory actions, and the observed sensorimo- tor contingencies. In this paper, we use relational histogram...... features and illustrate their effect on learning to predict a variety of “means end” actions’ outcomes. The results show that our vision features can make the learning problem significantly easier, leading to increased learning rates and higher maximum performance. This work is in particular important...

  15. Gender Perception From Faces Using Boosted LBPH (Local Binary Patten Histograms

    Directory of Open Access Journals (Sweden)

    U. U. Tariq

    2013-06-01

    Full Text Available Automatic Gender classification from faces has several applications such as surveillance, human computer interaction, targeted advertisement etc. Humans can recognize gender from faces quite accurately but for computer vision it is a difficult task. Many studies have targeted this problem but most of these studies used images of faces taken under constrained conditions. Real-world applications however require to process images from real-world, that have significant variation in lighting and pose, which makes the gender classification task very difficult. We have examined the problem of automatic gender classification from faces on real-world images. Using a face detector faces from images are extracted aligned and represented using Local binary pattern histogram. Discriminative features are selected using Adaboost and the boosted LBP features are used to train a support vector machine that provides a recognition rate of 93.29%.

  16. A histogram-free multicanonical Monte Carlo algorithm for the construction of analytical density of states

    Energy Technology Data Exchange (ETDEWEB)

    Eisenbach, Markus [ORNL; Li, Ying Wai [ORNL

    2017-06-01

    We report a new multicanonical Monte Carlo (MC) algorithm to obtain the density of states (DOS) for physical systems with continuous state variables in statistical mechanics. Our algorithm is able to obtain an analytical form for the DOS expressed in a chosen basis set, instead of a numerical array of finite resolution as in previous variants of this class of MC methods such as the multicanonical (MUCA) sampling and Wang-Landau (WL) sampling. This is enabled by storing the visited states directly in a data set and avoiding the explicit collection of a histogram. This practice also has the advantage of avoiding undesirable artificial errors caused by the discretization and binning of continuous state variables. Our results show that this scheme is capable of obtaining converged results with a much reduced number of Monte Carlo steps, leading to a significant speedup over existing algorithms.

  17. FPGA based high-performance multi-channel analyzer with local histogram memory

    International Nuclear Information System (INIS)

    Kulkarni, C.P.; Vaidya, P.P.; Paulson, M.

    2004-01-01

    Modern nuclear spectroscopy systems demand for a Multi-Channel Analyzer (MCA) with higher resolution, faster speed and other advanced features. The MCA described here is targeted for such demanding applications. The MCA has an in-built local histogram memory and a memory management unit integrated in an FPGA (Field Programmable Gate Array) chip. In addition to the integrated low power digital circuitry, the system utilizes state of the art advanced analog circuits like low power, high speed and high precision comparators, op-amps, ADC and DAC. The operating resolution is selectable from 256 channels to 16384 channels for pulse height analysis. It supports high count rate applications (typically 100 KHz) without significant dead time penalty. It can have an USB bus interface with simple changes. In general, the MCA gives a high performance, compact and low power alternative for portable and battery operated systems as well as for high end laboratory instruments. (author)

  18. A powerful, low-cost histogramming memory for digital radiography with multi-wire proportional counters

    International Nuclear Information System (INIS)

    Bateman, J.E.; Locke, C.E.R.; Ferrari, C.A.

    1986-01-01

    A powerful, low-cost histogramming memory for digital radiograph with multi-wire proportional counter is described. The memory is based on a commercial video display device coupled to an Apple II microcomputer which, at a total cost of around 2500 pounds gives a system with 512 x 512 pixel resolution and a counting range of 4095 counts per pixel. The system can take data at rates of up to 5000 Hz while providing a live-time display. No hardware modifications are necessary, the comprehensive storage and display facilities being implemented in a combined package of BASIC and ASSEMBLER software. An ACCELERATOR coprocessor card is used to enhance the performance of the system. (author)

  19. Adaptive Kalman filtering for histogram-based appearance learning in infrared imagery.

    Science.gov (United States)

    Venkataraman, Vijay; Fan, Guoliang; Havlicek, Joseph P; Fan, Xin; Zhai, Yan; Yeary, Mark B

    2012-11-01

    Targets of interest in video acquired from imaging infrared sensors often exhibit profound appearance variations due to a variety of factors, including complex target maneuvers, ego-motion of the sensor platform, background clutter, etc., making it difficult to maintain a reliable detection process and track lock over extended time periods. Two key issues in overcoming this problem are how to represent the target and how to learn its appearance online. In this paper, we adopt a recent appearance model that estimates the pixel intensity histograms as well as the distribution of local standard deviations in both the foreground and background regions for robust target representation. Appearance learning is then cast as an adaptive Kalman filtering problem where the process and measurement noise variances are both unknown. We formulate this problem using both covariance matching and, for the first time in a visual tracking application, the recent autocovariance least-squares (ALS) method. Although convergence of the ALS algorithm is guaranteed only for the case of globally wide sense stationary process and measurement noises, we demonstrate for the first time that the technique can often be applied with great effectiveness under the much weaker assumption of piecewise stationarity. The performance advantages of the ALS method relative to the classical covariance matching are illustrated by means of simulated stationary and nonstationary systems. Against real data, our results show that the ALS-based algorithm outperforms the covariance matching as well as the traditional histogram similarity-based methods, achieving sub-pixel tracking accuracy against the well-known AMCOM closure sequences and the recent SENSIAC automatic target recognition dataset.

  20. Quantitatively assessed CT imaging measures of pulmonary interstitial pneumonia: Effects of reconstruction algorithms on histogram parameters

    International Nuclear Information System (INIS)

    Koyama, Hisanobu; Ohno, Yoshiharu; Yamazaki, Youichi; Nogami, Munenobu; Kusaka, Akiko; Murase, Kenya; Sugimura, Kazuro

    2010-01-01

    This study aimed the influences of reconstruction algorithm for quantitative assessments in interstitial pneumonia patients. A total of 25 collagen vascular disease patients (nine male patients and 16 female patients; mean age, 57.2 years; age range 32-77 years) underwent thin-section MDCT examinations, and MDCT data were reconstructed with three kinds of reconstruction algorithm (two high-frequencies [A and B] and one standard [C]). In reconstruction algorithm B, the effect of low- and middle-frequency space was suppressed compared with reconstruction algorithm A. As quantitative CT parameters, kurtosis, skewness, and mean lung density (MLD) were acquired from a frequency histogram of the whole lung parenchyma in each reconstruction algorithm. To determine the difference of quantitative CT parameters affected by reconstruction algorithms, these parameters were compared statistically. To determine the relationships with the disease severity, these parameters were correlated with PFTs. In the results, all the histogram parameters values had significant differences each other (p < 0.0001) and those of reconstruction algorithm C were the highest. All MLDs had fair or moderate correlation with all parameters of PFT (-0.64 < r < -0.45, p < 0.05). Though kurtosis and skewness in high-frequency reconstruction algorithm A had significant correlations with all parameters of PFT (-0.61 < r < -0.45, p < 0.05), there were significant correlations only with diffusing capacity of carbon monoxide (DLco) and total lung capacity (TLC) in reconstruction algorithm C and with forced expiratory volume in 1 s (FEV1), DLco and TLC in reconstruction algorithm B. In conclusion, reconstruction algorithm has influence to quantitative assessments on chest thin-section MDCT examination in interstitial pneumonia patients.

  1. Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

    International Nuclear Information System (INIS)

    Levine, Benjamin G.; Stone, John E.; Kohlmeyer, Axel

    2011-01-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.

  2. Quantitatively assessed CT imaging measures of pulmonary interstitial pneumonia: Effects of reconstruction algorithms on histogram parameters

    Energy Technology Data Exchange (ETDEWEB)

    Koyama, Hisanobu [Department of Radiology, Hyogo Kaibara Hospital, 5208-1 Kaibara, Kaibara-cho, Tanba 669-3395 (Japan)], E-mail: hisanobu19760104@yahoo.co.jp; Ohno, Yoshiharu [Department of Radiology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017 (Japan)], E-mail: yosirad@kobe-u.ac.jp; Yamazaki, Youichi [Department of Medical Physics and Engineering, Faculty of Health Sciences, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita 565-0871 (Japan)], E-mail: y.yamazk@sahs.med.osaka-u.ac.jp; Nogami, Munenobu [Division of PET, Institute of Biomedical Research and Innovation, 2-2 MInamimachi, Minatojima, Chu0-ku, Kobe 650-0047 (Japan)], E-mail: aznogami@fbri.org; Kusaka, Akiko [Division of Radiology, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017 (Japan)], E-mail: a.kusaka@hosp.kobe-u.ac.jp; Murase, Kenya [Department of Medical Physics and Engineering, Faculty of Health Sciences, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita 565-0871 (Japan)], E-mail: murase@sahs.med.osaka-u.ac.jp; Sugimura, Kazuro [Department of Radiology, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017 (Japan)], E-mail: sugimura@med.kobe-u.ac.jp

    2010-04-15

    This study aimed the influences of reconstruction algorithm for quantitative assessments in interstitial pneumonia patients. A total of 25 collagen vascular disease patients (nine male patients and 16 female patients; mean age, 57.2 years; age range 32-77 years) underwent thin-section MDCT examinations, and MDCT data were reconstructed with three kinds of reconstruction algorithm (two high-frequencies [A and B] and one standard [C]). In reconstruction algorithm B, the effect of low- and middle-frequency space was suppressed compared with reconstruction algorithm A. As quantitative CT parameters, kurtosis, skewness, and mean lung density (MLD) were acquired from a frequency histogram of the whole lung parenchyma in each reconstruction algorithm. To determine the difference of quantitative CT parameters affected by reconstruction algorithms, these parameters were compared statistically. To determine the relationships with the disease severity, these parameters were correlated with PFTs. In the results, all the histogram parameters values had significant differences each other (p < 0.0001) and those of reconstruction algorithm C were the highest. All MLDs had fair or moderate correlation with all parameters of PFT (-0.64 < r < -0.45, p < 0.05). Though kurtosis and skewness in high-frequency reconstruction algorithm A had significant correlations with all parameters of PFT (-0.61 < r < -0.45, p < 0.05), there were significant correlations only with diffusing capacity of carbon monoxide (DLco) and total lung capacity (TLC) in reconstruction algorithm C and with forced expiratory volume in 1 s (FEV1), DLco and TLC in reconstruction algorithm B. In conclusion, reconstruction algorithm has influence to quantitative assessments on chest thin-section MDCT examination in interstitial pneumonia patients.

  3. Flow cytometric DNA analysis of ducks accumulating 137Cs on a reactor reservoir

    International Nuclear Information System (INIS)

    George, L.S.; Dallas, C.E.; Brisbin, I.L. Jr.; Evans, D.L.

    1991-01-01

    The objective of this study was to detect red blood cell (rbc) DNA abnormalities in male, game-farm mallard ducks as they ranged freely and accumulated 137Cs (radiocesium) from an abandoned nuclear reactor cooling reservoir. Prior to release, the ducks were tamed to enable recapture at will. Flow cytometric measurements conducted at intervals during the first year of exposure yielded cell cycle percentages of DNA (G0/G1, S, G2 + M phases) of rbc, as well as coefficients of variation (CV) in the G0/G1 phase. DNA histograms of exposed ducks were compared with two sets of controls which were maintained 30 and 150 miles from the study site. 137Cs live wholebody burdens were also measured in these animals in a parallel kinetics study, and an approximate steady-state equilibrium was attained after about 8 months. DNA histograms from 2 of the 14 contaminated ducks revealed DNA aneuploid-like patterns after 9 months exposure. These two ducks were removed from the experiment at this time, and when sampled again 1 month later, one continued to exhibit DNA aneuploidy. None of the control DNA histograms demonstrated DNA aneuploid-like patterns. There were no significant differences in cell cycle percentages at any time point between control and exposed animals. A significant increase in CV was observed at 9 months exposure, but after removal of the two ducks with DNA aneuploidy, no significant difference was detected in the group monitored after 12 months exposure. An increased variation in the DNA and DNA aneuploidy could, therefore, be detected in duck rbc using flow cytometric analysis, with the onset of these effects being related to the attainment of maximal levels of 137Cs body burdens in the exposed animals

  4. Implementation of digital image encryption algorithm using logistic function and DNA encoding

    Science.gov (United States)

    Suryadi, MT; Satria, Yudi; Fauzi, Muhammad

    2018-03-01

    Cryptography is a method to secure information that might be in form of digital image. Based on past research, in order to increase security level of chaos based encryption algorithm and DNA based encryption algorithm, encryption algorithm using logistic function and DNA encoding was proposed. Digital image encryption algorithm using logistic function and DNA encoding use DNA encoding to scramble the pixel values into DNA base and scramble it in DNA addition, DNA complement, and XOR operation. The logistic function in this algorithm used as random number generator needed in DNA complement and XOR operation. The result of the test show that the PSNR values of cipher images are 7.98-7.99 bits, the entropy values are close to 8, the histogram of cipher images are uniformly distributed and the correlation coefficient of cipher images are near 0. Thus, the cipher image can be decrypted perfectly and the encryption algorithm has good resistance to entropy attack and statistical attack.

  5. Gastrointestinal Dose-Histogram Effects in the Context of Dose-Volume–Constrained Prostate Radiation Therapy: Analysis of Data From the RADAR Prostate Radiation Therapy Trial

    Energy Technology Data Exchange (ETDEWEB)

    Ebert, Martin A., E-mail: Martin.Ebert@health.wa.gov.au [Department of Radiation Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia (Australia); School of Physics, University of Western Australia, Perth, Western Australia (Australia); Foo, Kerwyn [Sydney Medical School, University of Sydney, Sydney, New South Wales (Australia); Haworth, Annette [Department of Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne, Victoria (Australia); Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria (Australia); Gulliford, Sarah L. [Joint Department of Physics, Institute of Cancer Research and Royal Marsden National Health Service Foundation Trust, Sutton, Surrey (United Kingdom); Kennedy, Angel [Department of Radiation Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia (Australia); Joseph, David J. [Department of Radiation Oncology, Sir Charles Gairdner Hospital, Nedlands, Western Australia (Australia); School of Surgery, University of Western Australia, Perth, Western Australia (Australia); Denham, James W. [School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales (Australia)

    2015-03-01

    Purpose: To use a high-quality multicenter trial dataset to determine dose-volume effects for gastrointestinal (GI) toxicity following radiation therapy for prostate carcinoma. Influential dose-volume histogram regions were to be determined as functions of dose, anatomical location, toxicity, and clinical endpoint. Methods and Materials: Planning datasets for 754 participants in the TROG 03.04 RADAR trial were available, with Late Effects of Normal Tissues (LENT) Subjective, Objective, Management, and Analytic (SOMA) toxicity assessment to a median of 72 months. A rank sum method was used to define dose-volume cut-points as near-continuous functions of dose to 3 GI anatomical regions, together with a comprehensive assessment of significance. Univariate and multivariate ordinal regression was used to assess the importance of cut-points at each dose. Results: Dose ranges providing significant cut-points tended to be consistent with those showing significant univariate regression odds-ratios (representing the probability of a unitary increase in toxicity grade per percent relative volume). Ranges of significant cut-points for rectal bleeding validated previously published results. Separation of the lower GI anatomy into complete anorectum, rectum, and anal canal showed the impact of mid-low doses to the anal canal on urgency and tenesmus, completeness of evacuation and stool frequency, and mid-high doses to the anorectum on bleeding and stool frequency. Derived multivariate models emphasized the importance of the high-dose region of the anorectum and rectum for rectal bleeding and mid- to low-dose regions for diarrhea and urgency and tenesmus, and low-to-mid doses to the anal canal for stool frequency, diarrhea, evacuation, and bleeding. Conclusions: Results confirm anatomical dependence of specific GI toxicities. They provide an atlas summarizing dose-histogram effects and derived constraints as functions of anatomical region, dose, toxicity, and endpoint for

  6. Gastrointestinal Dose-Histogram Effects in the Context of Dose-Volume–Constrained Prostate Radiation Therapy: Analysis of Data From the RADAR Prostate Radiation Therapy Trial

    International Nuclear Information System (INIS)

    Ebert, Martin A.; Foo, Kerwyn; Haworth, Annette; Gulliford, Sarah L.; Kennedy, Angel; Joseph, David J.; Denham, James W.

    2015-01-01

    Purpose: To use a high-quality multicenter trial dataset to determine dose-volume effects for gastrointestinal (GI) toxicity following radiation therapy for prostate carcinoma. Influential dose-volume histogram regions were to be determined as functions of dose, anatomical location, toxicity, and clinical endpoint. Methods and Materials: Planning datasets for 754 participants in the TROG 03.04 RADAR trial were available, with Late Effects of Normal Tissues (LENT) Subjective, Objective, Management, and Analytic (SOMA) toxicity assessment to a median of 72 months. A rank sum method was used to define dose-volume cut-points as near-continuous functions of dose to 3 GI anatomical regions, together with a comprehensive assessment of significance. Univariate and multivariate ordinal regression was used to assess the importance of cut-points at each dose. Results: Dose ranges providing significant cut-points tended to be consistent with those showing significant univariate regression odds-ratios (representing the probability of a unitary increase in toxicity grade per percent relative volume). Ranges of significant cut-points for rectal bleeding validated previously published results. Separation of the lower GI anatomy into complete anorectum, rectum, and anal canal showed the impact of mid-low doses to the anal canal on urgency and tenesmus, completeness of evacuation and stool frequency, and mid-high doses to the anorectum on bleeding and stool frequency. Derived multivariate models emphasized the importance of the high-dose region of the anorectum and rectum for rectal bleeding and mid- to low-dose regions for diarrhea and urgency and tenesmus, and low-to-mid doses to the anal canal for stool frequency, diarrhea, evacuation, and bleeding. Conclusions: Results confirm anatomical dependence of specific GI toxicities. They provide an atlas summarizing dose-histogram effects and derived constraints as functions of anatomical region, dose, toxicity, and endpoint for

  7. Dynamic Contrast-enhanced MR Imaging in Renal Cell Carcinoma: Reproducibility of Histogram Analysis on Pharmacokinetic Parameters

    Science.gov (United States)

    Wang, Hai-yi; Su, Zi-hua; Xu, Xiao; Sun, Zhi-peng; Duan, Fei-xue; Song, Yuan-yuan; Li, Lu; Wang, Ying-wei; Ma, Xin; Guo, Ai-tao; Ma, Lin; Ye, Hui-yi

    2016-01-01

    Pharmacokinetic parameters derived from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) have been increasingly used to evaluate the permeability of tumor vessel. Histogram metrics are a recognized promising method of quantitative MR imaging that has been recently introduced in analysis of DCE-MRI pharmacokinetic parameters in oncology due to tumor heterogeneity. In this study, 21 patients with renal cell carcinoma (RCC) underwent paired DCE-MRI studies on a 3.0 T MR system. Extended Tofts model and population-based arterial input function were used to calculate kinetic parameters of RCC tumors. Mean value and histogram metrics (Mode, Skewness and Kurtosis) of each pharmacokinetic parameter were generated automatically using ImageJ software. Intra- and inter-observer reproducibility and scan–rescan reproducibility were evaluated using intra-class correlation coefficients (ICCs) and coefficient of variation (CoV). Our results demonstrated that the histogram method (Mode, Skewness and Kurtosis) was not superior to the conventional Mean value method in reproducibility evaluation on DCE-MRI pharmacokinetic parameters (K trans & Ve) in renal cell carcinoma, especially for Skewness and Kurtosis which showed lower intra-, inter-observer and scan-rescan reproducibility than Mean value. Our findings suggest that additional studies are necessary before wide incorporation of histogram metrics in quantitative analysis of DCE-MRI pharmacokinetic parameters. PMID:27380733

  8. A Whole-Tumor Histogram Analysis of Apparent Diffusion Coefficient Maps for Differentiating Thymic Carcinoma from Lymphoma.

    Science.gov (United States)

    Zhang, Wei; Zhou, Yue; Xu, Xiao-Quan; Kong, Ling-Yan; Xu, Hai; Yu, Tong-Fu; Shi, Hai-Bin; Feng, Qing

    2018-01-01

    To assess the performance of a whole-tumor histogram analysis of apparent diffusion coefficient (ADC) maps in differentiating thymic carcinoma from lymphoma, and compare it with that of a commonly used hot-spot region-of-interest (ROI)-based ADC measurement. Diffusion weighted imaging data of 15 patients with thymic carcinoma and 13 patients with lymphoma were retrospectively collected and processed with a mono-exponential model. ADC measurements were performed by using a histogram-based and hot-spot-ROI-based approach. In the histogram-based approach, the following parameters were generated: mean ADC (ADC mean ), median ADC (ADC median ), 10th and 90th percentile of ADC (ADC 10 and ADC 90 ), kurtosis, and skewness. The difference in ADCs between thymic carcinoma and lymphoma was compared using a t test. Receiver operating characteristic analyses were conducted to determine and compare the differentiating performance of ADCs. Lymphoma demonstrated significantly lower ADC mean , ADC median , ADC 10 , ADC 90 , and hot-spot-ROI-based mean ADC than those found in thymic carcinoma (all p values histogram analysis of ADC maps can improve the differentiating performance between thymic carcinoma and lymphoma.

  9. TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins.

    Science.gov (United States)

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2016-05-10

    The TaBoo SeArch (TBSA) algorithm [ Harada et al. J. Comput. Chem. 2015 , 36 , 763 - 772 and Harada et al. Chem. Phys. Lett. 2015 , 630 , 68 - 75 ] was recently proposed as an enhanced conformational sampling method for reproducing biologically relevant rare events of a given protein. In TBSA, an inverse histogram of the original distribution, mapped onto a set of reaction coordinates, is constructed from trajectories obtained by multiple short-time molecular dynamics (MD) simulations. Rarely occurring states of a given protein are statistically selected as new initial states based on the inverse histogram, and resampling is performed by restarting the MD simulations from the new initial states to promote the conformational transition. In this process, the definition of the inverse histogram, which characterizes the rarely occurring states, is crucial for the efficiency of TBSA. In this study, we propose a simple modification of the inverse histogram to further accelerate the convergence of TBSA. As demonstrations of the modified TBSA, we applied it to (a) hydrogen bonding rearrangements of Met-enkephalin, (b) large-amplitude domain motions of Glutamine-Binding Protein, and (c) folding processes of the B domain of Staphylococcus aureus Protein A. All demonstrations numerically proved that the modified TBSA reproduced these biologically relevant rare events with nanosecond-order simulation times, although a set of microsecond-order, canonical MD simulations failed to reproduce the rare events, indicating the high efficiency of the modified TBSA.

  10. A statistic to estimate the variance of the histogram-based mutual information estimator based on dependent pairs of observations

    NARCIS (Netherlands)

    Moddemeijer, R

    In the case of two signals with independent pairs of observations (x(n),y(n)) a statistic to estimate the variance of the histogram based mutual information estimator has been derived earlier. We present such a statistic for dependent pairs. To derive this statistic it is necessary to avail of a

  11. Comparison of the accuracy of two conventional phenotypic methods and two MALDI-TOF MS systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts.

    Science.gov (United States)

    Chao, Qiao-Ting; Lee, Tai-Fen; Teng, Shih-Hua; Peng, Li-Yun; Chen, Ping-Hung; Teng, Lee-Jene; Hsueh, Po-Ren

    2014-01-01

    We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Bruker Biotyper and Vitek MS) and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID) with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex) levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database), Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar) systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis) were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD) system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD) system, 39 (43.8%), including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5%) by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati) isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii complex

  12. Comparison of the accuracy of two conventional phenotypic methods and two MALDI-TOF MS systems with that of DNA sequencing analysis for correctly identifying clinically encountered yeasts.

    Directory of Open Access Journals (Sweden)

    Qiao-Ting Chao

    Full Text Available We assessed the accuracy of species-level identification of two commercially available matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS systems (Bruker Biotyper and Vitek MS and two conventional phenotypic methods (Phoenix 100 YBC and Vitek 2 Yeast ID with that of rDNA gene sequencing analysis among 200 clinical isolates of commonly encountered yeasts. The correct identification rates of the 200 yeast isolates to species or complex (Candida parapsilosis complex, C. guilliermondii complex and C. rugosa complex levels by the Bruker Biotyper, Vitek MS (using in vitro devices [IVD] database, Phoenix 100 YBC and Vitek 2 Yeast ID (Sabouraud's dextrose agar systems were 92.5%, 79.5%, 89%, and 74%, respectively. An additional 72 isolates of C. parapsilosis complex and 18 from the above 200 isolates (30 in each of C. parapsilosis, C. metapsilosis, and C. orthopsilosis were also evaluated separately. Bruker Biotyper system could accurately identify all C. parapsilosis complex to species level. Using Vitek 2 MS (IVD system, all C. parapsilosis but none of C. metapsilosis, or C. orthopsilosis could be accurately identified. Among the 89 yeasts misidentified by the Vitek 2 MS (IVD system, 39 (43.8%, including 27 C. orthopsilosis isolates, could be correctly identified Using the Vitek MS Plus SARAMIS database for research use only. This resulted in an increase in the rate of correct identification of all yeast isolates (87.5% by Vitek 2 MS. The two species in C. guilliermondii complex (C. guilliermondii and C. fermentati isolates were correctly identified by cluster analysis of spectra generated by the Bruker Biotyper system. Based on the results obtained in the current study, MALDI-TOF MS systems present a promising alternative for the routine identification of yeast species, including clinically commonly and rarely encountered yeast species and several species belonging to C. parapsilosis complex, C. guilliermondii

  13. Predicting pathologic tumor response to chemoradiotherapy with histogram distances characterizing longitudinal changes in 18F-FDG uptake patterns

    Science.gov (United States)

    Tan, Shan; Zhang, Hao; Zhang, Yongxue; Chen, Wengen; D’Souza, Warren D.; Lu, Wei

    2013-01-01

    Purpose: A family of fluorine-18 (18F)-fluorodeoxyglucose (18F-FDG) positron-emission tomography (PET) features based on histogram distances is proposed for predicting pathologic tumor response to neoadjuvant chemoradiotherapy (CRT). These features describe the longitudinal change of FDG uptake distribution within a tumor. Methods: Twenty patients with esophageal cancer treated with CRT plus surgery were included in this study. All patients underwent PET/CT scans before (pre-) and after (post-) CRT. The two scans were first rigidly registered, and the original tumor sites were then manually delineated on the pre-PET/CT by an experienced nuclear medicine physician. Two histograms representing the FDG uptake distribution were extracted from the pre- and the registered post-PET images, respectively, both within the delineated tumor. Distances between the two histograms quantify longitudinal changes in FDG uptake distribution resulting from CRT, and thus are potential predictors of tumor response. A total of 19 histogram distances were examined and compared to both traditional PET response measures and Haralick texture features. Receiver operating characteristic analyses and Mann-Whitney U test were performed to assess their predictive ability. Results: Among all tested histogram distances, seven bin-to-bin and seven crossbin distances outperformed traditional PET response measures using maximum standardized uptake value (AUC = 0.70) or total lesion glycolysis (AUC = 0.80). The seven bin-to-bin distances were: L2 distance (AUC = 0.84), χ2 distance (AUC = 0.83), intersection distance (AUC = 0.82), cosine distance (AUC = 0.83), squared Euclidean distance (AUC = 0.83), L1 distance (AUC = 0.82), and Jeffrey distance (AUC = 0.82). The seven crossbin distances were: quadratic-chi distance (AUC = 0.89), earth mover distance (AUC = 0.86), fast earth mover distance (AUC = 0.86), diffusion distance (AUC = 0.88), Kolmogorov-Smirnov distance (AUC = 0.88), quadratic form distance

  14. DNA fusion gene vaccines

    DEFF Research Database (Denmark)

    Holst, Peter Johannes; Bassi, Maria Rosaria; Thomsen, Allan Randrup

    2010-01-01

    DNA vaccines are versatile and safe, but limited immunogenicity has prevented their use in the clinical setting. Experimentally, immunogenicity may be enhanced by the use of new delivery technologies, by coadministration of cytokines and pathogen-associated molecular patterns, or by fusion...... of antigens into molecular domains that enhance antigen presentation. More specifically, the immunogenicity of DNA vaccines may benefit from increased protein synthesis, increased T-cell help and MHC class I presentation, and the addition of a range of specific cytokines and pathogen-associated molecular...... with viral-vectored vaccines, various synergistic components may need to be incorporated into DNA vaccines. From the perspective of the future clinical use of DNA vaccines, it has been suggested that antigen presentation should be improved and cytokine coadministration attempted. However, even...

  15. The relationship between the PD-1/PD-L1 pathway and DNA mismatch repair in cervical cancer and its clinical significance

    Directory of Open Access Journals (Sweden)

    Feng YC

    2018-01-01

    Full Text Available Yang-chun Feng,1,2 Wen-li Ji,3 Na Yue,3 Yan-chun Huang,2 Xiu-min Ma1 1Clinical Laboratory Center, The First Affiliated Hospital of Xinjiang Medical University, 2Clinical Laboratory Center, 3Clinical Pathology Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, People’s Republic of China Background: According to recent clinical observations, deficient DNA mismatch repair (dMMR is capable of improving antitumor effects of the PD-1/PD-L1 pathway, suggesting that dMMR may act as a prognostic indicator of PD-1/PD-L1 antibody drugs. In this study, we examined the dMMR and PD-1/PD-L1 expression, as well as explored the correlation of dMMR status with PD-1/PD-L1 expression in cervical cancer patients, in order to optimize cervical cancer patient selection for PD-1/PD-L1 antibody drug treatment, which is helpful to avoid adverse effects and keep costs manageable. Methods: Sixty-six tissue samples from patients with squamous cell carcinoma were collected, and data of their clinical characteristics were also gathered. Based on these samples, the expression levels of MLH1, MSH2, and PD-L1 in cancer cells were tested by immunohistochemical assay (IHC. Moreover, PD-1/PD-L1 expression in tumor-invading lymphocytes (TILs was detected by IHC as well. Six single-nucleotide-repeat markers of microsatellite instability (MSI, including NR-27, MONO-27, BAT-25, NR-24, NR-21, and BAT-26, were tested by capillary electrophoresis sequencer analysis. According to expression of MLH1, MSH2 and the MSI test, all 66 cases were divided into dMMR or proficient DNA mismatch repair (pMMR groups. The comparisons of dMMR and PD-L1 in cancer cells and of PD-1/PD-L1 in TILs were conducted categorized by age, childbearing history, history of abortion, ethnicity, and cancer cell differentiation subgroup. Furthermore, PD-L1 levels in cancer cells and PD-1/PD-L1 in TILs were analyzed and compared in both dMMR and pMMR subgroups. Results: Of the patient samples, 25

  16. Detection of Local Tumor Recurrence After Definitive Treatment of Head and Neck Squamous Cell Carcinoma: Histogram Analysis of Dynamic Contrast-Enhanced T1-Weighted Perfusion MRI.

    Science.gov (United States)

    Choi, Sang Hyun; Lee, Jeong Hyun; Choi, Young Jun; Park, Ji Eun; Sung, Yu Sub; Kim, Namkug; Baek, Jung Hwan

    2017-01-01

    This study aimed to explore the added value of histogram analysis of the ratio of initial to final 90-second time-signal intensity AUC (AUCR) for differentiating local tumor recurrence from contrast-enhancing scar on follow-up dynamic contrast-enhanced T1-weighted perfusion MRI of patients treated for head and neck squamous cell carcinoma (HNSCC). AUCR histogram parameters were assessed among tumor recurrence (n = 19) and contrast-enhancing scar (n = 27) at primary sites and compared using the t test. ROC analysis was used to determine the best differentiating parameters. The added value of AUCR histogram parameters was assessed when they were added to inconclusive conventional MRI results. Histogram analysis showed statistically significant differences in the 50th, 75th, and 90th percentiles of the AUCR values between the two groups (p Histogram analysis of AUCR can improve the diagnostic yield for local tumor recurrence during surveillance after treatment for HNSCC.

  17. Dynamic contrast-enhanced MR imaging of the rectum: Correlations between single-section and whole-tumor histogram analyses.

    Science.gov (United States)

    Choi, M H; Oh, S N; Park, G E; Yeo, D-M; Jung, S E

    2018-05-10

    To evaluate the interobserver and intermethod correlations of histogram metrics of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) parameters acquired by multiple readers using the single-section and whole-tumor volume methods. Four DCE parameters (K trans , K ep , V e , V p ) were evaluated in 45 patients (31 men and 14 women; mean age, 61±11 years [range, 29-83 years]) with locally advanced rectal cancer using pre-chemoradiotherapy (CRT) MRI. Ten histogram metrics were extracted using two methods of lesion selection performed by three radiologists: the whole-tumor volume method for the whole tumor on axial section-by-section images and the single-section method for the entire area of the tumor on one axial image. The interobserver and intermethod correlations were evaluated using the intraclass correlation coefficients (ICCs). The ICCs showed excellent interobserver and intermethod correlations in most of histogram metrics of the DCE parameters. The ICCs among the three readers were > 0.7 (Phistogram metrics, except for the minimum and maximum. The intermethod correlations for most of the histogram metrics were excellent for each radiologist, regardless of the differences in the radiologists' experience. The interobserver and intermethod correlations for most of the histogram metrics of the DCE parameters are excellent in rectal cancer. Therefore, the single-section method may be a potential alternative to the whole-tumor volume method using pre-CRT MRI, despite the fact that the high agreement between the two methods cannot be extrapolated to post-CRT MRI. Copyright © 2018 Société française de radiologie. Published by Elsevier Masson SAS. All rights reserved.

  18. Residential distance to major roadways and semen quality, sperm DNA integrity, chromosomal disomy, and serum reproductive hormones among men attending a fertility clinic.

    Science.gov (United States)

    Nassan, Feiby L; Chavarro, Jorge E; Mínguez-Alarcón, Lidia; Williams, Paige L; Tanrikut, Cigdem; Ford, Jennifer B; Dadd, Ramace; Perry, Melissa J; Hauser, Russ; Gaskins, Audrey J

    2018-06-01

    We examined associations of residential distance to major roadways, as a proxy for traffic-related air pollution exposures, with sperm characteristics and male reproductive hormones. The cohort included 797 men recruited from Massachusetts General Hospital Fertility Center between 2000 and 2015 to participate in fertility research studies. Men reported their residential addresses at enrollment and provided 1-6 semen samples and a blood sample during follow-up. We estimated the Euclidean distance to major roadways (e.g. interstates and highways: limited access highways, multi-lane highways (not limited access), other numbered routes, and major roads) using information from the Massachusetts Department of Geographic Information Systems. Semen parameters (1238 semen samples), sperm DNA integrity (389 semen samples), chromosomal disomy (101 semen samples), and serum reproductive hormones (405 serum samples) were assessed following standard procedures. Men in this cohort were primarily Caucasian (86%), not current smokers (92%), with a college or higher education (88%), and had an average age of 36 years and BMI of 27.7 kg/m 2 . The median (interquartile range) residential distance to a major roadway was 111 (37, 248) meters. Residential proximity to major roadways was not associated with semen parameters, sperm DNA integrity, chromosomal disomy, or serum reproductive hormone concentrations. The adjusted percent change (95% CI) in semen quality parameters associated with a 500 m increase in residential distance to a major roadway was -1.0% (-6.3, 4.5) for semen volume, 4.3% (-5.8, 15.7) for sperm concentration, 3.1% (-7.2, 14.5) for sperm count, 1.1% (-1.2, 3.4) for % total motile sperm, and 0.1% (-0.3, 0.5) for % morphologically normal sperm. Results were consistent when we modeled the semen parameters dichotomized according to WHO 2010 reference values. Residential distance to major roadways, as a proxy for traffic-related air pollution exposure, was not related

  19. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  20. Genomic DNA fingerprinting of clinical Haemophilus influenzae isolates by polymerase chain reaction amplification: comparison with major outer-membrane protein and restriction fragment length polymorphism analysis

    NARCIS (Netherlands)

    van Belkum, A.; Duim, B.; Regelink, A.; Möller, L.; Quint, W.; van Alphen, L.

    1994-01-01

    Non-capsulate strains of Haemophilus influenzae were genotyped by analysis of variable DNA segments obtained by amplification of genomic DNA with the polymerase chain reaction (PCR fingerprinting). Discrete fragments of 100-2000 bp were obtained. The reproducibility of the procedure was assessed by

  1. Impact of the radiotherapy technique on the correlation between dose–volume histograms of the bladder wall defined on MRI imaging and dose–volume/surface histograms in prostate cancer patients

    International Nuclear Information System (INIS)

    Maggio, Angelo; Carillo, Viviana; Perna, Lucia; Fiorino, Claudio; Cozzarini, Cesare; Rancati, Tiziana; Valdagni, Riccardo; Gabriele, Pietro

    2013-01-01

    The aim of this study was to evaluate the correlation between the ‘true’ absolute and relative dose–volume histograms (DVHs) of the bladder wall, dose–wall histogram (DWH) defined on MRI imaging and other surrogates of bladder dosimetry in prostate cancer patients, planned both with 3D-conformal and intensity-modulated radiation therapy (IMRT) techniques. For 17 prostate cancer patients, previously treated with radical intent, CT and MRI scans were acquired and matched. The contours of bladder walls were drawn by using MRI images. External bladder surfaces were then used to generate artificial bladder walls by performing automatic contractions of 5, 7 and 10 mm. For each patient a 3D conformal radiotherapy (3DCRT) and an IMRT treatment plan was generated with a prescription dose of 77.4 Gy (1.8 Gy/fr) and DVH of the whole bladder of the artificial walls (DVH-5/10) and dose–surface histograms (DSHs) were calculated and compared against the DWH in absolute and relative value, for both treatment planning techniques. A specific software (VODCA v. 4.4.0, MSS Inc.) was used for calculating the dose–volume/surface histogram. Correlation was quantified for selected dose–volume/surface parameters by the Spearman correlation coefficient. The agreement between %DWH and DVH5, DVH7 and DVH10 was found to be very good (maximum average deviations below 2%, SD < 5%): DVH5 showed the best agreement. The correlation was slightly better for absolute (R = 0.80–0.94) compared to relative (R = 0.66–0.92) histograms. The DSH was also found to be highly correlated with the DWH, although slightly higher deviations were generally found. The DVH was not a good surrogate of the DWH (R < 0.7 for most of parameters). When comparing the two treatment techniques, more pronounced differences between relative histograms were seen for IMRT with respect to 3DCRT (p < 0.0001). (note)

  2. Registration for Optical Multimodal Remote Sensing Images Based on FAST Detection, Window Selection, and Histogram Specification

    Directory of Open Access Journals (Sweden)

    Xiaoyang Zhao

    2018-04-01

    Full Text Available In recent years, digital frame cameras have been increasingly used for remote sensing applications. However, it is always a challenge to align or register images captured with different cameras or different imaging sensor units. In this research, a novel registration method was proposed. Coarse registration was first applied to approximately align the sensed and reference images. Window selection was then used to reduce the search space and a histogram specification was applied to optimize the grayscale similarity between the images. After comparisons with other commonly-used detectors, the fast corner detector, FAST (Features from Accelerated Segment Test, was selected to extract the feature points. The matching point pairs were then detected between the images, the outliers were eliminated, and geometric transformation was performed. The appropriate window size was searched and set to one-tenth of the image width. The images that were acquired by a two-camera system, a camera with five imaging sensors, and a camera with replaceable filters mounted on a manned aircraft, an unmanned aerial vehicle, and a ground-based platform, respectively, were used to evaluate the performance of the proposed method. The image analysis results showed that, through the appropriate window selection and histogram specification, the number of correctly matched point pairs had increased by 11.30 times, and that the correct matching rate had increased by 36%, compared with the results based on FAST alone. The root mean square error (RMSE in the x and y directions was generally within 0.5 pixels. In comparison with the binary robust invariant scalable keypoints (BRISK, curvature scale space (CSS, Harris, speed up robust features (SURF, and commercial software ERDAS and ENVI, this method resulted in larger numbers of correct matching pairs and smaller, more consistent RMSE. Furthermore, it was not necessary to choose any tie control points manually before registration

  3. Evaluation of dose-volume histograms after prostate seed implantation. 4-year experience

    International Nuclear Information System (INIS)

    Hoinkis, C.; Lehmann, D.; Winkler, C.; Herrmann, T.; Hakenberg, O.W.; Wirth, M.P.

    2004-01-01

    Background and purpose: permanent interstitial brachytherapy by seed implantation is a treatment alternative for low-volume low-risk prostate cancer and a complex interdisciplinary treatment with a learning curve. Dose-volume histograms are used to assess postimplant quality. The authors evaluated their learning curve based on dose-volume histograms and analyzed factors influencing implantation quality. Patients and methods: since 1999, 38 patients with a minimum follow-up of 6 months were treated at the authors' institution with seed implantation using palladium-103 or iodine-125, initially using the preplan method and later real-time planning. Postimplant CT was performed after 4 weeks. The dose-volume indices D90, V100, V150, the D max of pre- and postplans, and the size and position of the volume receiving the prescribed dose (high-dose volume) of the postplans were evaluated. In six patients, postplan imaging both by CT and MRI was used and prostate volumes were compared with preimplant transrectal ultrasound volumes. The first five patients were treated under external supervision. Results: patients were divided into three consecutive groups for analysis of the learning curve (group 1: n = 5 patients treated under external supervision; group 2: n = 13 patients; group 3: n = 20 patients). D90 post for the three groups were 79.3%, 74.2%, and 99.9%, the V100 post were 78.6%, 73.5%, and 88.2%, respectively. The relationship between high-dose volume and prostate volume showed a similar increase as the D90, while the relationship between high-dose volume lying outside the prostate and prostate volume remained constant. The ratio between prostate volumes from transrectal ultrasound and CT imaging decreased with increasing D90 post , while the preplanning D90 and V100 remained constant. The different isotopes used, the method of planning, and the implanted activity per prostate volume did not influence results. Conclusion: a learning curve characterized by an increase

  4. Efficient Sleeping Beauty DNA Transposition From DNA Minicircles

    Directory of Open Access Journals (Sweden)

    Nynne Sharma

    2013-01-01

    Full Text Available DNA transposon-based vectors have emerged as new potential delivery tools in therapeutic gene transfer. Such vectors are now showing promise in hematopoietic stem cells and primary human T cells, and clinical trials with transposon-engineered cells are on the way. However, the use of plasmid DNA as a carrier of the vector raises safety concerns due to the undesirable administration of bacterial sequences. To optimize vectors based on the Sleeping Beauty (SB DNA transposon for clinical use, we examine here SB transposition from DNA minicircles (MCs devoid of the bacterial plasmid backbone. Potent DNA transposition, directed by the hyperactive SB100X transposase, is demonstrated from MC donors, and the stable transfection rate is significantly enhanced by expressing the SB100X transposase from MCs. The stable transfection rate is inversely related to the size of circular donor, suggesting that a MC-based SB transposition system benefits primarily from an increased cellular uptake and/or enhanced expression which can be observed with DNA MCs. DNA transposon and transposase MCs are easily produced, are favorable in size, do not carry irrelevant DNA, and are robust substrates for DNA transposition. In accordance, DNA MCs should become a standard source of DNA transposons not only in therapeutic settings but also in the daily use of the SB system.

  5. Comparison of the clinical performances of the AdvanSure HPV Screening Real-Time PCR, the Abbott Real-Time High-Risk HPV Test, and the Hybrid Capture High-Risk HPV DNA Test for Cervical Cancer Screening.

    Science.gov (United States)

    Chung, Hae-Sun; Hahm, Chorong; Lee, Miae

    2014-09-01

    The clinical performance of three human papillomavirus (HPV) DNA commercial assays for cervical cancer screening was evaluated; the AdvanSure HPV Screening Real-Time PCR (AdvanSure PCR; LG Life Sciences) that was developed recently for the detection of both high-risk and low-risk genotypes, the Abbott RealTime High-Risk HPV Test (Abbott PCR; Abbott Molecular) and the Hybrid Capture High-Risk HPV DNA test (HC2; Qiagen). The three different HPV DNA tests were compared using cytology samples obtained from 619 women who underwent routine cervical cancer screening. The gold-standard assay was histopathological confirmation of cervical intraepithelial neoplasia of grade 2 or worse. The clinical sensitivities of the AdvanSure PCR, the Abbott PCR and the HC2 for the detection of cervical intraepithelial neoplasia of grade 2 or worse were 95.5%, 95.5% and 100%, respectively, while the clinical specificities were 61.6%, 86.4% and 83.3%, respectively. There were no significant differences in the clinical sensitivities of the Abbott PCR and the AdvanSure PCR compared to the HC2. The clinical specificities of the Abbott PCR and the AdvanSure PCR for the detection of HPV types 16/18 were 97.8% and 98.5%, respectively. For cervical cancer screening, all three tests showed relatively good clinical sensitivities, but the AdvanSure PCR had lower clinical specificity than the Abbott PCR and the HC2. The AdvanSure PCR and the Abbott PCR assays have the advantage of being automated and the ability to distinguish between HPV types 16/18 and other HPV types. The two real-time PCR assays could be useful tools in HPV testing for cervical cancer screening. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Epigenome-Wide Tumor DNA Methylation Profiling Identifies Novel Prognostic Biomarkers of Metastatic-Lethal Progression in Men Diagnosed with Clinically Localized Prostate Cancer.

    Science.gov (United States)

    Zhao, Shanshan; Geybels, Milan S; Leonardson, Amy; Rubicz, Rohina; Kolb, Suzanne; Yan, Qingxiang; Klotzle, Brandy; Bibikova, Marina; Hurtado-Coll, Antonio; Troyer, Dean; Lance, Raymond; Lin, Daniel W; Wright, Jonathan L; Ostrander, Elaine A; Fan, Jian-Bing; Feng, Ziding; Stanford, Janet L

    2017-01-01

    Aside from Gleason sum, few factors accurately identify the subset of prostate cancer patients at high risk for metastatic progression. We hypothesized that epigenetic alterations could distinguish prostate tumors with life-threatening potential. Epigenome-wide DNA methylation profiling was performed in surgically resected primary tumor tissues from a population-based (n = 430) and a replication (n = 80) cohort of prostate cancer patients followed prospectively for at least 5 years. Metastasis was confirmed by positive bone scan, MRI, CT, or biopsy, and death certificates confirmed cause of death. AUC, partial AUC (pAUC, 95% specificity), and P value criteria were used to select differentially methylated CpG sites that robustly stratify patients with metastatic-lethal from nonrecurrent tumors, and which were complementary to Gleason sum. Forty-two CpG biomarkers stratified patients with metastatic-lethal versus nonrecurrent prostate cancer in the discovery cohort, and eight of these CpGs replicated in the validation cohort based on a significant (P prostate cancer include CpGs in five genes (ALKBH5, ATP11A, FHAD1, KLHL8, and PI15) and three intergenic regions. In the validation dataset, the AUC for Gleason sum alone (0.82) significantly increased with the addition of four individual CpGs (range, 0.86-0.89; all P epigenetic biomarkers warrant further investigation as they may improve prognostic classification of patients with clinically localized prostate cancer and provide new insights on tumor aggressiveness. Clin Cancer Res; 23(1); 311-9. ©2016 AACR. ©2016 American Association for Cancer Research.

  7. Histogram Analysis of CT Perfusion of Hepatocellular Carcinoma for Predicting Response to Transarterial Radioembolization: Value of Tumor Heterogeneity Assessment

    International Nuclear Information System (INIS)

    Reiner, Caecilia S.; Gordic, Sonja; Puippe, Gilbert; Morsbach, Fabian; Wurnig, Moritz; Schaefer, Niklaus; Veit-Haibach, Patrick; Pfammatter, Thomas; Alkadhi, Hatem

    2016-01-01

    PurposeTo evaluate in patients with hepatocellular carcinoma (HCC), whether assessment of tumor heterogeneity by histogram analysis of computed tomography (CT) perfusion helps predicting response to transarterial radioembolization (TARE).Materials and MethodsSixteen patients (15 male; mean age 65 years; age range 47–80 years) with HCC underwent CT liver perfusion for treatment planning prior to TARE with Yttrium-90 microspheres. Arterial perfusion (AP) derived from CT perfusion was measured in the entire tumor volume, and heterogeneity was analyzed voxel-wise by histogram analysis. Response to TARE was evaluated on follow-up imaging (median follow-up, 129 days) based on modified Response Evaluation Criteria in Solid Tumors (mRECIST). Results of histogram analysis and mean AP values of the tumor were compared between responders and non-responders. Receiver operating characteristics were calculated to determine the parameters’ ability to discriminate responders from non-responders.ResultsAccording to mRECIST, 8 patients (50 %) were responders and 8 (50 %) non-responders. Comparing responders and non-responders, the 50th and 75th percentile of AP derived from histogram analysis was significantly different [AP 43.8/54.3 vs. 27.6/34.3 mL min −1  100 mL −1 ); p < 0.05], while the mean AP of HCCs (43.5 vs. 27.9 mL min −1  100 mL −1 ; p > 0.05) was not. Further heterogeneity parameters from histogram analysis (skewness, coefficient of variation, and 25th percentile) did not differ between responders and non-responders (p > 0.05). If the cut-off for the 75th percentile was set to an AP of 37.5 mL min −1  100 mL −1 , therapy response could be predicted with a sensitivity of 88 % (7/8) and specificity of 75 % (6/8).ConclusionVoxel-wise histogram analysis of pretreatment CT perfusion indicating tumor heterogeneity of HCC improves the pretreatment prediction of response to TARE

  8. SU-F-R-50: Radiation-Induced Changes in CT Number Histogram During Chemoradiation Therapy for Pancreatic Cancer

    International Nuclear Information System (INIS)

    Chen, X; Schott, D; Song, Y; Li, D; Hall, W; Erickson, B; Li, X

    2016-01-01

    Purpose: In an effort of early assessment of treatment response, we investigate radiation induced changes in CT number histogram of GTV during the delivery of chemoradiation therapy (CRT) for pancreatic cancer. Methods: Diagnostic-quality CT data acquired daily during routine CT-guided CRT using a CT-on-rails for 20 pancreatic head cancer patients were analyzed. All patients were treated with a radiation dose of 50.4 in 28 fractions. On each daily CT set, the contours of the pancreatic head and the spinal cord were delineated. The Hounsfiled Units (HU) histogram in these contourswere extracted and processed using MATLAB. Eight parameters of the histogram including the mean HU over all the voxels, peak position, volume, standard deviation (SD), skewness, kurtosis, energy, and entropy were calculated for each fraction. The significances were inspected using paired two-tailed t-test and the correlations were analyzed using Spearman rank correlation tests. Results: In general, HU histogram in pancreatic head (but not in spinal cord) changed during the CRT delivery. Changes from the first to the last fraction in mean HU in pancreatic head ranged from −13.4 to 3.7 HU with an average of −4.4 HU, which was significant (P<0.001). Among other quantities, the volume decreased, the skewness increased (less skewed), and the kurtosis decreased (less sharp) during the CRT delivery. The changes of mean HU, volume, skewness, and kurtosis became significant after two weeks of treatment. Patient pathological response status is associated with the changes of SD (ΔSD), i.e., ΔSD= 1.85 (average of 7 patients) for good reponse, −0.08 (average of 6 patients) for moderate and poor response. Conclusion: Significant changes in HU histogram and the histogram-based metrics (e.g., meam HU, skewness, and kurtosis) in tumor were observed during the course of chemoradiation therapy for pancreas cancer. These changes may be potentially used for early assessment of treatment response.

  9. Utility of whole-lesion ADC histogram metrics for assessing the malignant potential of pancreatic intraductal papillary mucinous neoplasms (IPMNs).

    Science.gov (United States)

    Hoffman, David H; Ream, Justin M; Hajdu, Christina H; Rosenkrantz, Andrew B

    2017-04-01

    To evaluate whole-lesion ADC histogram metrics for assessing the malignant potential of pancreatic intraductal papillary mucinous neoplasms (IPMNs), including in comparison with conventional MRI features. Eighteen branch-duct IPMNs underwent MRI with DWI prior to resection (n = 16) or FNA (n = 2). A blinded radiologist placed 3D volumes-of-interest on the entire IPMN on the ADC map, from which whole-lesion histogram metrics were generated. The reader also assessed IPMN size, mural nodularity, and adjacent main-duct dilation. Benign (low-to-intermediate grade dysplasia; n = 10) and malignant (high-grade dysplasia or invasive adenocarcinoma; n = 8) IPMNs were compared. Whole-lesion ADC histogram metrics demonstrating significant differences between benign and malignant IPMNs were: entropy (5.1 ± 0.2 vs. 5.4 ± 0.2; p = 0.01, AUC = 86%); mean of the bottom 10th percentile (2.2 ± 0.4 vs. 1.6 ± 0.7; p = 0.03; AUC = 81%); and mean of the 10-25th percentile (2.8 ± 0.4 vs. 2.3 ± 0.6; p = 0.04; AUC = 79%). The overall mean ADC, skewness, and kurtosis were not significantly different between groups (p ≥ 0.06; AUC = 50-78%). For entropy (highest performing histogram metric), an optimal threshold of >5.3 achieved a sensitivity of 100%, a specificity of 70%, and an accuracy of 83% for predicting malignancy. No significant difference (p = 0.18-0.64) was observed between benign and malignant IPMNs for cyst size ≥3 cm, adjacent main-duct dilatation, or mural nodule. At multivariable analysis of entropy in combination with all other ADC histogram and conventional MRI features, entropy was the only significant independent predictor of malignancy (p = 0.004). Although requiring larger studies, ADC entropy obtained from 3D whole-lesion histogram analysis may serve as a biomarker for identifying the malignant potential of IPMNs, independent of conventional MRI features.

  10. SU-F-R-50: Radiation-Induced Changes in CT Number Histogram During Chemoradiation Therapy for Pancreatic Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Chen, X; Schott, D; Song, Y; Li, D; Hall, W; Erickson, B; Li, X [Medical College of Wisconsin, Milwaukee, WI (United States)

    2016-06-15

    Purpose: In an effort of early assessment of treatment response, we investigate radiation induced changes in CT number histogram of GTV during the delivery of chemoradiation therapy (CRT) for pancreatic cancer. Methods: Diagnostic-quality CT data acquired daily during routine CT-guided CRT using a CT-on-rails for 20 pancreatic head cancer patients were analyzed. All patients were treated with a radiation dose of 50.4 in 28 fractions. On each daily CT set, the contours of the pancreatic head and the spinal cord were delineated. The Hounsfiled Units (HU) histogram in these contourswere extracted and processed using MATLAB. Eight parameters of the histogram including the mean HU over all the voxels, peak position, volume, standard deviation (SD), skewness, kurtosis, energy, and entropy were calculated for each fraction. The significances were inspected using paired two-tailed t-test and the correlations were analyzed using Spearman rank correlation tests. Results: In general, HU histogram in pancreatic head (but not in spinal cord) changed during the CRT delivery. Changes from the first to the last fraction in mean HU in pancreatic head ranged from −13.4 to 3.7 HU with an average of −4.4 HU, which was significant (P<0.001). Among other quantities, the volume decreased, the skewness increased (less skewed), and the kurtosis decreased (less sharp) during the CRT delivery. The changes of mean HU, volume, skewness, and kurtosis became significant after two weeks of treatment. Patient pathological response status is associated with the changes of SD (ΔSD), i.e., ΔSD= 1.85 (average of 7 patients) for good reponse, −0.08 (average of 6 patients) for moderate and poor response. Conclusion: Significant changes in HU histogram and the histogram-based metrics (e.g., meam HU, skewness, and kurtosis) in tumor were observed during the course of chemoradiation therapy for pancreas cancer. These changes may be potentially used for early assessment of treatment response.

  11. Histogram Analysis of CT Perfusion of Hepatocellular Carcinoma for Predicting Response to Transarterial Radioembolization: Value of Tumor Heterogeneity Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Reiner, Caecilia S., E-mail: caecilia.reiner@usz.ch; Gordic, Sonja; Puippe, Gilbert; Morsbach, Fabian; Wurnig, Moritz [University Hospital Zurich, Institute of Diagnostic and Interventional Radiology (Switzerland); Schaefer, Niklaus; Veit-Haibach, Patrick [University Hospital Zurich, Division of Nuclear Medicine (Switzerland); Pfammatter, Thomas; Alkadhi, Hatem [University Hospital Zurich, Institute of Diagnostic and Interventional Radiology (Switzerland)

    2016-03-15

    PurposeTo evaluate in patients with hepatocellular carcinoma (HCC), whether assessment of tumor heterogeneity by histogram analysis of computed tomography (CT) perfusion helps predicting response to transarterial radioembolization (TARE).Materials and MethodsSixteen patients (15 male; mean age 65 years; age range 47–80 years) with HCC underwent CT liver perfusion for treatment planning prior to TARE with Yttrium-90 microspheres. Arterial perfusion (AP) derived from CT perfusion was measured in the entire tumor volume, and heterogeneity was analyzed voxel-wise by histogram analysis. Response to TARE was evaluated on follow-up imaging (median follow-up, 129 days) based on modified Response Evaluation Criteria in Solid Tumors (mRECIST). Results of histogram analysis and mean AP values of the tumor were compared between responders and non-responders. Receiver operating characteristics were calculated to determine the parameters’ ability to discriminate responders from non-responders.ResultsAccording to mRECIST, 8 patients (50 %) were responders and 8 (50 %) non-responders. Comparing responders and non-responders, the 50th and 75th percentile of AP derived from histogram analysis was significantly different [AP 43.8/54.3 vs. 27.6/34.3 mL min{sup −1} 100 mL{sup −1}); p < 0.05], while the mean AP of HCCs (43.5 vs. 27.9 mL min{sup −1} 100 mL{sup −1}; p > 0.05) was not. Further heterogeneity parameters from histogram analysis (skewness, coefficient of variation, and 25th percentile) did not differ between responders and non-responders (p > 0.05). If the cut-off for the 75th percentile was set to an AP of 37.5 mL min{sup −1} 100 mL{sup −1}, therapy response could be predicted with a sensitivity of 88 % (7/8) and specificity of 75 % (6/8).ConclusionVoxel-wise histogram analysis of pretreatment CT perfusion indicating tumor heterogeneity of HCC improves the pretreatment prediction of response to TARE.

  12. Classification of amyloid status using machine learning with histograms of oriented 3D gradients

    Directory of Open Access Journals (Sweden)

    Liam Cattell

    2016-01-01

    Full Text Available Brain amyloid burden may be quantitatively assessed from positron emission tomography imaging using standardised uptake value ratios. Using these ratios as an adjunct to visual image assessment has been shown to improve inter-reader reliability, however, the amyloid positivity threshold is dependent on the tracer and specific image regions used to calculate the uptake ratio. To address this problem, we propose a machine learning approach to amyloid status classification, which is independent of tracer and does not require a specific set of regions of interest. Our method extracts feature vectors from amyloid images, which are based on histograms of oriented three-dimensional gradients. We optimised our method on 133 18F-florbetapir brain volumes, and applied it to a separate test set of 131 volumes. Using the same parameter settings, we then applied our method to 209 11C-PiB images and 128 18F-florbetaben images. We compared our method to classification results achieved using two other methods: standardised uptake value ratios and a machine learning method based on voxel intensities. Our method resulted in the largest mean distances between the subjects and the classification boundary, suggesting that it is less likely to make low-confidence classification decisions. Moreover, our method obtained the highest classification accuracy for all three tracers, and consistently achieved above 96% accuracy.

  13. Pedestrian detection in crowded scenes with the histogram of gradients principle

    Science.gov (United States)

    Sidla, O.; Rosner, M.; Lypetskyy, Y.

    2006-10-01

    This paper describes a close to real-time scale invariant implementation of a pedestrian detector system which is based on the Histogram of Oriented Gradients (HOG) principle. Salient HOG features are first selected from a manually created very large database of samples with an evolutionary optimization procedure that directly trains a polynomial Support Vector Machine (SVM). Real-time operation is achieved by a cascaded 2-step classifier which uses first a very fast linear SVM (with the same features as the polynomial SVM) to reject most of the irrelevant detections and then computes the decision function with a polynomial SVM on the remaining set of candidate detections. Scale invariance is achieved by running the detector of constant size on scaled versions of the original input images and by clustering the results over all resolutions. The pedestrian detection system has been implemented in two versions: i) fully body detection, and ii) upper body only detection. The latter is especially suited for very busy and crowded scenarios. On a state-of-the-art PC it is able to run at a frequency of 8 - 20 frames/sec.

  14. Towards the elimination of Monte Carlo statistical fluctuation from dose volume histograms for radiotherapy treatment planning

    International Nuclear Information System (INIS)

    Sempau, J.; Bielajew, A.F.

    2000-01-01

    The Monte Carlo calculation of dose for radiotherapy treatment planning purposes introduces unavoidable statistical noise into the prediction of dose in a given volume element (voxel). When the doses in these voxels are summed to produce dose volume histograms (DVHs), this noise translates into a broadening of differential DVHs and correspondingly flatter DVHs. A brute force approach would entail calculating dose for long periods of time - enough to ensure that the DVHs had converged. In this paper we introduce an approach for deconvolving the statistical noise from DVHs, thereby obtaining estimates for converged DVHs obtained about 100 times faster than the brute force approach described above. There are two important implications of this work: (a) decisions based upon DVHs may be made much more economically using the new approach and (b) inverse treatment planning or optimization methods may employ Monte Carlo dose calculations at all stages of the iterative procedure since the prohibitive cost of Monte Carlo calculations at the intermediate calculation steps can be practically eliminated. (author)

  15. Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

    Directory of Open Access Journals (Sweden)

    Yan Koon-Kiu

    2007-11-01

    Full Text Available Abstract Background The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins. Results We introduce a simple mathematical framework based on a stochastic birth-and-death model that allows one to extract some of this information and apply it to the set of all pairs of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster, and H. sapiens. It was found that the histogram of sequence identities p generated by an all-to-all alignment of all protein sequences encoded in a genome is well fitted with a power-law form ~ p-γ with the value of the exponent γ around 4 for the majority of organisms used in this study. This implies that the intra-protein variability of substitution rates is best described by the Gamma-distribution with the exponent α ≈ 0.33. Different features of the shape of such histograms allow us to quantify the ratio between the genome-wide average deletion/duplication rates and the amino-acid substitution rate. Conclusion We separately measure the short-term ("raw" duplication and deletion rates rdup∗ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemOCai3aa0baaSqaaiabbsgaKjabbwha1jabbchaWbqaaiabgEHiQaaaaaa@3283@, rdel∗ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGacaGaaiaabeqaaeqabiWaaaGcbaGaemOCai3aa0baaSqaaiabbsga

  16. Underwater image quality enhancement of sea cucumbers based on improved histogram equalization and wavelet transform

    Directory of Open Access Journals (Sweden)

    Xi Qiao

    2017-09-01

    Full Text Available Sea cucumbers usually live in an environment where lighting and visibility are generally not controllable, which cause the underwater image of sea cucumbers to be distorted, blurred, and severely attenuated. Therefore, the valuable information from such an image cannot be fully extracted for further processing. To solve the problems mentioned above and improve the quality of the underwater images of sea cucumbers, pre-processing of a sea cucumber image is attracting increasing interest. This paper presents a new method based on contrast limited adaptive histogram equalization and wavelet transform (CLAHE-WT to enhance the sea cucumber image quality. CLAHE was used to process the underwater image for increasing contrast based on the Rayleigh distribution, and WT was used for de-noising based on a soft threshold. Qualitative analysis indicated that the proposed method exhibited better performance in enhancing the quality and retaining the image details. For quantitative analysis, the test with 120 underwater images showed that for the proposed method, the mean square error (MSE, peak signal to noise ratio (PSNR, and entropy were 49.2098, 13.3909, and 6.6815, respectively. The proposed method outperformed three established methods in enhancing the visual quality of sea cucumber underwater gray image.

  17. Face Recognition Performance Improvement using a Similarity Score of Feature Vectors based on Probabilistic Histograms

    Directory of Open Access Journals (Sweden)

    SRIKOTE, G.

    2016-08-01

    Full Text Available This paper proposes an improved performance algorithm of face recognition to identify two face mismatch pairs in cases of incorrect decisions. The primary feature of this method is to deploy the similarity score with respect to Gaussian components between two previously unseen faces. Unlike the conventional classical vector distance measurement, our algorithms also consider the plot of summation of the similarity index versus face feature vector distance. A mixture of Gaussian models of labeled faces is also widely applicable to different biometric system parameters. By comparative evaluations, it has been shown that the efficiency of the proposed algorithm is superior to that of the conventional algorithm by an average accuracy of up to 1.15% and 16.87% when compared with 3x3 Multi-Region Histogram (MRH direct-bag-of-features and Principal Component Analysis (PCA-based face recognition systems, respectively. The experimental results show that similarity score consideration is more discriminative for face recognition compared to feature distance. Experimental results of Labeled Face in the Wild (LFW data set demonstrate that our algorithms are suitable for real applications probe-to-gallery identification of face recognition systems. Moreover, this proposed method can also be applied to other recognition systems and therefore additionally improves recognition scores.

  18. Directional Histogram Ratio at Random Probes: A Local Thresholding Criterion for Capillary Images

    Science.gov (United States)

    Lu, Na; Silva, Jharon; Gu, Yu; Gerber, Scott; Wu, Hulin; Gelbard, Harris; Dewhurst, Stephen; Miao, Hongyu

    2013-01-01

    With the development of micron-scale imaging techniques, capillaries can be conveniently visualized using methods such as two-photon and whole mount microscopy. However, the presence of background staining, leaky vessels and the diffusion of small fluorescent molecules can lead to significant complexity in image analysis and loss of information necessary to accurately quantify vascular metrics. One solution to this problem is the development of accurate thresholding algorithms that reliably distinguish blood vessels from surrounding tissue. Although various thresholding algorithms have been proposed, our results suggest that without appropriate pre- or post-processing, the existing approaches may fail to obtain satisfactory results for capillary images that include areas of contamination. In this study, we propose a novel local thresholding algorithm, called directional histogram ratio at random probes (DHR-RP). This method explicitly considers the geometric features of tube-like objects in conducting image binarization, and has a reliable performance in distinguishing small vessels from either clean or contaminated background. Experimental and simulation studies suggest that our DHR-RP algorithm is superior over existing thresholding methods. PMID:23525856

  19. First impressions of 3D visual tools and dose volume histograms for plan evaluation

    International Nuclear Information System (INIS)

    Rattray, G.; Simitcioglu, A.; Parkinson, M.; Biggs, J.

    1999-01-01

    Converting from 2D to 3D treatment planning offers numerous challenges. The practices that have evolved in the 2D environment may not be applicable when translated into the 3D environment. One such practice is the methods used to evaluate a plan. In 2D planning a plane by plane comparison method is generally practiced. This type of evaluation method would not be appropriate for plans produced by a 3D planning system. To this end 3D dose displays and Dose Volume Histograms (DVHs) have been developed to facilitate the evaluation of such plans. A survey was conducted to determine the impressions of Radiation Therapists as they used these tools for the first time. The survey involved comparing a number of plans for a small group of patients and selecting the best plan for each patient. Three evaluation methods were assessed. These included the traditional plane by plane, 3D dose display, and DVHs. Those surveyed found the DVH to be the easiest of the three methods to use, with the 3D display being the next easiest. Copyright (1999) Blackwell Science Pty Ltd

  20. Thai Finger-Spelling Recognition Using a Cascaded Classifier Based on Histogram of Orientation Gradient Features

    Directory of Open Access Journals (Sweden)

    Kittasil Silanon

    2017-01-01

    Full Text Available Hand posture recognition is an essential module in applications such as human-computer interaction (HCI, games, and sign language systems, in which performance and robustness are the primary requirements. In this paper, we proposed automatic classification to recognize 21 hand postures that represent letters in Thai finger-spelling based on Histogram of Orientation Gradient (HOG feature (which is applied with more focus on the information within certain region of the image rather than each single pixel and Adaptive Boost (i.e., AdaBoost learning technique to select the best weak classifier and to construct a strong classifier that consists of several weak classifiers to be cascaded in detection architecture. We collected 21 static hand posture images from 10 subjects for testing and training in Thai letters finger-spelling. The parameters for the training process have been adjusted in three experiments, false positive rates (FPR, true positive rates (TPR, and number of training stages (N, to achieve the most suitable training model for each hand posture. All cascaded classifiers are loaded into the system simultaneously to classify different hand postures. A correlation coefficient is computed to distinguish the hand postures that are similar. The system achieves approximately 78% accuracy on average on all classifier experiments.

  1. Action Recognition Using 3D Histograms of Texture and A Multi-Class Boosting Classifier.

    Science.gov (United States)

    Zhang, Baochang; Yang, Yun; Chen, Chen; Yang, Linlin; Han, Jungong; Shao, Ling

    2017-10-01

    Human action recognition is an important yet challenging task. This paper presents a low-cost descriptor called 3D histograms of texture (3DHoTs) to extract discriminant features from a sequence of depth maps. 3DHoTs are derived from projecting depth frames onto three orthogonal Cartesian planes, i.e., the frontal, side, and top planes, and thus compactly characterize the salient information of a specific action, on which texture features are calculated to represent the action. Besides this fast feature descriptor, a new multi-class boosting classifier (MBC) is also proposed to efficiently exploit different kinds of features in a unified framework for action classification. Compared with the existing boosting frameworks, we add a new multi-class constraint into the objective function, which helps to maintain a better margin distribution by maximizing the mean of margin, whereas still minimizing the variance of margin. Experiments on the MSRAction3D, MSRGesture3D, MSRActivity3D, and UTD-MHAD data sets demonstrate that the proposed system combining 3DHoTs and MBC is superior to the state of the art.

  2. Histogram-Based Thresholding for Detection and Quantification of Hemorrhages in Retinal Images

    Directory of Open Access Journals (Sweden)

    Hussain Fadhel Hamdan Jaafar

    2016-12-01

    Full Text Available Retinal image analysis is commonly used for the detection and quantification of retinal diabetic retinopathy. In retinal images, dark lesions including hemorrhages and microaneurysms are the earliest warnings of vision loss. In this paper, new algorithm for extraction and quantification of hemorrhages in fundus images is presented. Hemorrhage candidates are extracted in a preliminary step as a coarse segmentation followed by a fine segmentation step. Local variation processes are applied in the coarse segmentation step to determine boundaries of all candidates with distinct edges. Fine segmentation processes are based on histogram thresholding to extract real hemorrhages from the segmented candidates locally. The proposed method was trained and tested using an image dataset of 153 manually labeled retinal images. At the pixel level, the proposed method could identify abnormal retinal images with 90.7% sensitivity and 85.1% predictive value. Due to its distinctive performance measurements, this technique demonstrates that it could be used for a computer-aided mass screening of retinal diseases.

  3. Fast and efficient search for MPEG-4 video using adjacent pixel intensity difference quantization histogram feature

    Science.gov (United States)

    Lee, Feifei; Kotani, Koji; Chen, Qiu; Ohmi, Tadahiro

    2010-02-01

    In this paper, a fast search algorithm for MPEG-4 video clips from video database is proposed. An adjacent pixel intensity difference quantization (APIDQ) histogram is utilized as the feature vector of VOP (video object plane), which had been reliably applied to human face recognition previously. Instead of fully decompressed video sequence, partially decoded data, namely DC sequence of the video object are extracted from the video sequence. Combined with active search, a temporal pruning algorithm, fast and robust video search can be realized. The proposed search algorithm has been evaluated by total 15 hours of video contained of TV programs such as drama, talk, news, etc. to search for given 200 MPEG-4 video clips which each length is 15 seconds. Experimental results show the proposed algorithm can detect the similar video clip in merely 80ms, and Equal Error Rate (ERR) of 2 % in drama and news categories are achieved, which are more accurately and robust than conventional fast video search algorithm.

  4. Automatic Samples Selection Using Histogram of Oriented Gradients (HOG Feature Distance

    Directory of Open Access Journals (Sweden)

    Inzar Salfikar

    2018-01-01

    Full Text Available Finding victims at a disaster site is the primary goal of Search-and-Rescue (SAR operations. Many technologies created from research for searching disaster victims through aerial imaging. but, most of them are difficult to detect victims at tsunami disaster sites with victims and backgrounds which are look similar. This research collects post-tsunami aerial imaging data from the internet to builds dataset and model for detecting tsunami disaster victims. Datasets are built based on distance differences from features every sample using Histogram-of-Oriented-Gradient (HOG method. We use the longest distance to collect samples from photo to generate victim and non-victim samples. We claim steps to collect samples by measuring HOG feature distance from all samples. the longest distance between samples will take as a candidate to build the dataset, then classify victim (positives and non-victim (negatives samples manually. The dataset of tsunami disaster victims was re-analyzed using cross-validation Leave-One-Out (LOO with Support-Vector-Machine (SVM method. The experimental results show the performance of two test photos with 61.70% precision, 77.60% accuracy, 74.36% recall and f-measure 67.44% to distinguish victim (positives and non-victim (negatives.

  5. Autonomous dynamic obstacle avoidance for bacteria-powered microrobots (BPMs with modified vector field histogram.

    Directory of Open Access Journals (Sweden)

    Hoyeon Kim

    Full Text Available In order to broaden the use of microrobots in practical fields, autonomous control algorithms such as obstacle avoidance must be further developed. However, most previous studies of microrobots used manual motion control to navigate past tight spaces and obstacles while very few studies demonstrated the use of autonomous motion. In this paper, we demonstrated a dynamic obstacle avoidance algorithm for bacteria-powered microrobots (BPMs using electric field in fluidic environments. A BPM consists of an artificial body, which is made of SU-8, and a high dense layer of harnessed bacteria. BPMs can be controlled using externally applied electric fields due to the electrokinetic property of bacteria. For developing dynamic obstacle avoidance for BPMs, a kinematic model of BPMs was utilized to prevent collision and a finite element model was used to characteristic the deformation of an electric field near the obstacle walls. In order to avoid fast moving obstacles, we modified our previously static obstacle avoidance approach using a modified vector field histogram (VFH method. To validate the advanced algorithm in experiments, magnetically controlled moving obstacles were used to intercept the BPMs as the BPMs move from the initial position to final position. The algorithm was able to successfully guide the BPMs to reach their respective goal positions while avoiding the dynamic obstacles.

  6. Autonomous dynamic obstacle avoidance for bacteria-powered microrobots (BPMs) with modified vector field histogram.

    Science.gov (United States)

    Kim, Hoyeon; Cheang, U Kei; Kim, Min Jun

    2017-01-01

    In order to broaden the use of microrobots in practical fields, autonomous control algorithms such as obstacle avoidance must be further developed. However, most previous studies of microrobots used manual motion control to navigate past tight spaces and obstacles while very few studies demonstrated the use of autonomous motion. In this paper, we demonstrated a dynamic obstacle avoidance algorithm for bacteria-powered microrobots (BPMs) using electric field in fluidic environments. A BPM consists of an artificial body, which is made of SU-8, and a high dense layer of harnessed bacteria. BPMs can be controlled using externally applied electric fields due to the electrokinetic property of bacteria. For developing dynamic obstacle avoidance for BPMs, a kinematic model of BPMs was utilized to prevent collision and a finite element model was used to characteristic the deformation of an electric field near the obstacle walls. In order to avoid fast moving obstacles, we modified our previously static obstacle avoidance approach using a modified vector field histogram (VFH) method. To validate the advanced algorithm in experiments, magnetically controlled moving obstacles were used to intercept the BPMs as the BPMs move from the initial position to final position. The algorithm was able to successfully guide the BPMs to reach their respective goal positions while avoiding the dynamic obstacles.

  7. Apparent diffusion coefficient histogram shape analysis for monitoring early response in patients with advanced cervical cancers undergoing concurrent chemo-radiotherapy.

    Science.gov (United States)

    Meng, Jie; Zhu, Lijing; Zhu, Li; Wang, Huanhuan; Liu, Song; Yan, Jing; Liu, Baorui; Guan, Yue; Ge, Yun; He, Jian; Zhou, Zhengyang; Yang, Xiaofeng

    2016-10-22

    To explore the role of apparent diffusion coefficient (ADC) histogram shape related parameters in early assessment of treatment response during the concurrent chemo-radiotherapy (CCRT) course of advanced cervical cancers. This prospective study was approved by the local ethics committee and informed consent was obtained from all patients. Thirty-two patients with advanced cervical squamous cell carcinomas underwent diffusion weighted magnetic resonance imaging (b values, 0 and 800 s/mm 2 ) before CCRT, at the end of 2nd and 4th week during CCRT and immediately after CCRT completion. Whole lesion ADC histogram analysis generated several histogram shape related parameters including skewness, kurtosis, s-sD av , width, standard deviation, as well as first-order entropy and second-order entropies. The averaged ADC histograms of 32 patients were generated to visually observe dynamic changes of the histogram shape following CCRT. All parameters except width and standard deviation showed significant changes during CCRT (all P histogram also changed obviously following CCRT. ADC histogram shape analysis held the potential in monitoring early tumor response in patients with advanced cervical cancers undergoing CCRT.

  8. [Characteristics of high resolution diffusion weighted imaging apparent diffusion coefficient histogram and its correlations with cancer stages in patients with nasopharyngeal carcinoma].

    Science.gov (United States)

    Wang, G J; Wang, Y; Ye, Y; Chen, F; Lu, Y T; Li, S L

    2017-11-07

    Objective: To investigate the features of apparent diffusion coefficient (ADC) histogram parameters based on entire tumor volume data in high resolution diffusion weighted imaging of nasopharyngeal carcinoma (NPC) and to evaluate its correlations with cancer stages. Methods: This retrospective study included 154 cases of NPC patients[102 males and 52 females, mean age (48±11) years]who had received readout segmentation of long variable echo trains of MRI scan before radiation therapy. The area of tumor was delineated on each section of axial ADC maps to generate ADC histogram by using Image J. ADC histogram of entire tumor along with the histogram parameters-the tumor voxels, ADC(mean), ADC(25%), ADC(50%), ADC(75%), skewness and kurtosis were obtained by merging all sections with SPSS 22.0 software. Intra-observer repeatability was assessed by using intra-class correlation coefficients (ICC). The patients were subdivided into two groups according to cancer volume: small cancer group (histogram parameters and cancer stages was evaluated with Spearman test. Results: The ICC of measuring ADC histogram parameters of tumor voxels, ADC(mean), ADC(25%), ADC(50%), ADC(75%), skewness, kurtosis was 0.938, 0.861, 0.885, 0.838, 0.836, 0.358 and 0.456, respectively. The tumor voxels was positively correlated with T staging ( r =0.368, P histogram (ADC(mean), ADC(25%), ADC(50%)) increases with T staging in NPC smaller than 2 cm(3).

  9. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens.

    Science.gov (United States)

    Loudig, Olivier; Wang, Tao; Ye, Kenny; Lin, Juan; Wang, Yihong; Ramnauth, Andrew; Liu, Christina; Stark, Azadeh; Chitale, Dhananjay; Greenlee, Robert; Multerer, Deborah; Honda, Stacey; Daida, Yihe; Spencer Feigelson, Heather; Glass, Andrew; Couch, Fergus J; Rohan, Thomas; Ben-Dov, Iddo Z

    2017-03-14

    Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.

  10. The incorporation of specific tissue/nuclide attenuation data into the Anderson method for producing brachytherapy volume-dose histograms

    International Nuclear Information System (INIS)

    Loft, S.M.; Dale, R.G.

    1990-01-01

    Anderson (1986) has proposed an analytical method for deriving volume-dose histograms relating to three-dimensional brachytherapy distributions. Because the mathematical transformation allows the otherwise dominant effects of the inverse-square fall-off about individual sources to be effectively suppressed, resulting histograms provide the potential for visually and numerically assessing overall quality of a brachytherapy treatment. In this paper the Anderson equations have been combined with the radial-dose polynomials of Dale, which are applicable to a number of tissue/nuclide combinations, and the predictions of the combined formalism used to further investigate the physical aspects of brachytherapy dosimetry. The problems associated with the dosimetry of low-energy γ-emitters such as 125 I are once again highlighted, as are potential advantages of using a radionuclide with an intermediate γ-ray energy. (author)

  11. Online: a program to display histograms and control monitor processes on the WA62 VAX data acquisition system at CERN

    International Nuclear Information System (INIS)

    Hand, R.P.

    1981-02-01

    ONLINE is a program which can be launched from any terminal on the WA62 experiment's DEC VAX 11/780 computer when the Native mode data acquisition system is running. It is used to display histograms produced by the various experiment monitor processes running under the system and can establish links with such processes to allow the user to issue monitor commands and change internal monitor process parameters. This report describes the criteria used in the design of ONLINE and shows some of the features of the VAX/VMS Operating System which are used to access histograms produced by monitor processes, to establish communications links with monitor processes and to provide the user with an easy to learn system for the examination of online experimental data in a graphical form. Also given, is a brief account of the way monitor processes are structured and how this structure facilitates user-monitor dialogue. (author)

  12. Histogramming in the LATOME-firmware for the Phase-1 upgrade of the ATLAS LAr calorimeter readout

    Energy Technology Data Exchange (ETDEWEB)

    Horn, Philipp; Hentges, Rainer; Straessner, Arno [Institut fuer Kern- und Teilchenphysik, Dresden (Germany)

    2016-07-01

    Due to the increased luminosity and the higher effective event rate after the phase 1 upgrade the ATLAS LAr detector needs new trigger electronics. The so-called LATOME-Board was designed as a LAr Digital Processing Blade (LPDB) to reconstruct the energy deposited by the particles and is an important part of the read out system. A prototype has already been build and the firmware for the on-board FPGA is under development. The insertion of a histogram-builder in this device gives the unique opportunity to look at untriggered data. This talk provides an insight in the LATOME-firmware and shows the different possibilities to implement the histogram-builder.

  13. Background estimation and player detection in badminton video clips using histogram of pixel values along temporal dimension

    Science.gov (United States)

    Peng, Yahui; Ma, Xiao; Gao, Xinyu; Zhou, Fangxu

    2015-12-01

    Computer vision is an important tool for sports video processing. However, its application in badminton match analysis is very limited. In this study, we proposed a straightforward but robust histogram-based background estimation and player detection methods for badminton video clips, and compared the results with the naive averaging method and the mixture of Gaussians methods, respectively. The proposed method yielded better background estimation results than the naive averaging method and more accurate player detection results than the mixture of Gaussians player detection method. The preliminary results indicated that the proposed histogram-based method could estimate the background and extract the players accurately. We conclude that the proposed method can be used for badminton player tracking and further studies are warranted for automated match analysis.

  14. Clinical experience of laboratory follow-up with noninvasive prena