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Sample records for quantitative histological validation

  1. Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

    Directory of Open Access Journals (Sweden)

    Mekkaoui Choukri

    2012-10-01

    Full Text Available Abstract Background The study of myofiber reorganization in the remote zone after myocardial infarction has been performed in 2D. Microstructural reorganization in remodeled hearts, however, can only be fully appreciated by considering myofibers as continuous 3D entities. The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods Diffusion Tensor CMR of normal human, sheep, and rat hearts, as well as infarcted sheep hearts was performed ex vivo. Fiber tracts were generated with a fourth-order Runge-Kutta integration technique and classified statistically by the median, mean, maximum, or minimum helix angle (HA along the tract. An index of tract coherence was derived from the relationship between these HA statistics. Histological validation was performed using phase-contrast microscopy. Results In normal hearts, the subendocardial and subepicardial myofibers had a positive and negative HA, respectively, forming a symmetric distribution around the midmyocardium. However, in the remote zone of the infarcted hearts, a significant positive shift in HA was observed. The ratio between negative and positive HA variance was reduced from 0.96 ± 0.16 in normal hearts to 0.22 ± 0.08 in the remote zone of the remodeled hearts (p Conclusions A significant reorganization of the 3D fiber continuum is observed in the remote zone of remodeled hearts. The positive (rightward shift in HA in the remote zone is greatest in the subepicardium, but involves all layers of the myocardium. Tractography-based quantification, performed here for the first time in remodeled hearts, may provide a framework for assessing regional changes in the left ventricle following infarction.

  2. Fiber architecture in remodeled myocardium revealed with a quantitative diffusion CMR tractography framework and histological validation

    National Research Council Canada - National Science Library

    Choukri Mekkaoui; Shuning Huang; Howard H Chen; Guangping Dai; Timothy G Reese; William J Kostis; Aravinda Thiagalingam; Pal Maurovich-Horvat; Jeremy N Ruskin; Udo Hoffmann; Marcel P Jackowski; David E Sosnovik

    2012-01-01

    .... The aim of this study was therefore to develop a technique for quantitative 3D diffusion CMR tractography of the heart, and to apply this method to quantify fiber architecture in the remote zone of remodeled hearts. Methods...

  3. Development and validation of a quantitative PCR to detect Parvicapsula minibicornis and comparison to histologically ranked infection of juvenile Chinook salmon, Oncorhynchus tshawytscha (Walbaum), from the Klamath River, USA

    Science.gov (United States)

    True, K.; Purcell, M.K.; Foott, J.S.

    2009-01-01

    Parvicapsula minibicornis is a myxosporean parasite that is associated with disease in Pacific salmon during their freshwater life history phase. This study reports the development of a quantitative (real-time) polymerase chain reaction (QPCR) to detect P. minibicornis DNA. The QPCR assay targets the 18S ribosomal subunit gene. A plasmid DNA control was developed to calibrate cycle threshold (CT) score to plasmid molecular equivalent (PME) units, a measure of gene copy number. Assay validation revealed that the QPCR was sensitive and able to detect 50 ag of plasmid DNA, which was equivalent to 12.5 PME. The QPCR assay could detect single P. minibicornis actinospores well above assay sensitivity, indicating a single spore contains at least 100 times the 18S DNA copies required for detection. The QPCR assay was repeatable and highly specific; no detectable amplification was observed using DNA from related myxozoan parasites. The method was validated using kidney tissues from 218 juvenile Chinook salmon sampled during the emigration period of March to July 2005 from the Klamath River. The QPCR assay was compared with histological examination. The QPCR assay detected P. minibicornis infection in 88.1% of the fish sampled, while histological examination detected infection in 71.1% of the fish sampled. Good concordance was found between the methods as 80% of the samples were in agreement. The majority of the disconcordant fish were positive by QPCR, with low levels of P. minibicornis DNA, but negative by histology. The majority of the fish rated histologically as having subclinical or clinical infections had high QPCR levels. The results of this study demonstrate that QPCR is a sensitive quantitative tool for evaluating P. minibicornis infection in fish health monitoring studies. ?? 2008 Blackwell Publishing Ltd.

  4. Towards Quantitative Ocean Precipitation Validation

    Science.gov (United States)

    Klepp, C.; Bakan, S.; Andersson, A.

    2009-04-01

    A thorough knowledge of global ocean precipitation is an indispensable prerequisite for the understanding and successful modelling of the global climate system as it is an important component of the water cycle. However, reliable detection of quantitative precipitation over the global oceans, especially at high latitudes during the cold season remains a challenging task for remote sensing and model based estimates. Quantitative ship validation data using reliable instruments for measuring rain and snowfall hardly exist but are highly demanded for ground validation of such products. The satellite based HOAPS (Hamburg Ocean Atmosphere Parameters and Fluxes from Satellite Data) climatology contains fields of precipitation, evaporation and the resulting freshwater flux along with 12 additional atmospheric parameters over the global ice-free ocean between 1987 and 2005. Except for the NOAA Pathfinder SST, all basic state variables are calculated from SSM/I passive microwave radiometer measurements. HOAPS contains three main data subsets that originate from one common pixel-level data source. Gridded 0.5 degree monthly, pentad and twice daily data products are freely available from www.hoaps.org. Especially for North Atlantic mid-latitude mix-phase precipitation, the HOAPS precipitation retrieval has been investigated in some depth. This analysis revealed that the HOAPS retrieval qualitatively well represents cyclonic and intense mesoscale precipitation in agreement with ship observations and Cloudsat data, while GPCP, ECMWF forecast, ERA-40 and regional model data miss mesoscale precipitation substantially. As the differences between the investigated data sets are already large under mix-phase precipitation conditions, further work is carried out on snowfall validation during the cold season at high-latitudes. A Norwegian Sea field campaign in winter 2005 was carried out using an optical disdrometer capable of measuring quantitative amounts of snowfall over the ocean

  5. Regional quantitative histological variations in human oral mucosa.

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    Ciano, Joseph; Beatty, Brian Lee

    2015-03-01

    Oral mucosa demonstrates regional variations that reflect contact with food during mastication. Though known qualitatively, our aim was to quantitatively assess regions to establish a measurable baseline from which one could compare in pathological and comparative studies, in which the abrasiveness of diets may differ. We assessed variations in the epithelial-connective tissue junction (rete ridges counts), collagen organization within the lamina propria, and elastin composition of the lamina propria of 15 regions of the labial (buccal) gingiva, lingual gingiva, vestibule, and palate. All characteristics varied more between regions within the same individual than between individuals. Lingual gingiva had high rete ridges counts, high level of collagen organization, and moderate elastin composition compared to other regions. The labial gingiva had few rete ridges, high collagen organization, and low elastin. The vestibule had the fewest average of rete ridges, least organized collagen, and high elastin. The hard palate had the highest average of rete ridges, high collagen organization, and the lowest elastin content. The soft palate conversely had the smallest average of rete ridges, moderate collagen organization, and the highest elastin composition. Our results indicate that comparison of these quantitative histological differences is warranted only for collagen organization and elastin composition. Differences in rete ridges counts were not statistically significant. Most histological characteristics observed were not significantly different between dentulous and edentulous cadavers, and the group containing all individuals. An exception was the level of collagen fiber organization within the lamina propria, which was higher in most regions when teeth were present.

  6. Histological validation of myocardial microstructure obtained from diffusion tensor magnetic resonance imaging.

    Science.gov (United States)

    Scollan, D F; Holmes, A; Winslow, R; Forder, J

    1998-12-01

    Diffusion tensor magnetic resonance imaging (MRI) is a possible new means of elucidating the anatomic structure of the myocardium. It enjoys several advantages over traditional histological approaches, including the ability to rapidly measure fiber organization in isolated, perfused, arrested hearts, thereby avoiding fixation and sectioning of artifacts. However, quantitative validation of this MRI method has been lacking. Here, fiber orientations estimated in the same locations in the same heart using both diffusion tensor MRI and histology are compared in a total of two perfused rabbit hearts. Fiber orientations were statistically similar for both methods and differed on average by 12 degrees at any single location. This is similar to the 10 degrees uncertainty in fiber orientation achieved with histology. In addition, imaging studies performed in a total of seven hearts support a level of organization beyond the myofiber, the recently described laminar organization of the ventricular myocardium.

  7. Derivation and validation of murine histologic alterations resembling asthma, with two proposed histologic grade parameters

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    Sutherland Mhairi

    2009-10-01

    Full Text Available Abstract Background The objective was to define murine histologic alterations resembling asthma in a BALB/c OVA model and to suggest grading criteria. Identified were six salient histologic findings in lungs with putative allergic inflammation: 1 bronchoarterial space inflammation; 2 peri-venular inflammation; 3 inflammation about amuscular blood vessels; 4 inter-alveolar space inflammation, not about capillaries; 5 pleural inflammation; and 6 eosinophils within the inflammatory aggregates. An initial study comprised six groups of twelve mice each: 1 stressed, control; 2 stressed, sensitized; 3 stressed, challenged; 4 not physically stressed, control; 5 not physically stressed, sensitized; 6 not physically stressed, challenged. A second study comprised four experimental groups of twenty mice each: 1 stressed, control; 2 stressed, challenged; 3 not physically stressed, control; 4 not physically stressed, challenged. A third study evaluated two grading criteria, 1 the proportion of non-tracheal respiratory passages with inflammatory aggregates and 2 mitoses in the largest two non-tracheal respiratory passages, in five groups of five mice each, evaluated at different times after the last exposure. Results The first study suggested the six histological findings might reliably indicate the presence of alterations resembling asthma: whereas 82.4% of mice with a complete response had detectable interleukin (IL-5, only 3.8% of mice without one did; whereas 77.8% of mice with a complete response were challenged mice, only 6.7% of mice without complete responses were. The second study revealed that the six histological findings provided a definition that was 97.4% sensitive and 100% specific. The third study found that the odds of a bronchial passage's having inflammation declined 1 when mitoses were present (OR = 0.73, 0.60 - 0.90, and 2 with one day increased time (OR = 0.75, 0.65 - 0.86. Conclusion A definition of murine histologic alterations

  8. Pneumatic distension of ventricular mural architecture validated histologically

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    Burg, M.C.; Heindel, W. [University Hospital Muenster (Germany). Dept. of Clinical Radiology; Lunkenheimer, P. [University Hospital Muenster (Germany). Dept. of Experimental Thoraco-vascular Surgery; Niederer, P. [ETH and University of Zuerich (Switzerland). Inst. for Biomedical Engineering; Brune, C. [Twente Univ. (Netherlands). Dept. of Applied Mathematics; Redmann, K. [University Hospital Muenster (Germany). Center for Reproductive Medicine and Andrology; Smerup, M. [Aarhus University Hospital (Denmark). Dept. of Cardiothoracic and Vascular Surgery; Spiegel, U.; Becker, F. [University Hospital Muenster (Germany). Dept. Surgical Research; Maintz, D. [University Hospital Muenster (Germany). Dept. of Clinical Radiology; Cologne Univ. (Germany). Dept. of Radiology; Anderson, R.H. [Newcastle Univ., London (United Kingdom). Inst. of Genetic Medicine

    2016-11-15

    There are ongoing arguments as to how cardiomyocytes are aggregated together within the ventricular walls. We used pneumatic distension through the coronary arteries to exaggerate the gaps between the aggregated cardiomyocytes, analyzing the pattern revealed using computed tomography, and validating our findings by histology. We distended 10 porcine hearts, arresting 4 in diastole by infusion of cardioplegic solutions, and 4 in systole by injection of barium chloride. Mural architecture was revealed by computed tomography, measuring also the angulations of the long chains of cardiomyocytes. We prepared the remaining 2 hearts for histology by perfusion with formaldehyde. Increasing pressures of pneumatic distension elongated the ventricular walls, but produced insignificant changes in mural thickness. The distension exaggerated the spaces between the aggregated cardiomyocytes, compartmenting the walls into epicardial, central, and endocardial regions, with a feathered arrangement of transitions between them. Marked variation was noted in the thicknesses of the parts in the different ventricular segments, with no visible anatomical boundaries between them. Measurements of angulations revealed intruding and extruding populations of cardiomyocytes that deviated from a surface-parallel alignment. Scrolling through the stacks of tomographic images revealed marked spiraling of the aggregated cardiomyocytes when traced from base to apex. Our findings call into question the current assumption that cardiomyocytes are uniformly aggregated together in a tangential fashion. There is marked heterogeneity in the architecture of the different ventricular segments, with the aggregated units never extending in a fully transmural fashion.

  9. A combined post-mortem magnetic resonance imaging and quantitative histological study of multiple sclerosis pathology.

    Science.gov (United States)

    Kolasinski, James; Stagg, Charlotte J; Chance, Steven A; Deluca, Gabriele C; Esiri, Margaret M; Chang, Eun-Hyuk; Palace, Jacqueline A; McNab, Jennifer A; Jenkinson, Mark; Miller, Karla L; Johansen-Berg, Heidi

    2012-10-01

    Multiple sclerosis is a chronic inflammatory neurological condition characterized by focal and diffuse neurodegeneration and demyelination throughout the central nervous system. Factors influencing the progression of pathology are poorly understood. One hypothesis is that anatomical connectivity influences the spread of neurodegeneration. This predicts that measures of neurodegeneration will correlate most strongly between interconnected structures. However, such patterns have been difficult to quantify through post-mortem neuropathology or in vivo scanning alone. In this study, we used the complementary approaches of whole brain post-mortem magnetic resonance imaging and quantitative histology to assess patterns of multiple sclerosis pathology. Two thalamo-cortical projection systems were considered based on their distinct neuroanatomy and their documented involvement in multiple sclerosis: lateral geniculate nucleus to primary visual cortex and mediodorsal nucleus of the thalamus to prefrontal cortex. Within the anatomically distinct thalamo-cortical projection systems, magnetic resonance imaging derived cortical thickness was correlated significantly with both a measure of myelination in the connected tract and a measure of connected thalamic nucleus cell density. Such correlations did not exist between these markers of neurodegeneration across different thalamo-cortical systems. Magnetic resonance imaging lesion analysis depicted clearly demarcated subcortical lesions impinging on the white matter tracts of interest; however, quantitation of the extent of lesion-tract overlap failed to demonstrate any appreciable association with the severity of markers of diffuse pathology within each thalamo-cortical projection system. Diffusion-weighted magnetic resonance imaging metrics in both white matter tracts were correlated significantly with a histologically derived measure of tract myelination. These data demonstrate for the first time the relevance of functional

  10. Validation of the prognostic value of histologic scoring systems in primary sclerosing cholangitis

    DEFF Research Database (Denmark)

    de Vries, Elisabeth M G; de Krijger, Manon; Färkkilä, Martti

    2017-01-01

    Histologic scoring systems specific for primary sclerosing cholangitis (PSC) are not validated. We recently determined the applicability and prognostic value of three histological scoring systems in a single PSC cohort. The aim of this study was to validate their prognostic use and reproducibility...

  11. Quantitative model validation techniques: new insights

    CERN Document Server

    Ling, You

    2012-01-01

    This paper develops new insights into quantitative methods for the validation of computational model prediction. Four types of methods are investigated, namely classical and Bayesian hypothesis testing, a reliability-based method, and an area metric-based method. Traditional Bayesian hypothesis testing is extended based on interval hypotheses on distribution parameters and equality hypotheses on probability distributions, in order to validate models with deterministic/stochastic output for given inputs. Two types of validation experiments are considered - fully characterized (all the model/experimental inputs are measured and reported as point values) and partially characterized (some of the model/experimental inputs are not measured or are reported as intervals). Bayesian hypothesis testing can minimize the risk in model selection by properly choosing the model acceptance threshold, and its results can be used in model averaging to avoid Type I/II errors. It is shown that Bayesian interval hypothesis testing...

  12. Multiparametric MRI of Epiphyseal Cartilage Necrosis (Osteochondrosis with Histological Validation in a Goat Model.

    Directory of Open Access Journals (Sweden)

    Luning Wang

    Full Text Available To evaluate multiple MRI parameters in a surgical model of osteochondrosis (OC in goats.Focal ischemic lesions of two different sizes were induced in the epiphyseal cartilage of the medial femoral condyles of goats at 4 days of age by surgical transection of cartilage canal blood vessels. Goats were euthanized and specimens harvested 3, 4, 5, 6, 9 and 10 weeks post-op. Ex vivo MRI scans were conducted at 9.4 Tesla for mapping the T1, T2, T1ρ, adiabatic T1ρ and TRAFF relaxation times of articular cartilage, unaffected epiphyseal cartilage, and epiphyseal cartilage within the area of the induced lesion. After MRI scans, safranin O staining was conducted to validate areas of ischemic necrosis induced in the medial femoral condyles of six goats, and to allow comparison of MRI findings with the semi-quantitative proteoglycan assessment in corresponding safranin O-stained histological sections.All relaxation time constants differentiated normal epiphyseal cartilage from lesions of ischemic cartilage necrosis, and the histological staining results confirmed the proteoglycan (PG loss in the areas of ischemia. In the scanned specimens, all of the measured relaxation time constants were higher in the articular than in the normal epiphyseal cartilage, consistently allowing differentiation between these two tissues.Multiparametric MRI provided a sensitive approach to discriminate between necrotic and viable epiphyseal cartilage and between articular and epiphyseal cartilage, which may be useful for diagnosing and monitoring OC lesions and, potentially, for assessing effectiveness of treatment interventions.

  13. Association of noninvasive quantitative decline in liver fat content on MRI with histologic response in nonalcoholic steatohepatitis

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    Patel, Janki; Bettencourt, Ricki; Cui, Jeffrey; Salotti, Joanie; Hooker, Jonathan; Bhatt, Archana; Hernandez, Carolyn; Nguyen, Phirum; Aryafar, Hamed; Valasek, Mark; Haufe, William; Hooker, Catherine; Richards, Lisa; Sirlin, Claude B.; Loomba, Rohit

    2016-01-01

    Background: Magnetic resonance imaging-estimated proton-density-fat-fraction (MRI-PDFF) has been shown to be a noninvasive, accurate and reproducible imaging-based biomarker for assessing steatosis and treatment response in nonalcoholic steatohepatitis (NASH) clinical trials. However, there are no data on the magnitude of MRI-PDFF reduction corresponding to histologic response in the setting of a NASH clinical trial. The aim of this study was to quantitatively compare the magnitude of MRI-PDFF reduction between histologic responders versus histologic nonresponders in NASH patients. Methods: This study is a secondary analysis of the MOZART trial, which included 50 patients with biopsy-proven NASH randomized to ezetimibe 10 mg/day orally or placebo for 24 weeks. The primary aim was to perform a head-to-head comparative analysis of histologic responders [defined as a ⩾2-point reduction in the nonalcoholic fatty liver disease (NAFLD) Activity Score (NAS) without worsening fibrosis] versus nonresponders, and the corresponding quantitative change in liver fat content measured via MRI-PDFF. Results: Of the 35 patients who underwent paired liver biopsy and MRI-PDFF assessment at the beginning and end of treatment, 10 demonstrated a histologic response. Compared with histologic nonresponders, histologic responders had a statistically significant reduction in MRI-PDFF of −4.1% ± 4.9 versus −0.6 ± 4.1 (p < 0.04) with a mean relative percent change of −29.3% ± 33.0 versus +2.0% ± 24.0 (p < 0.004), respectively. Conclusions: Utilizing paired MRI-PDFF and liver histology data, we demonstrate that a relative reduction of 29% in liver fat on MRI-PDFF is associated with a histologic response in NASH. After external validation by independent research groups, these results can be incorporated into designing future NASH clinical trials, especially those utilizing change in hepatic fat quantified by MRI-PDFF, as a treatment endpoint. PMID:27582882

  14. Quantitative Analysis of Chemotherapeutic Effects in Tumors Using In Vivo Staining and Correlative Histology

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    Heung Kook Choi

    2005-01-01

    Full Text Available Aims: To microscopically analyze the chemotherapeutic response of tumors using in vivo staining based on an annexinV-Cy5.5 probe and independently asses their apoptotic count using quantitative histological analysis. Methods: Lewis Lung Carcinomas cells, that are sensitive (CS-LLC and resistant (CR-LLC to chemotherapy were implanted in nude mice and grown to tumours. Mice were treated with cyclophosphamide and injected with a Cy5.5-annexinV fluorescent probe. In vivo imaging was performed using Fluorescence Molecular Tomography. Subsequently tumours were excised and prepared for histology. The histological tumour sections were stained for apoptosis using a terminal deoxynucleotidyl transferase-mediated nick end labeling (TUNEL assay. A minimum of ten tissue sections were analyzed per tumour for apoptosis quantification by TUNEL staining and corresponding Cy5.5 distribution. Results: We detected higher levels of apoptosis and corresponding higher levels of Cy5.5 fluorescence in the CS-LLC vs. the CR-LLC tumours. The cell count rate on CS-LLC sections over CR-LLC was found to be ∼2 :1 where the corresponding area observed on Cy5.5 distribution measurements revealed a ∼1.7 :1 ratio of CS-LLC over CR-LLC. These observations are consistent with the higher apoptotic index expected from the CS-LLC cell line. Conclusions: Quantitative analysis of histological slices revealed higher fluorescence and higher apoptotic count in the CS-LLC tumour images compared to the CR-LLC tumour images. These observations demonstrate that the annexinV-Cy5.5 probe sensed the chemotherapeutic effect of cyclophospamide and further confirmed in vivo FMT measurements.

  15. Neuronal hypertrophy and mast cells in histologically negative, clinically diagnosed acute appendicitis: a quantitative immunophenotypical analysis.

    Science.gov (United States)

    Amber, Safeena; Mathai, Alka Mary; Naik, Ramadas; Pai, Muktha R; Kumar, Suneet; Prasad, Keerthana

    2010-03-01

    In about 20-25% of appendicectomies performed for clinically suspected acute appendicitis, definite morphological changes are lacking on histopathological examination. The present study was done to investigate whether any changes in neurons and mast cells could be detected in patients presenting with clinical acute appendicitis but found to have normal appendix at histopathology. A descriptive study was conducted on 50 appendix specimens which were categorized as histology-positive acute appendicitis (HPAA), clinically acute appendicitis but histologically negative (HNAA), appendices resected for other causes and appendices from forensic autopsy. A morphometric and quantitative evaluation of nerve fibers and ganglion plexus and its relation to mast cell density were studied. All sections were subjected to hematoxylin and eosin stain, toluidine blue stain, S 100 protein and neuron specific enolase (NSE) immunostaining and a quantitative image analysis system. Mucosal and submucosal neuronal components highlighted by NSE and S100 immunostaining observed in cases of HNAA were comparable to cases of HPAA. With S 100 immunostaining in HNAA cases, the increase in number and size of myentric neuronal plexus were mild in 40% (10/25) cases, moderate in 40% (10/25) and marked in 20% (5/25) cases as compared to 66.7% (10/15) cases of HPAA showing moderate and 33.3% (5/15) cases showing marked increase (p = 0.018). The mean mast cell count was highest in the HNAA cases (2.74) in all the four layers as compared to the HPAA (1.85) and control group (2.05). There was no difference in the relationship of the size of ganglion cells and the mast cell concentration. Neuronal hypertrophy and mast cells may play a role in the pathogenesis of appendicitis-like pain in patients with histologically normal appendices.

  16. Optimisation and validation of methods to assess single nucleotide polymorphisms (SNPs) in archival histological material

    DEFF Research Database (Denmark)

    Andreassen, Christian Nicolaj; Sørensen, Flemming Brandt; Overgaard, J.;

    2004-01-01

    only archival specimens are available. This study was conducted to validate protocols optimised for assessment of SNPs based on paraffin embedded, formalin fixed tissue samples. PATIENTS AND METHODS: In 137 breast cancer patients, three TGFB1 SNPs were assessed based on archival histological specimens...... TGFB1 SNPs was used to provide an indirect validation of the genotyping results. Furthermore, two different methods for DNA extraction were compared (semi-automatic DNA extraction using the ABI Prism 6100 Nucleic Acid PrepStation versus Proteinase K digestion for 5 days followed by boiling and DNA...... precipitation). RESULTS: Assessment of SNPs based on archival histological material is encumbered by a number of obstacles and pitfalls. However, these can be widely overcome by careful optimisation of the methods used for sample selection, DNA extraction and PCR. Within 130 samples that fulfil the criteria...

  17. Quantitative system validation in model driven design

    DEFF Research Database (Denmark)

    Hermanns, Hilger; Larsen, Kim Guldstrand; Raskin, Jean-Francois;

    2010-01-01

    The European STREP project Quasimodo1 develops theory, techniques and tool components for handling quantitative constraints in model-driven development of real-time embedded systems, covering in particular real-time, hybrid and stochastic aspects. This tutorial highlights the advances made, focus...

  18. Stereological assessment of mouse lung parenchyma via nondestructive, multiscale micro-CT imaging validated by light microscopic histology.

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    Vasilescu, Dragos M; Klinge, Christine; Knudsen, Lars; Yin, Leilei; Wang, Ge; Weibel, Ewald R; Ochs, Matthias; Hoffman, Eric A

    2013-03-15

    Quantitative assessment of the lung microstructure using standard stereological methods such as volume fractions of tissue, alveolar surface area, or number of alveoli, are essential for understanding the state of normal and diseased lung. These measures are traditionally obtained from histological sections of the lung tissue, a process that ultimately destroys the three-dimensional (3-D) anatomy of the tissue. In comparison, a novel X-ray-based imaging method that allows nondestructive sectioning and imaging of fixed lungs at multiple resolutions can overcome this limitation. Scanning of the whole lung at high resolution and subsequent regional sampling at ultrahigh resolution without physically dissecting the organ allows the application of design-based stereology for assessment of the whole lung structure. Here we validate multiple stereological estimates performed on micro-computed tomography (μCT) images by comparing them with those obtained via conventional histology on the same mouse lungs. We explore and discuss the potentials and limitations of the two approaches. Histological examination offers higher resolution and the qualitative differentiation of tissues by staining, but ultimately loses 3-D tissue relationships, whereas μCT allows for the integration of morphometric data with the spatial complexity of lung structure. However, μCT has limited resolution satisfactory for the sterological estimates presented in this study but not for differentiation of tissues. We conclude that introducing stereological methods in μCT studies adds value by providing quantitative information on internal structures while not curtailing more complex approaches to the study of lung architecture in the context of physiological or pathological studies.

  19. Quantitative diagnosis of tongue cancer from histological images in an animal model

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    Lu, Guolan; Qin, Xulei; Wang, Dongsheng; Muller, Susan; Zhang, Hongzheng; Chen, Amy; Chen, Zhuo G.; Fei, Baowei

    2016-03-01

    We developed a chemically-induced oral cancer animal model and a computer aided method for tongue cancer diagnosis. The animal model allows us to monitor the progress of the lesions over time. Tongue tissue dissected from mice was sent for histological processing. Representative areas of hematoxylin and eosin stained tissue from tongue sections were captured for classifying tumor and non-tumor tissue. The image set used in this paper consisted of 214 color images (114 tumor and 100 normal tissue samples). A total of 738 color, texture, morphometry and topology features were extracted from the histological images. The combination of image features from epithelium tissue and its constituent nuclei and cytoplasm has been demonstrated to improve the classification results. With ten iteration nested cross validation, the method achieved an average sensitivity of 96.5% and a specificity of 99% for tongue cancer detection. The next step of this research is to apply this approach to human tissue for computer aided diagnosis of tongue cancer.

  20. HisTOOLogy: an open-source tool for quantitative analysis of histological sections.

    Science.gov (United States)

    Magliaro, C; Tirella, A; Mattei, G; Pirone, A; Ahluwalia, A

    2015-12-01

    HisTOOLogy is an open-source software for the quantification of digital colour images of histological sections. The simple graphical user interface enables both expert and non-expert users to rapidly extract useful information from stained tissue sections. The software's main feature is a generalizable colour separation algorithm based on k-means clustering which accurately and reproducibly returns the amount of colour per unit area for any stain, thus allowing the quantification of tissue components. Here we describe HisTOOLogy's algorithms and graphical user interface structure, showing how it can be used to separate different dye colours in several classical stains. In addition, to demonstrate how the tool can be employed to obtain quantitative information on biological tissues, the effect of different hepatic tissue decellularization protocols on cell removal and matrix preservation was assessed through image analysis using HisTOOLogy and compared with conventional DNA and total protein content assays. HisTOOLogy's performance was also compared with ImageJ's colour deconvolution plug-in, demonstrating its advantages in terms of ease of use and speed of colour separation.

  1. Histology as a Valid Tool To Differentiate Fresh from Frozen-Thawed Marinated Fish.

    Science.gov (United States)

    Meistro, Serena; Pezzolato, Marzia; Muscolino, Daniele; Giarratana, Filippo; Baioni, Elisa; Panebianco, Antonio; Bozzetta, Elena

    2016-08-01

    European Commission Regulation (EU) 1276/2011 requires that fishery products intended for raw consumption be frozen at -20°C for not less than 24 h or at -35°C for at least 15 h in order to kill viable parasites other than trematodes. But because marinating processes are not always effective in destroying nematode larvae, raw marinated fish preparations should be frozen before consumption. This study evaluated the performance of a standardized histological method to distinguish between fresh and frozen-thawed raw marinated fish. Sixty anchovy (Engraulis encrasicolus) fillets were sampled: 30 were marinated at +4°C for 24 h, and 30 were frozen at -20°C for 24 h before being marinated for 24 h. All 60 samples were fixed in formalin, processed for paraffin embedding, cut, and stained with hematoxylin and eosin. The slide preparations were examined microscopically by three independent histopathologists and classified as frozen-thawed or negative according to standard operating procedure criteria in use at our laboratory. Performance evaluation of the method showed 100% sensitivity (95% confidence interval [CI], 88.4 to 100%) and 100% specificity (95% CI, 88.4 to 100%), and the interrater agreement (Cohen's kappa) was 1 (95% CI, 0.85 to 1). Histology proved a valid and reliable tool to distinguish fresh from frozen-thawed marinated fish. It can be applied to deliver safe raw fishery products to consumers in order to minimize the risk of anisakidosis.

  2. Photothermal multispectral image cytometry for quantitative histology of nanoparticles and micrometastasis in intact, stained and selectively burned tissues.

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    Nedosekin, Dmitry A; Shashkov, Evgeny V; Galanzha, Ekaterina I; Hennings, Leah; Zharov, Vladimir P

    2010-11-01

    There is a rapidly growing interest in the advanced analysis of histological data and the development of appropriate detection technologies in particular for mapping of nanoparticle distributions in tissue in nanomedicine applications. We evaluated photothermal (PT) scanning cytometry for color-coded imaging, spectral identification, and quantitative detection of individual nanoparticles and abnormal cells in histological samples with and without staining. Using this tool, individual carbon nanotubes, gold nanorods, and melanoma cells with intrinsic melanin markers were identified in unstained (e.g. sentinel lymph nodes) and conventionally-stained tissues. In addition, we introduced a spectral burning technique for histology through selective laser bleaching areas with nondesired absorption background and nanobubble-based PT signal amplification. The obtained data demonstrated the promise of PT cytometry in the analysis of low-absorption samples and mapping of various individual nanoparticles' distribution that would be impossible with existing assays. Comparison of PT cytometry and photoacoustic (PA) cytometry previously developed by us, revealed that these methods supplement each other with a sensitivity advantage (up to 10-fold) of contactless PT technique in assessment of thin (≤100 μm) histological samples, while PA imaging provides characterization of thicker samples which, however, requires an acoustic contact with transducers. A potential of high-speed integrated PT-PA cytometry for express histology and immunohistochemistry of both intact and stained heterogeneous tissues with high sensitivity at the zepromolar concentration level is further highlighted.

  3. Quantitative measurement of retinal ganglion cell populations via histology-based random forest classification.

    Science.gov (United States)

    Hedberg-Buenz, Adam; Christopher, Mark A; Lewis, Carly J; Fernandes, Kimberly A; Dutca, Laura M; Wang, Kai; Scheetz, Todd E; Abràmoff, Michael D; Libby, Richard T; Garvin, Mona K; Anderson, Michael G

    2016-05-01

    The inner surface of the retina contains a complex mixture of neurons, glia, and vasculature, including retinal ganglion cells (RGCs), the final output neurons of the retina and primary neurons that are damaged in several blinding diseases. The goal of the current work was two-fold: to assess the feasibility of using computer-assisted detection of nuclei and random forest classification to automate the quantification of RGCs in hematoxylin/eosin (H&E)-stained retinal whole-mounts; and if possible, to use the approach to examine how nuclear size influences disease susceptibility among RGC populations. To achieve this, data from RetFM-J, a semi-automated ImageJ-based module that detects, counts, and collects quantitative data on nuclei of H&E-stained whole-mounted retinas, were used in conjunction with a manually curated set of images to train a random forest classifier. To test performance, computer-derived outputs were compared to previously published features of several well-characterized mouse models of ophthalmic disease and their controls: normal C57BL/6J mice; Jun-sufficient and Jun-deficient mice subjected to controlled optic nerve crush (CONC); and DBA/2J mice with naturally occurring glaucoma. The result of these efforts was development of RetFM-Class, a command-line-based tool that uses data output from RetFM-J to perform random forest classification of cell type. Comparative testing revealed that manual and automated classifications by RetFM-Class correlated well, with 83.2% classification accuracy for RGCs. Automated characterization of C57BL/6J retinas predicted 54,642 RGCs per normal retina, and identified a 48.3% Jun-dependent loss of cells at 35 days post CONC and a 71.2% loss of RGCs among 16-month-old DBA/2J mice with glaucoma. Output from automated analyses was used to compare nuclear area among large numbers of RGCs from DBA/2J mice (n = 127,361). In aged DBA/2J mice with glaucoma, RetFM-Class detected a decrease in median and mean nucleus size

  4. In vivo optical imaging of human retinal capillary networks using speckle variance optical coherence tomography with quantitative clinico-histological correlation.

    Science.gov (United States)

    Chan, Geoffrey; Balaratnasingam, Chandrakumar; Xu, Jing; Mammo, Zaid; Han, Sherry; Mackenzie, Paul; Merkur, Andrew; Kirker, Andrew; Albiani, David; Sarunic, Marinko V; Yu, Dao-Yi

    2015-07-01

    Retinal capillary networks are critically linked to neuronal health and disease. The ability to perform accurate in vivo examination of human retinal capillary networks is therefore valuable for studying mechanisms that govern retinal homeostasis and retinal vascular diseases. Speckle variance optical coherence tomography (svOCT) is a non-invasive imaging technique that has the capacity to provide angiographic information about the retinal circulation. The application of this technology for studying human retinal capillary networks however has not been validated in a quantifiable manner. We use a custom-built svOCT device to qualitatively and quantitatively study the various capillary networks in the human perifovea. Capillary networks corresponding to the nerve fibre layer (NFL), the retinal ganglion cell/superficial inner plexiform layer (RGC/sIPL), the deep inner plexiform layer/superficial inner nuclear layer (dIPL/sINL) and the deep inner nuclear layer (dINL) are imaged in 9 normal human subjects. Measurements of capillary diameter and capillary density are made from each of these networks and results are compared to post-mortem histological data acquired with confocal scanning laser microscopy. Additionally, retinal capillary measurements from high-resolution fundus fluorescein angiogram (FA) are directly compared with svOCT images from 6 eyes. We demonstrate that svOCT images of capillary networks are morphologically comparable to microscopic images of histological specimens. Similar to histological images in svOCT images, the capillaries in the NFL network run parallel to the direction of RGC axons while capillaries in the dINL network comprise a planar configuration with multiple closed loops. Capillaries in remaining networks are convoluted with a complex three-dimensional architecture. We demonstrate that there is no significant difference in capillary density measurements between svOCT and histology images for all networks. Capillary diameter was

  5. Simple clinical variables predict liver histology in hepatitis C: prospective validation of a clinical prediction model.

    Science.gov (United States)

    Romagnuolo, Joseph; Andrews, Christopher N; Bain, Vincent G; Bonacini, Maurizio; Cotler, Scott J; Ma, Mang; Sherman, Morris

    2005-11-01

    A recent single-center multivariate analysis of hepatitis C (HCV) patients showed that having any two criteria: 1) ferritin > or =200 microg/l and 2) spider nevi and/or albumin clinical prediction model using an independent multicenter sample. Eighty-one patients with previously untreated active chronic HCV underwent physical examination, laboratory investigation, and liver biopsy. Biopsies were read, in blinded fashion, by a single pathologist, using a modified Hytiroglou (1995) scale. The clinical scoring system was correlated with histology; likelihood ratios (LRs), Fisher's exact p-values, and receiver operating characteristics (ROCs) were calculated. Data recording was complete in 77 and 38 patients regarding fibrotic stage and inflammatory grade, respectively. For fibrosis, 3/3 patients with any three criteria (LR 17, positive predictive value (PPV) 100%), 4/5 patients with any two criteria (LR 5.1), and 15/47 with no criteria (LR 0.6, negative predictive value (NPV) 68%) had stage 2 or greater fibrosis on biopsy (p=0.01). For inflammation, 5/5 patients with both criteria (LR 15, PPV 100%), and 8/19 patients with no criteria (LR 0.5, NPV 58%) had moderate-severe inflammation on liver biopsy (p=0.036). When missing variables were assumed to be normal, recalculated LRs were almost identical. An alanine aminotransferase (ALAT) level data set has validated our published model which uses simple clinical variables accurately and significantly to predict hepatic fibrosis and inflammation in HCV patients.

  6. Guided protein extraction from formalin-fixed tissues for quantitative multiplex analysis avoids detrimental effects of histological stains.

    Science.gov (United States)

    Becker, Karl-Friedrich; Schott, Christina; Becker, Ingrid; Höfler, Heinz

    2008-05-01

    Formalin fixed and paraffin embedded (FFPE) tissues are the basis for histopathological diagnosis of many diseases around the world. For translational research and routine diagnostics, protein analysis from FFPE tissues is very important. We evaluated the potential influence of six histological stains, including hematoxylin (Mayer and Gill), fast red, light green, methyl blue and toluidine blue, for yield, electrophoretic mobility in 1-D gels, and immunoreactivity of proteins isolated from formalin-fixed breast cancer tissues. Proteins extracted from stained FFPE tissues using a recently established technique were compared with proteins obtained from the same tissues but without prior histological staining. Western blot and quantitative protein lysate microarray analysis demonstrated that histological staining can result in decreased protein yield but may not have much influence on immunoreactivity and electrophoretic mobility. Interestingly, not all staining protocols tested are compatible with subsequent protein analysis. The commonly used hematoxylin staining was found to be suitable for multiplexed quantitative protein measurement technologies although protein extraction was less efficient. For best results we suggest a guided protein extraction method, in which an adjacent hematoxylin/eosin-stained tissue section is used to control dissection of an unstained specimen for subsequent protein extraction and quantification for research and diagnosis.

  7. Validation of In utero Tractography of Human Fetal Commissural and Internal Capsule Fibers with Histological Structure Tensor Analysis.

    Science.gov (United States)

    Mitter, Christian; Jakab, András; Brugger, Peter C; Ricken, Gerda; Gruber, Gerlinde M; Bettelheim, Dieter; Scharrer, Anke; Langs, Georg; Hainfellner, Johannes A; Prayer, Daniela; Kasprian, Gregor

    2015-01-01

    Diffusion tensor imaging (DTI) and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establish in utero DTI as a clinical imaging tool, an independent comparison between macroscopic imaging and microscopic histology data in the same subject is needed. The present study aimed to cross-validate normal as well as abnormal in utero tractography results of commissural and internal capsule fibers in human fetal brains using postmortem histological structure tensor (ST) analysis. In utero tractography findings from two structurally unremarkable and five abnormal fetal brains were compared to the results of postmortem ST analysis applied to digitalized whole hemisphere sections of the same subjects. An approach to perform ST-based deterministic tractography in histological sections was implemented to overcome limitations in correlating in utero tractography to postmortem histology data. ST analysis and histology-based tractography of fetal brain sections enabled the direct assessment of the anisotropic organization and main fiber orientation of fetal telencephalic layers on a micro- and macroscopic scale, and validated in utero tractography results of corpus callosum and internal capsule fiber tracts. Cross-validation of abnormal in utero tractography results could be achieved in four subjects with agenesis of the corpus callosum (ACC) and in two cases with malformations of internal capsule fibers. In addition, potential limitations of current DTI-based in utero tractography could be demonstrated in several brain regions. Combining the three-dimensional nature of DTI-based in utero tractography with the microscopic resolution provided by histological ST analysis may ultimately facilitate a more complete morphologic

  8. Validation of In utero Tractography of Human Fetal Commissural and Internal Capsule Fibers with Histological Structure Tensor Analysis

    Science.gov (United States)

    Mitter, Christian; Jakab, András; Brugger, Peter C.; Ricken, Gerda; Gruber, Gerlinde M.; Bettelheim, Dieter; Scharrer, Anke; Langs, Georg; Hainfellner, Johannes A.; Prayer, Daniela; Kasprian, Gregor

    2015-01-01

    Diffusion tensor imaging (DTI) and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establish in utero DTI as a clinical imaging tool, an independent comparison between macroscopic imaging and microscopic histology data in the same subject is needed. The present study aimed to cross-validate normal as well as abnormal in utero tractography results of commissural and internal capsule fibers in human fetal brains using postmortem histological structure tensor (ST) analysis. In utero tractography findings from two structurally unremarkable and five abnormal fetal brains were compared to the results of postmortem ST analysis applied to digitalized whole hemisphere sections of the same subjects. An approach to perform ST-based deterministic tractography in histological sections was implemented to overcome limitations in correlating in utero tractography to postmortem histology data. ST analysis and histology-based tractography of fetal brain sections enabled the direct assessment of the anisotropic organization and main fiber orientation of fetal telencephalic layers on a micro- and macroscopic scale, and validated in utero tractography results of corpus callosum and internal capsule fiber tracts. Cross-validation of abnormal in utero tractography results could be achieved in four subjects with agenesis of the corpus callosum (ACC) and in two cases with malformations of internal capsule fibers. In addition, potential limitations of current DTI-based in utero tractography could be demonstrated in several brain regions. Combining the three-dimensional nature of DTI-based in utero tractography with the microscopic resolution provided by histological ST analysis may ultimately facilitate a more complete morphologic

  9. Validation of in utero tractography of human fetal commissural and internal capsule fibers with histological structure tensor analysis

    Directory of Open Access Journals (Sweden)

    Christian eMitter

    2015-12-01

    Full Text Available Diffusion tensor imaging (DTI and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establish in utero DTI as a clinical imaging tool, an independent comparison between macroscopic imaging and microscopic histology data in the same subject is needed. The present study aimed to cross-validate normal as well as abnormal in utero tractography results of commissural and internal capsule fibers in human fetal brains using postmortem histological structure tensor (ST analysis. In utero tractography findings from two structurally unremarkable and five abnormal fetal brains were compared to the results of postmortem ST analysis applied to digitalized whole hemisphere sections of the same subjects. An approach to perform ST-based deterministic tractography in histological sections was implemented to overcome limitations in correlating in utero tractography to postmortem histology data. ST analysis and histology-based tractography of fetal brain sections enabled the direct assessment of the anisotropic organization and main fiber orientation of fetal telencephalic layers on a micro- and macroscopic scale, and validated in utero tractography results of corpus callosum and internal capsule fiber tracts. Cross-validation of abnormal in utero tractography results could be achieved in four subjects with agenesis of the corpus callosum and in two cases with malformations of internal capsule fibers. In addition, potential limitations of current DTI-based in utero tractography could be demonstrated in several brain regions. Combining the three-dimensional nature of DTI-based in utero tractography with the microscopic resolution provided by histological ST analysis may ultimately facilitate a more complete

  10. The ageing and myasthenic thymus: a morphometric study validating a standard procedure in the histological workup of thymic specimens.

    Science.gov (United States)

    Ströbel, Philipp; Moritz, Regina; Leite, Maria Isabel; Willcox, Nick; Chuang, Wen-Yu; Gold, Ralf; Nix, Wilfred; Schalke, Berthold; Kiefer, Reinhard; Müller-Hermelink, Hans-Konrad; Jaretzki Iii, Alfred; Newsom-Davis, John; Marx, Alexander

    2008-09-15

    The thymus is believed to play an important role in the pathogenesis of myasthenia gravis (MG). The 80% of MG patients with anti-acetylcholine receptor autoantibodies fall into three clinical subgroups: 1) thymoma; 2) early-onset MG (histology. We here describe the validated, standardized histological workup and reporting system used in this trial.

  11. Quantitative validation of PEDFLOW for description of unidirectional pedestrian dynamics

    CERN Document Server

    Zhang, J; Chraibi, M; Loehner, R; Haug, E; Gawenat, B

    2015-01-01

    The results of a systematic quantitative validation of PEDFLOW based on the experimental data from FZJ are presented. Unidirectional flow experiments, totaling 28 different combinations with varying entry, corridor and exit widths, were considered. The condition imposed on PEDFLOW was that all the cases should be run with the same input parameters. The exit times and fundamental diagrams for the measuring region were evaluated and compared. This validation process led to modifications and enhancements of the model underlying PEDFLOW. The preliminary conclusions indicate that the results agree well for densities smaller than 3 m-2 and a good agreement is observed even at high densities for the corridors with bcor = 2.4 m, and bcor = 3.0 m. For densities between 1 and 2 m-2 the specific flow and velocities are underpredicted by PEDFLOW.

  12. Quantitative validation of a habitat suitability index for oyster restoration

    Directory of Open Access Journals (Sweden)

    Seth eTheuerkauf

    2016-05-01

    Full Text Available Habitat suitability index (HSI models provide spatially explicit information on the capacity of a given habitat to support a species of interest, and their prevalence has increased dramatically in recent years. Despite caution that the reliability of HSIs must be validated using independent, quantitative data, most HSIs intended to inform terrestrial and marine species management remain unvalidated. Furthermore, of the eight HSI models developed for eastern oyster (Crassostrea virginica restoration and fishery production, none has been validated. Consequently, we developed, calibrated, and validated an HSI for the eastern oyster to identify optimal habitat for restoration in a tributary of Chesapeake Bay, the Great Wicomico River (GWR. The GWR harbors a high density, restored oyster population, and therefore serves as an excellent model system for assessing the validity of the HSI. The HSI was derived from GIS layers of bottom type, salinity, and water depth (surrogate for dissolved oxygen, and was tested using live adult oyster density data from a survey of high vertical relief reefs (HRR and low vertical relief reefs (LRR in the sanctuary network. Live adult oyster density was a statistically-significant sigmoid function of the HSI, which validates the HSI as a robust predictor of suitable oyster reef habitat for rehabilitation or restoration. In addition, HRR had on average 103-116 more adults m^−2 than LRR at a given level of the HSI. For HRR, HSI values ≥0.3 exceeded the accepted restoration target of 50 live adult oysters m^−2. For LRR, the HSI was generally able to predict live adult oyster densities that meet or exceed the target at HSI values ≥0.3. The HSI indicated that there remain large areas of suitable habitat for restoration in the GWR. This study provides a robust framework for HSI model development and validation, which can be refined and applied to other systems and previously developed HSIs to improve the efficacy of

  13. Virtual microscopy: an evaluation of its validity and diagnostic performance in routine histologic diagnosis of skin tumors

    DEFF Research Database (Denmark)

    Nielsen, Patricia Switten; Lindebjerg, Jan; Rasmussen, Jan;

    2010-01-01

    Digitization of histologic slides is associated with many advantages, and its use in routine diagnosis holds great promise. Nevertheless, few articles evaluate virtual microscopy in routine settings. This study is an evaluation of the validity and diagnostic performance of virtual microscopy...... that it is feasible to make histologic diagnosis on the skin tumor types represented in this study using virtual microscopy after pathologists have completed a period of training. Larger studies should be conducted to verify whether virtual microscopy can replace conventional microscopy in routine practice....... in routine histologic diagnosis of skin tumors. Our aim is to investigate whether conventional microscopy of skin tumors can be replaced by virtual microscopy. Ninety-six skin tumors and skin-tumor-like changes were consecutively gathered over a 1-week period. Specimens were routinely processed, and digital...

  14. A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability.

    Science.gov (United States)

    Calabrese, Evan; Badea, Alexandra; Watson, Charles; Johnson, G Allan

    2013-05-01

    There has been growing interest in the role of postnatal brain development in the etiology of several neurologic diseases. The rat has long been recognized as a powerful model system for studying neuropathology and the safety of pharmacologic treatments. However, the complex spatiotemporal changes that occur during rat neurodevelopment remain to be elucidated. This work establishes the first magnetic resonance histology (MRH) atlas of the developing rat brain, with an emphasis on quantitation. The atlas comprises five specimens at each of nine time points, imaged with eight distinct MR contrasts and segmented into 26 developmentally defined brain regions. The atlas was used to establish a timeline of morphometric changes and variability throughout neurodevelopment and represents a quantitative database of rat neurodevelopment for characterizing rat models of human neurologic disease. Published by Elsevier Inc.

  15. MR measurement of luminal water in prostate gland: Quantitative correlation between MRI and histology.

    Science.gov (United States)

    Sabouri, Shirin; Fazli, Ladan; Chang, Silvia D; Savdie, Richard; Jones, Edward C; Goldenberg, S Larry; Black, Peter C; Kozlowski, Piotr

    2017-09-01

    To determine the relationship between parameters measured from luminal water imaging (LWI), a new magnetic resonance imaging (MRI) T2 mapping technique, and the corresponding tissue composition in prostate. In all, 17 patients with prostate cancer were examined with a 3D multiecho spin echo sequence at 3T prior to undergoing radical prostatectomy. Maps of seven MR parameters, called N, T2-short , T2-long , Ashort , Along , geometric mean T2 time (gmT2 ), and luminal water fraction (LWF), were generated using nonnegative least squares (NNLS) analysis of the T2 decay curves. MR parametric maps were correlated to digitized whole-mount histology sections. Percentage area of tissue components, including luminal space, nuclei, and cytoplasm plus stroma, was measured on the histology sections by using color-based image segmentation. Spearman's rank correlation test was used to evaluate the correlation between MR parameters and the corresponding tissue components, with particular attention paid to the correlation between LWF and percentage area of luminal space. N, T2-short , Along , gmT2 , and LWF showed significant correlation (P correlation (P correlation was observed between LWF and luminal space (Spearman's coefficient of rank correlation = 0.75, P correlated with the fractional amount of luminal space in prostatic tissue. This result suggests that LWI can potentially be applied for evaluation of prostatic diseases in which the extent of luminal space differs between normal and abnormal tissues. 1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:861-869. © 2017 International Society for Magnetic Resonance in Medicine.

  16. Quantitative Assessment of Synovial Vascularity Using Contrast-Enhanced Power Doppler Ultrasonography: Correlation with Histologic Findings and MR Imaging Findings in Arthritic Rabbit Knee Model

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sang Hoon; Shin, Myung Jin; Kim, Seong Moon; Kim, Namkug; Suh, Sang Hyun [Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of); Suh, Jin Suck [Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2008-02-15

    To validate contrast-enhanced power Doppler ultrasonography (PD US) for the evaluation of synovial vascularity in an arthritic rabbit knee model in correlation with MR and histological findings. Power Doppler ultrasonography was performed for carrageenin-induced arthritic left knee and control right knee of 13 rabbits, first without and then with sonic contrast agent enhancement (Levovist, Schering, Berlin Germany), followed by gadolinium-enhanced MR imaging. Synovial vascularity was quantitatively assessed by calculating the color pixel area in power Doppler sonography using a computer-aided image analysis program and by grading the enhancement on MR images: grade 1, enhancement of knee joint is less than one-third of the area; grade 2, one-third to two-thirds enhancement; and grade 3, more than two-thirds enhancement. Microvessel density (MVD) was measured on slides stained immunohistochemically for CD31 antigen for histological assessment. The mean area of color pixels in PD US changed from 4.37 to 16.42 mm{sup 2} in the arthritic knee after enhancement (p < 0.05), whereas it changed from 0.77 to 2.31 mm{sup 2} in the control knee (p < 0.05). Arthritic knees had greater power Doppler signal than control knees both before and after contrast administration (p < 0.05). The average MVD was 88 in arthritic knees and 46 in control knees. MVDs correlated with color pixel areas of contrast-enhanced power Doppler imaging in arthritic knees. In MR grading of arthritic knees, five were grade 2 and eight were grade 3. MVD and PD US revealed no significant difference between grade 2 and 3 arthritic knees (p > 0.05). Sonic contrast-enhanced PD US improves the visualization of synovial vascularity and allows quantitative measurement in experimentally induced rabbit arthritic knees.

  17. Histological Validity and Clinical Evidence for Use of Fractional Lasers for Acne Scars

    Science.gov (United States)

    Sardana, Kabir; Garg, Vijay K; Arora, Pooja; Khurana, Nita

    2012-01-01

    Though fractional lasers are widely used for acne scars, very little clinical or histological data based on the objective clinical assessment or the depth of penetration of lasers on in vivo facial tissue are available. The depth probably is the most important aspect that predicts the improvement in acne scars but the studies on histology have little uniformity in terms of substrate (tissue) used, processing and stains used. The variability of the laser setting (dose, pulses and density) makes comparison of the studies difficult. It is easier to compare the end results, histological depth and clinical results. We analysed all the published clinical and histological studies on fractional lasers in acne scars and analysed the data, both clinical and histological, by statistical software to decipher their significance. On statistical analysis, the depth was found to be variable with the 1550-nm lasers achieving a depth of 679 μm versus 10,600 nm (895 μm) and 2940 nm (837 μm) lasers. The mean depth of penetration (in μm) in relation to the energy used, in millijoules (mj), varies depending on the laser studied. This was statistically found to be 12.9–28.5 for Er:glass, 3–54.38 for Er:YAG and 6.28–53.66 for CO2. The subjective clinical improvement was a modest 46%. The lack of objective evaluation of clinical improvement and scar-specific assessment with the lack of appropriate in vivo studies is a case for combining conventional modalities like subcision, punch excision and needling with fractional lasers to achieve optimal results. PMID:23060702

  18. Histological validity and clinical evidence for use of fractional lasers for acne scars

    Directory of Open Access Journals (Sweden)

    Kabir Sardana

    2012-01-01

    Full Text Available Though fractional lasers are widely used for acne scars, very little clinical or histological data based on the objective clinical assessment or the depth of penetration of lasers on in vivo facial tissue are available. The depth probably is the most important aspect that predicts the improvement in acne scars but the studies on histology have little uniformity in terms of substrate (tissue used, processing and stains used. The variability of the laser setting (dose, pulses and density makes comparison of the studies difficult. It is easier to compare the end results, histological depth and clinical results. We analysed all the published clinical and histological studies on fractional lasers in acne scars and analysed the data, both clinical and histological, by statistical software to decipher their significance. On statistical analysis, the depth was found to be variable with the 1550-nm lasers achieving a depth of 679 μm versus 10,600 nm (895 μm and 2940 nm (837 μm lasers. The mean depth of penetration (in μm in relation to the energy used, in millijoules (mj, varies depending on the laser studied. This was statistically found to be 12.9-28.5 for Er:glass, 3-54.38 for Er:YAG and 6.28-53.66 for CO 2 . The subjective clinical improvement was a modest 46%. The lack of objective evaluation of clinical improvement and scar-specific assessment with the lack of appropriate in vivo studies is a case for combining conventional modalities like subcision, punch excision and needling with fractional lasers to achieve optimal results.

  19. Quantitative Histology Studies on the Test in Hybrid Bull of Wild and Domestic Yak

    Institute of Scientific and Technical Information of China (English)

    阎萍

    2005-01-01

    The testicular tissue of three types of yak bull (1/2 wild yak,cross 1/2 wild yak and domestic yak) were studied quantitatively at 6,12,18 and 24 months old. The results showed that the average values changed from breed to breed at the same age. But there were no significant difference. The volume density and the height of seminiferous tubule and epithelium increased with the age and testicular weight. The capacity rate of the testicular seminiferous tubule in three types were 78.71% ,75.78% and 78.58% respectively, which nearly reached the level of mature bull.

  20. A comparative study of the quantitative accuracy of three-dimensional reconstructions of spinal cord from serial histological sections.

    Science.gov (United States)

    Duerstock, B S; Bajaj, C L; Borgens, R B

    2003-05-01

    We evaluated the accuracy of estimating the volume of biological soft tissues from their three-dimensional (3D) computer wireframe models, reconstructed from histological data sets obtained from guinea-pig spinal cords. We compared quantification from two methods of three-dimensional surface reconstruction to standard quantitative techniques, Cavalieri method employing planimetry and point counting and Geometric Best-Fitting. This involved measuring a group of spinal cord segments and test objects to evaluate the accuracy of our novel quantification approaches. Once a quantitative methodology was standardized there was no statistical difference in volume measurement of spinal segments between quantification methods. We found that our 3D surface reconstructions' ability to model precisely actual soft tissues provided an accurate volume quantification of complex anatomical structures as standard approaches of Cavalieri estimation and Geometric Best-Fitting. Additionally, 3D reconstruction quantitatively interrogates and three-dimensionally images spinal cord segments and obscured internal pathological features with approximately the same effort required for standard quantification alone.

  1. A Framework for Mixing Methods in Quantitative Measurement Development, Validation, and Revision: A Case Study

    Science.gov (United States)

    Luyt, Russell

    2012-01-01

    A framework for quantitative measurement development, validation, and revision that incorporates both qualitative and quantitative methods is introduced. It extends and adapts Adcock and Collier's work, and thus, facilitates understanding of quantitative measurement development, validation, and revision as an integrated and cyclical set of…

  2. A Framework for Mixing Methods in Quantitative Measurement Development, Validation, and Revision: A Case Study

    Science.gov (United States)

    Luyt, Russell

    2012-01-01

    A framework for quantitative measurement development, validation, and revision that incorporates both qualitative and quantitative methods is introduced. It extends and adapts Adcock and Collier's work, and thus, facilitates understanding of quantitative measurement development, validation, and revision as an integrated and cyclical set of…

  3. Quantitative assessment of optical properties in healthy cartilage and repair tissue by optical coherence tomography and histology (Conference Presentation)

    Science.gov (United States)

    Jansen, Sanne M. A.; Cernohorsky, Paul; de Bruin, Daniel M.; van der Pol, Edwin; Savci-Heijink, Cemile D.; Strackee, Simon D.; Faber, Dirk J.; van Leeuwen, Ton G.

    2016-02-01

    Quantification of the OCT signal is an important step toward clinical implementation of a diagnostic tool in cartilage imaging. Discrimination of structural cartilage differences in patients with osteoarthritis is critical, yet challenging. This study assesses the variation in the optical attenuation coefficient (μOCT) between healthy cartilage, repair tissue, bone and layers within repair tissue in a controlled setting. OCT and histology was used to assess goat talus articular surfaces in which central osteochondral defects were created. Exact matches of OCT and histology were selected for research. μOCT measurements were taken from healthy cartilage, repair tissue and bone. Measured μOCT in healthy cartilage was higher compared to both repair tissue and bone tissue. Two possible mechanisms for the difference in attenuation were investigated. We studied morphological parameters in terms of nucleus count, nucleus size and inter-nucleus distance. Collagen content in healthy cartilage and repair tissue was assessed using polarization microscopy. Quantitative analysis of the nuclei did not demonstrate a difference in nucleus size and count between healthy cartilage and repair tissue. In healthy cartilage, cells were spaced farther apart and had a lower variation in local nuclear density compared to repair tissue. Polarization microscopy suggested higher collagen content in healthy cartilage compared to repair tissue. μOCT measurements can distinguish between healthy cartilage, repair tissue and bone. Results suggest that cartilage OCT attenuation measurements could be of great impact in clinical diagnostics of osteoarthritis.

  4. Assessing agreement between preclinical magnetic resonance imaging and histology: An evaluation of their image qualities and quantitative results.

    Science.gov (United States)

    Elschner, Cindy; Korn, Paula; Hauptstock, Maria; Schulz, Matthias C; Range, Ursula; Jünger, Diana; Scheler, Ulrich

    2017-01-01

    One consequence of demographic change is the increasing demand for biocompatible materials for use in implants and prostheses. This is accompanied by a growing number of experimental animals because the interactions between new biomaterials and its host tissue have to be investigated. To evaluate novel materials and engineered tissues the use of non-destructive imaging modalities have been identified as a strategic priority. This provides the opportunity for studying interactions repeatedly with individual animals, along with the advantages of reduced biological variability and decreased number of laboratory animals. However, histological techniques are still the golden standard in preclinical biomaterial research. The present article demonstrates a detailed method comparison between histology and magnetic resonance imaging. This includes the presentation of their image qualities as well as the detailed statistical analysis for assessing agreement between quantitative measures. Exemplarily, the bony ingrowth of tissue engineered bone substitutes for treatment of a cleft-like maxillary bone defect has been evaluated. By using a graphical concordance analysis the mean difference between MRI results and histomorphometrical measures has been examined. The analysis revealed a slightly but significant bias in the case of the bone volume [Formula: see text] and a clearly significant deviation for the remaining defect width [Formula: see text] But the study although showed a considerable effect of the analyzed section position to the quantitative result. It could be proven, that the bias of the data sets was less originated due to the imaging modalities, but mainly on the evaluation of different slice positions. The article demonstrated that method comparisons not always need the use of an independent animal study, additionally.

  5. Histology as a valid and reliable tool to differentiate fresh from frozen-thawed fish.

    Science.gov (United States)

    Bozzetta, E; Pezzolato, M; Cencetti, E; Varello, K; Abramo, F; Mutinelli, F; Ingravalle, F; Teneggi, E

    2012-08-01

    Selling fish products as fresh when they have actually been frozen and thawed is a common fraudulent practice in seafood retailing. Unlike fish products frozen to protect them against degenerative changes during transportation and to extend the product's storage life, fish intended for raw consumption in European countries must be previously frozen at -20° C for at least 24 h to kill parasites. The aim of this study was to use histological analysis to distinguish between fresh and frozen-thawed fish and to evaluate this method for use as a routine screening technique in compliance with the requirements of European Commission Regulation No. 882/2004 on official food and feed controls. Method performance (i.e., accuracy and precision) was evaluated on tissue samples from three common Mediterranean fish species; the evaluation was subsequently extended to include samples from 35 fish species in a second experiment to test for method robustness. Method accuracy was tested by comparing histological results against a "gold standard" obtained from the analysis of frozen and unfrozen fish samples prepared for the study. Method precision was evaluated according to interrater agreement (i.e., three laboratories with expertise in histopathology in the first experiment and three expert analysts in the second experiment) by estimating Cohen's kappa (and corresponding 95 % confidence intervals) for each pair of laboratories and experts and the combined Cohen's kappa for all three experts and laboratories. The observed interrater agreement among the three laboratories and the three experts indicated high levels of method accuracy and precision (high sensitivity and specificity) and method reproducibility. Our results suggest that histology is a rapid, simple, and highly accurate method for distinguishing between fresh and frozen-thawed fish, regardless of the fish species analyzed.

  6. Microradiography of Microcalcifications in Breast Specimen: A New Histological Correlation Procedure and the Effect of Improved Resolution on Diagnostic Validity

    Directory of Open Access Journals (Sweden)

    H.-J. Langen

    2012-01-01

    Full Text Available Introduction. Does high-resolution visualization of microcalcifications improve diagnostic reliability? Method. X-rays were taken of mamma specimens with microcalcifications in 32 patients (10 malignant; 22 benign using conventional radiography (12 Lp/mm and high-resolution radiography (2000 Lp/mm. Histological sections were subsequently prepared and correlated to the microradiographic image and every calcification was assigned an exact malignant or benign histological diagnosis. Five radiologists classified single groups of calcifications in both methods according to the BIRADS classification system. Results. Using microradiography microcalcifications can be shown in high resolution at the cell level including histological correlation. In some cases, the diagnostic validity was improved by the high resolution in microradiography. In other cases, the high resolution resulted in more visible calcifications, thus giving benign calcifications a malignant appearance. In the BIRADS 2 and 3 group, the probability of malignancy was 28.6% in the conventional radiography evaluation and 37.8% in the microradiography evaluation. In the BIRADS 4 and 5 group, the probability of malignancy was 34.2% in the conventional radiography evaluation and 24.4% in the microradiography evaluation. The differences were not significant. Summary. Overall, the improved resolution in microradiography did not show an improvement in diagnostic accuracy compared to conventional radiography.

  7. Microradiography of microcalcifications in breast specimen: a new histological correlation procedure and the effect of improved resolution on diagnostic validity.

    Science.gov (United States)

    Langen, H-J; Koehler, S; Bielmeier, J; Jocher, R; Kranzfelder, D; Jagusch, N; Treutlein, G; Wetzler, Th; Müller, J; Ott, G

    2012-01-01

    Introduction. Does high-resolution visualization of microcalcifications improve diagnostic reliability? Method. X-rays were taken of mamma specimens with microcalcifications in 32 patients (10 malignant; 22 benign) using conventional radiography (12 Lp/mm) and high-resolution radiography (2000 Lp/mm). Histological sections were subsequently prepared and correlated to the microradiographic image and every calcification was assigned an exact malignant or benign histological diagnosis. Five radiologists classified single groups of calcifications in both methods according to the BIRADS classification system. Results. Using microradiography microcalcifications can be shown in high resolution at the cell level including histological correlation. In some cases, the diagnostic validity was improved by the high resolution in microradiography. In other cases, the high resolution resulted in more visible calcifications, thus giving benign calcifications a malignant appearance. In the BIRADS 2 and 3 group, the probability of malignancy was 28.6% in the conventional radiography evaluation and 37.8% in the microradiography evaluation. In the BIRADS 4 and 5 group, the probability of malignancy was 34.2% in the conventional radiography evaluation and 24.4% in the microradiography evaluation. The differences were not significant. Summary. Overall, the improved resolution in microradiography did not show an improvement in diagnostic accuracy compared to conventional radiography.

  8. Validation of MRI-based 3D digital atlas registration with histological and autoradiographic volumes: an anatomofunctional transgenic mouse brain imaging study.

    Science.gov (United States)

    Lebenberg, J; Hérard, A-S; Dubois, A; Dauguet, J; Frouin, V; Dhenain, M; Hantraye, P; Delzescaux, T

    2010-07-01

    Murine models are commonly used in neuroscience to improve our knowledge of disease processes and to test drug effects. To accurately study neuroanatomy and brain function in small animals, histological staining and ex vivo autoradiography remain the gold standards to date. These analyses are classically performed by manually tracing regions of interest, which is time-consuming. For this reason, only a few 2D tissue sections are usually processed, resulting in a loss of information. We therefore proposed to match a 3D digital atlas with previously 3D-reconstructed post mortem data to automatically evaluate morphology and function in mouse brain structures. We used a freely available MRI-based 3D digital atlas derived from C57Bl/6J mouse brain scans (9.4T). The histological and autoradiographic volumes used were obtained from a preliminary study in APP(SL)/PS1(M146L) transgenic mice, models of Alzheimer's disease, and their control littermates (PS1(M146L)). We first deformed the original 3D MR images to match our experimental volumes. We then applied deformation parameters to warp the 3D digital atlas to match the data to be studied. The reliability of our method was qualitatively and quantitatively assessed by comparing atlas-based and manual segmentations in 3D. Our approach yields faster and more robust results than standard methods in the investigation of post mortem mouse data sets at the level of brain structures. It also constitutes an original method for the validation of an MRI-based atlas using histology and autoradiography as anatomical and functional references, respectively.

  9. Rationalisation and Validation of an Acrylamide-Free Procedure in Three-Dimensional Histological Imaging.

    Directory of Open Access Journals (Sweden)

    Hei Ming Lai

    Full Text Available Three-dimensional visualization of intact tissues is now being achieved by turning tissues transparent. CLARITY is a unique tissue clearing technique, which features the use of detergents to remove lipids from fixed tissues to achieve optical transparency. To preserve tissue integrity, an acrylamide-based hydrogel has been proposed to embed the tissue. In this study, we examined the rationale behind the use of acrylamide in CLARITY, and presented evidence to suggest that the omission of acrylamide-hydrogel embedding in CLARITY does not alter the preservation of tissue morphology and molecular information in fixed tissues. We therefore propose a novel and simplified workflow for formaldehyde-fixed tissue clearing, which will facilitate the laboratory implementation of this technique. Furthermore, we have investigated the basic tissue clearing process in detail and have highlighted some areas for targeted improvement of technologies essential for the emerging subject of three-dimensional histology.

  10. Histology-validated x-ray tomography for imaging human coronary arteries

    Science.gov (United States)

    Buscema, Marzia; Schulz, Georg; Deyhle, Hans; Khimchenko, Anna; Matviykiv, Sofiya; Holme, Margaret N.; Hipp, Alexander; Beckmann, Felix; Saxer, Till; Michaud, Katarzyna; Müller, Bert

    2016-10-01

    Heart disease is the number one cause of death worldwide. To improve therapy and patient outcome, the knowledge of anatomical changes in terms of lumen morphology and tissue composition of constricted arteries is crucial for designing a localized drug delivery to treat atherosclerosis disease. Traditional tissue characterization by histology is a pivotal tool, although it brings disadvantages such as vessel morphology modification during decalcification and slicing. X-ray tomography in absorption and phase contrast modes yields a deep understanding in blood vessel anatomy in healthy and diseased stages: measurements in absorption mode make visible highly absorbing tissue components including cholesterol plaques, whereas phase contrast tomography gains better contrast of the soft tissue components such as vessel walls. Established synchrotron radiation-based micro-CT techniques ensure high performance in terms of 3D visualization of highly absorbing and soft tissues.

  11. Validity of histology for the diagnosis of paediatric coeliac disease: a Swedish multicentre study.

    Science.gov (United States)

    Montén, Caroline; Bjelkenkrantz, Kaj; Gudjonsdottir, Audur H; Browaldh, Lars; Arnell, Henrik; Naluai, Åsa Torinsson; Agardh, Daniel

    2016-01-01

    OBJECTIVE Histological evaluation of intestinal biopsies for the diagnosis of coeliac disease can be challenging and compatible with risk of misdiagnosis. The aim was to evaluate the agreement of pathological diagnosis for coeliac disease in children investigated at four major paediatric university hospitals in Sweden. MATERIALS AND METHODS Intestinal duodenal biopsies were collected from 402 children at median 9.7 years (1.4-18.3 years). A pathologist at each hospital performed the primary evaluation. A designated pathologist, blinded to the primary evaluation, performed a second Marsh classification of biopsies (M0 to M3c) taken from the bulb and duodenum separately. Kappa (κ) scores between first and second evaluation determined the agreement. Plasma samples were collected at the day of intestinal biopsy and analysed for tissue transglutaminase autoantibodies (tTGA) using radioligand-binding assays. RESULTS Marsh scores were concordant in 229/356 biopsies (64%, κ = 0.52, p coeliac disease in 22 children of whom seven children were tTGA positive. CONCLUSIONS The variation between university hospitals on the pathological evaluation of biopsies may lead to misdiagnosis of coeliac disease in paediatric patients. Access to clinical and endoscopic information as well as tTGA levels may be useful for the pathologist to complement the evaluation in dubious cases.

  12. Needle muscle biopsy: technique validation and histological and histochemical methods for evaluating canine skeletal muscles

    Directory of Open Access Journals (Sweden)

    Sérgio de Almeida Braga

    2017-05-01

    Full Text Available This study evaluated the needle muscle biopsy technique using a 6G Bergström percutaneous needle combined with histological and histochemical methods to analyze the skeletal muscle of dogs. There are few studies about canine skeletal muscles and a lack of reports in the literature about tissue collection and analysis for canine species. Evaluation of 32 German Shepherd samples collected from the gluteus medius, at a depth of 3 cm, was performed. The choice of gluteus medius and the 3-cm depth provided good quantity fragments with sufficient sizes (3–5 mm, which permitted optimal visualization of muscle fibers. Myosin ATPase, at pH 9.4, 4.6, and 4.3, and SDH reactions revealed that all muscle samples analyzed had fibers in the classic mosaic arrangement, enabling counting and typification. The mean percentages of fibers were 29.95% for type I and 70.05% for type II. On the basis of these results, we concluded that the percutaneous needle biopsy technique for canine skeletal muscles is a safe and easy procedure that obtains fragments of proper sizes, thereby enabling the study of muscle fibers. Standardization of the muscle of choice and the depth of muscle sample collection significantly contributed to this success. This is an important method to evaluate muscle fiber types of dogs and diagnose important diseases affecting the skeletal muscles.

  13. Application of a quantitative histological health index for Antarctic rock cod (Trematomus bernacchii) from Davis Station, East Antarctica.

    Science.gov (United States)

    Corbett, Patricia A; King, Catherine K; Mondon, Julie A

    2015-08-01

    A quantitative Histological Health Index (HHI) was applied to Antarctic rock cod (Trematomus bernacchii) using gill, liver, spleen, kidney and gonad to assess the impact of wastewater effluent from Davis Station, East Antarctica. A total of 120 fish were collected from 6 sites in the Prydz Bay region of East Antarctica at varying distances from the wastewater outfall. The HHI revealed a greater severity of alteration in fish at the wastewater outfall, which decreased stepwise with distance. Gill and liver displayed the greatest severity of alteration in fish occurring in close proximity to the wastewater outfall, showing severe and pronounced alteration respectively. Findings of the HHI add to a growing weight of evidence indicating that the current level of wastewater treatment at Davis Station is insufficient to prevent impact to the surrounding environment. The HHI for T. bernacchii developed in this study is recommended as a useful risk assessment tool for assessing in situ, sub-lethal impacts from station-derived contamination in coastal regions throughout Antarctica.

  14. Optical-sectioning microscopy of protoporphyrin IX fluorescence in human gliomas: standardization and quantitative comparison with histology

    Science.gov (United States)

    Wei, Linpeng; Chen, Ye; Yin, Chengbo; Borwege, Sabine; Sanai, Nader; Liu, Jonathan T. C.

    2017-04-01

    Systemic delivery of 5-aminolevulinic acid leads to enhanced fluorescence image contrast in many tumors due to the increased accumulation of protoporphyrin IX (PpIX), a fluorescent porphyrin that is associated with tumor burden and proliferation. The value of PpIX-guided resection of malignant gliomas has been demonstrated in prospective randomized clinical studies in which a twofold greater extent of resection and improved progression-free survival have been observed. In low-grade gliomas and at the diffuse infiltrative margins of all gliomas, PpIX fluorescence is often too weak to be detected with current low-resolution surgical microscopes that are used in operating rooms. However, it has been demonstrated that high-resolution optical-sectioning microscopes are capable of detecting the sparse and punctate accumulations of PpIX that are undetectable via conventional low-power surgical fluorescence microscopes. To standardize the performance of high-resolution optical-sectioning devices for future clinical use, we have developed an imaging phantom and methods to ensure that the imaging of PpIX-expressing brain tissues can be performed reproducibly. Ex vivo imaging studies with a dual-axis confocal microscope demonstrate that these methods enable the acquisition of images from unsectioned human brain tissues that quantitatively and consistently correlate with images of histologically processed tissue sections.

  15. Validation, Uncertainty, and Quantitative Reliability at Confidence (QRC)

    Energy Technology Data Exchange (ETDEWEB)

    Logan, R W; Nitta, C K

    2002-12-06

    This paper represents a summary of our methodology for Verification and Validation and Uncertainty Quantification. A graded scale methodology is presented and related to other concepts in the literature. We describe the critical nature of quantified Verification and Validation with Uncertainty Quantification at specified Confidence levels in evaluating system certification status. Only after Verification and Validation has contributed to Uncertainty Quantification at specified confidence can rational tradeoffs of various scenarios be made. Verification and Validation methods for various scenarios and issues are applied in assessments of Quantified Reliability at Confidence and we summarize briefly how this can lead to a Value Engineering methodology for investment strategy.

  16. Primary histologic diagnosis using automated whole slide imaging: a validation study

    Directory of Open Access Journals (Sweden)

    Jukic Drazen M

    2006-04-01

    Full Text Available Abstract Background Only prototypes 5 years ago, high-speed, automated whole slide imaging (WSI systems (also called digital slide systems, virtual microscopes or wide field imagers are becoming increasingly capable and robust. Modern devices can capture a slide in 5 minutes at spatial sampling periods of less than 0.5 micron/pixel. The capacity to rapidly digitize large numbers of slides should eventually have a profound, positive impact on pathology. It is important, however, that pathologists validate these systems during development, not only to identify their limitations but to guide their evolution. Methods Three pathologists fully signed out 25 cases representing 31 parts. The laboratory information system was used to simulate real-world sign-out conditions including entering a full diagnostic field and comment (when appropriate and ordering special stains and recuts. For each case, discrepancies between diagnoses were documented by committee and a "consensus" report was formed and then compared with the microscope-based, sign-out report from the clinical archive. Results In 17 of 25 cases there were no discrepancies between the individual study pathologist reports. In 8 of the remaining cases, there were 12 discrepancies, including 3 in which image quality could be at least partially implicated. When the WSI consensus diagnoses were compared with the original sign-out diagnoses, no significant discrepancies were found. Full text of the pathologist reports, the WSI consensus diagnoses, and the original sign-out diagnoses are available as an attachment to this publication. Conclusion The results indicated that the image information contained in current whole slide images is sufficient for pathologists to make reliable diagnostic decisions and compose complex diagnostic reports. This is a very positive result; however, this does not mean that WSI is as good as a microscope. Virtually every slide had focal areas in which image quality (focus

  17. Experimental validation and clinical comparison of quantitative coronary analysis systems

    NARCIS (Netherlands)

    J. Haase (Jürgen)

    1993-01-01

    textabstractThe kernel topic of this thesis is the validation of QCA systems by a new experimental approach involving the percutaneous insertion of coronary stenosis phantoms in swine coronary arteries. The reliability of digital as well as cinefilm-based QCA systems has been compared on the basis

  18. Improving the validity of quantitative measures in applied linguistics research

    NARCIS (Netherlands)

    Purpura, J.E.; Brown, J.D.; Schoonen, R.

    2015-01-01

    In empirical applied linguistics research it is essential that the key variables are operationalized in a valid and reliable way, and that the scores are treated appropriately, allowing for a proper testing of the hypotheses under investigation. The current article addresses several theoretical and

  19. Improving the Validity of Quantitative Measures in Applied Linguistics Research

    Science.gov (United States)

    Purpura, James E.; Brown, James Dean; Schoonen, Rob

    2015-01-01

    In empirical applied linguistics research it is essential that the key variables are operationalized in a valid and reliable way, and that the scores are treated appropriately, allowing for a proper testing of the hypotheses under investigation. The current article addresses several theoretical and practical issues regarding the use of measurement…

  20. Validation quantitative de quelques procedes de correction phonetique (Quantitative Validation of a Few Procedures of Phonetic Correction)

    Science.gov (United States)

    Intravaia, Pietro

    1977-01-01

    A report on a diagnostic study of the Sicilian way of pronouncing the French /y/. On the basis of this study, a quantitative analysis of verbo-tonal methods of correction is made. Some such methods are based on intonation, rhythm, syllabication and combinatory phonetics. (Text is in French.) (AMH)

  1. Preschool Temperament Assessment: A Quantitative Assessment of the Validity of Behavioral Style Questionnaire Data

    Science.gov (United States)

    Huelsman, Timothy J.; Gagnon, Sandra Glover; Kidder-Ashley, Pamela; Griggs, Marissa Swaim

    2014-01-01

    Research Findings: Child temperament is an important construct, but its measurement has been marked by a number of weaknesses that have diminished the frequency with which it is assessed in practice. We address this problem by presenting the results of a quantitative construct validation study. We calculated validity indices by hypothesizing the…

  2. The Reliability and Validity of Discrete and Continuous Measures of Psychopathology: A Quantitative Review

    Science.gov (United States)

    Markon, Kristian E.; Chmielewski, Michael; Miller, Christopher J.

    2011-01-01

    In 2 meta-analyses involving 58 studies and 59,575 participants, we quantitatively summarized the relative reliability and validity of continuous (i.e., dimensional) and discrete (i.e., categorical) measures of psychopathology. Overall, results suggest an expected 15% increase in reliability and 37% increase in validity through adoption of a…

  3. The Reliability and Validity of Discrete and Continuous Measures of Psychopathology: A Quantitative Review

    Science.gov (United States)

    Markon, Kristian E.; Chmielewski, Michael; Miller, Christopher J.

    2011-01-01

    In 2 meta-analyses involving 58 studies and 59,575 participants, we quantitatively summarized the relative reliability and validity of continuous (i.e., dimensional) and discrete (i.e., categorical) measures of psychopathology. Overall, results suggest an expected 15% increase in reliability and 37% increase in validity through adoption of a…

  4. Quantitative measurement of hypertrophic scar: interrater reliability and concurrent validity.

    Science.gov (United States)

    Nedelec, Bernadette; Correa, José A; Rachelska, Grazyna; Armour, Alexis; LaSalle, Léo

    2008-01-01

    Research into the pathophysiology and treatment of hypertrophic scar (HSc) remains limited by the heterogeneity of scar and the imprecision with which its severity is measured. The objective of this study was to test the interrater reliability and concurrent validity of the Cutometer measurement of elasticity, the Mexameter measurement of erythema and pigmentation, and total thickness measure of the DermaScan C relative to the modified Vancouver Scar Scale (mVSS) in patient-matched normal skin, normal scar, and HSc. Three independent investigators evaluated 128 sites (severe HSc, moderate or mild HSc, donor site, and normal skin) on 32 burn survivors using all of the above measurement tools. The intraclass correlation coefficient, which was used to measure interrater reliability, reflects the inherent amount of error in the measure and is considered acceptable when it is >0.75. Interrater reliability of the totals of the height, pliability, and vascularity subscales of the mVSS fell below the acceptable limit ( congruent with0.50). The individual subscales of the mVSS fell well below the acceptable level (0.89) for each study site with the exception of severe scar. Mexameter and DermaScan C reliability measurements were acceptable for all sites (>0.82). Concurrent validity correlations with the mVSS were significant except for the comparison of the mVSS pliability subscale and the Cutometer maximum deformation measure comparison in severe scar. In conclusion, the Mexameter and DermaScan C measurements of scar color and thickness of all sites, as well as the Cutometer measurement of elasticity in all but the most severe scars shows high interrater reliability. Their significant concurrent validity with the mVSS confirms that these tools are measuring the same traits as the mVSS, and in a more objective way.

  5. Validation of a quantitative phosphorus loss assessment tool.

    Science.gov (United States)

    White, Michael J; Storm, Daniel E; Smolen, Michael D; Busteed, Philip R; Zhang, Hailin; Fox, Garey A

    2014-01-01

    Pasture Phosphorus Management Plus (PPM Plus) is a tool that allows nutrient management and conservation planners to evaluate phosphorus (P) loss from agricultural fields. This tool uses a modified version of the widely used Soil and Water Assessment Tool model with a vastly simplified interface. The development of PPM Plus has been fully described in previous publications; in this article we evaluate the accuracy of PPM Plus using 286 field-years of runoff, sediment, and P validation data from runoff studies at various locations in Oklahoma, Texas, Arkansas, and Georgia. Land uses include pasture, small grains, and row crops with rainfall ranging from 630 to 1390 mm yr, with and without animal manure application. PPM Plus explained 68% of the variability in total P loss, 56% of runoff, and 73% of the variability of sediment yield. An empirical model developed from these data using soil test P, total applied P, slope, and precipitation only accounted for 15% of the variability in total P loss, which implies that a process-based model is required to account for the diversity present in these data. PPM Plus is an easy-to-use conservation planning tool for P loss prediction, which, with modification, could be applicable at the regional and national scales. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  6. The Use of Ex Vivo Whole-organ Imaging and Quantitative Tissue Histology to Determine the Bio-distribution of Fluorescently Labeled Molecules.

    Science.gov (United States)

    McGowan, Jeremy W D; Bidwell, Gene L

    2016-12-24

    Fluorescent labeling is a well-established process for examining the fate of labeled molecules under a variety of experimental conditions both in vitro and in vivo. Fluorescent probes are particularly useful in determining the bio-distribution of administered large molecules, where the addition of a small-molecule fluorescent label is unlikely to affect the kinetics or bio-distribution of the compound. A variety of methods exist to examine bio-distribution that vary significantly in the amount of effort required and whether the resulting measurements are fully quantitative, but using multiple methods in conjunction can provide a rapid and effective system for analyzing bio-distributions. Ex vivo whole-organ imaging is a method that can be used to quickly compare the relative concentrations of fluorescent molecules within tissues and between multiple types of tissues or treatment groups. Using an imaging platform designed for live-animal or whole-organ imaging, fluorescence within intact tissues can be determined without further processing, saving time and labor while providing an accurate picture of the overall bio-distribution. This process is ideal in experiments attempting to determine the tissue specificity of a compound or for the comparison of multiple different compounds. Quantitative tissue histology on the other hand requires extensive further processing of tissues in order to create a quantitative measure of the labeled compounds. To accurately assess bio-distribution, all tissues of interest must be sliced, scanned, and analyzed relative to standard curves in order to make comparisons between tissues or groups. Quantitative tissue histology is the gold standard for determining absolute compound concentrations within tissues. Here, we describe how both methods can be used together effectively to assess the ability of different administration methods and compound modifications to target and deliver fluorescently labeled molecules to the central nervous

  7. Preliminary Evidence of the Reliability and Validity of a Quantitative Measure of Self-Authorship

    Science.gov (United States)

    Creamer, Elizabeth G.; Magolda, Marcia Baxter; Yue, Jessica

    2010-01-01

    This article presents preliminary evidence of the reliability and validity of a measure of self-authorship derived from 18 items in the Career Decision Making Survey. The research conceptualizes a quantitative measure of self-authorship as a three-part score that reflects level of agreement with statements at each of the first three phases of…

  8. Equine preantral follicles obtained via the Biopsy Pick-Up method: histological evaluation and validation of a mechanical isolation technique.

    Science.gov (United States)

    Haag, K T; Magalhães-Padilha, D M; Fonseca, G R; Wischral, A; Gastal, M O; King, S S; Jones, K L; Figueiredo, J R; Gastal, E L

    2013-03-15

    The aims of this study in mares were to: (1) compare preantral follicle parameters between in vitro Biopsy Pick-Up (BPU) and scalpel blade collection methods and between histological and mechanical isolation processing (experiment 1); (2) histologically evaluate preantral follicles (experiment 2); and (3) compare histological analysis with a previously established mechanical isolation technique using a tissue chopper (experiment 3) for ovarian cortical fragments obtained in vivo using a BPU instrument. In experiment 1, preantral follicles were analyzed (N = 220; 90% primordial and 10% primary). Proportions of primordial and primary follicles did not differ (P > 0.05) between tissue collection (BPU vs. scalpel blade dissection) or processing (mechanical isolation vs. histology) methods. Follicle viability and morphology rates were similar (P > 0.05) between tissue collection methods, but mechanical isolation produced more (P 0.05) by processing methods. In conclusion, most parameters evaluated for preantral follicles were similar between histological and tissue chopper processing techniques; hence, mechanical isolation efficiently dissociated equine preantral follicles from the ovarian cortex. Therefore, the tissue chopper could be used to isolate large numbers of morphologically normal equine preantral follicles for cryopreservation and/or in vitro culture.

  9. Laboratory and field validation of a Cry1Ab protein quantitation method for water.

    Science.gov (United States)

    Strain, Katherine E; Whiting, Sara A; Lydy, Michael J

    2014-10-01

    The widespread planting of crops expressing insecticidal proteins derived from the soil bacterium Bacillus thuringiensis (Bt) has given rise to concerns regarding potential exposure to non-target species. These proteins are released from the plant throughout the growing season into soil and surface runoff and may enter adjacent waterways as runoff, erosion, aerial deposition of particulates, or plant debris. It is crucial to be able to accurately quantify Bt protein concentrations in the environment to aid in risk analyses and decision making. Enzyme-linked immunosorbent assay (ELISA) is commonly used for quantitation of Bt proteins in the environment; however, there are no published methods detailing and validating the extraction and quantitation of Bt proteins in water. The objective of the current study was to optimize the extraction of a Bt protein, Cry1Ab, from three water matrices and validate the ELISA method for specificity, precision, accuracy, stability, and sensitivity. Recovery of the Cry1Ab protein was matrix-dependent and ranged from 40 to 88% in the validated matrices, with an overall method detection limit of 2.1 ng/L. Precision among two plates and within a single plate was confirmed with a coefficient of variation less than 20%. The ELISA method was verified in field and laboratory samples, demonstrating the utility of the validated method. The implementation of a validated extraction and quantitation protocol adds consistency and reliability to field-collected data regarding transgenic products.

  10. Validity of gradient-echo three-dimensional delayed gadolinium-enhanced magnetic resonance imaging of hip joint cartilage: A histologically controlled study

    Energy Technology Data Exchange (ETDEWEB)

    Zilkens, Christoph, E-mail: christoph.zilkens@med.uni-duesseldorf.de [Univ Dusseldorf, Medical Faculty, Department of Orthopaedic Surgery, Moorenstraße 5, D-40225 Dusseldorf (Germany); Miese, Falk, E-mail: falk.miese@med.uni-duesseldorf.de [Univ Dusseldorf, Medical Faculty, Department of Diagnostic and Interventional Radiology, Moorenstraße 5, D-40225 Dusseldorf (Germany); Herten, Monika, E-mail: Moherten@web.de [Univ Dusseldorf, Medical Faculty, Department of Orthopaedic Surgery, Moorenstraße 5, D-40225 Dusseldorf (Germany); Kurzidem, Sabine, E-mail: sabine.kurzidem@uni-duesseldorf.de [Univ Dusseldorf, Medical Faculty, Department of Orthopaedic Surgery, Moorenstraße 5, D-40225 Dusseldorf (Germany); Jäger, Marcus [Univ Essen, Medical Faculty, Department of Orthopaedic Surgery, D-45147 Essen (Germany); König, Dietmar, E-mail: Dietmarpierre.koenig@lvr.de [LVR Clinic for Orthopedic Surgery, D-41749 Viersen (Germany); Antoch, Gerald, E-mail: antoch@med.uni-duesseldorf.de [Univ Dusseldorf, Medical Faculty, Department of Diagnostic and Interventional Radiology, Moorenstraße 5, D-40225 Dusseldorf (Germany); Krauspe, Rüdiger, E-mail: krauspe@med.uni-duesseldorf.de [Univ Dusseldorf, Medical Faculty, Department of Orthopaedic Surgery, Moorenstraße 5, D-40225 Dusseldorf (Germany); Bittersohl, Bernd, E-mail: bernd.bittersohl@med.uni-duesseldorf.de [Univ Dusseldorf, Medical Faculty, Department of Orthopaedic Surgery, Moorenstraße 5, D-40225 Dusseldorf (Germany)

    2013-02-15

    Objective: To validate gradient-echo three-dimensional (3D) delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) by means of histological analyses in the assessment of hip joint cartilage. Materials and methods: Twenty-one femoral head specimens collected from 21 patients (7 males, 14 females, mean age: 60.9 ± 9.6 years; range: 37.6–77.3 years), who underwent total hip replacement for symptomatic hip joint osteoarthritis, underwent MRI and histological assessment. A region of 2 cm{sup 2} at the weight-bearing area was marked with four pins to enable multi-planar MRI reformatting to be matched with histological sections. MRI was performed at 3 T with a 3D double-echo steady-state (DESS) sequence for morphological cartilage assessment and 3D Volumetric Interpolated Breathhold Examination (VIBE) for T1{sub Gd} mapping. Histological sections were evaluated according to the Mankin score system. Total Mankin score, grade of toluidine staining (sensitive for glycosaminoglycan content) and a modified Mankin score classification system with four sub-groups of cartilage damage were correlated with MRI data. Results: Spearman's rho correlation analyses revealed a statistically significant correlation between T1{sub Gd} mapping and histological analyses in all categories including total Mankin score (r = −0.658, p-value ≤ 0.001), toluidine staining (r = −0.802, p-value < 0.001) and modified Mankin score (r = −0.716, p-value < 0.001). The correlation between morphological MRI and histological cartilage assessment was statistically significant but inferior to the biochemical cartilage MRI (r-values ranging from −0.411 to 0.525, p-values < 0.001). Conclusions: Gradient-echo dGEMRIC is reliable while offering the unique features of high image resolution and 3D biochemically sensitive MRI for the assessment of early cartilage degeneration.

  11. Placental development in the sheep and its relation to fetal development. A qualitative and quantitative anatomic and histologic study

    NARCIS (Netherlands)

    Stegeman, Jenny H.J.

    1974-01-01

    A quantitative macroscopic and microscopic investigation was performed upon the placenta of the sheep. Macroscopic data were obtained from 235 cases of single pregnancy, 285 cases of twin pregnancy, 45 cases of triplet pregnancy, and from one case of quadrulet pregnancy. Macroscopic data obtained in

  12. The Quantitative Reasoning for College Science (QuaRCS) Assessment, 1: Development and Validation

    CERN Document Server

    Follette, Katherine B; Dokter, Erin; Buxner, Sanlyn; Prather, Edward

    2015-01-01

    Science is an inherently quantitative endeavor, and general education science courses are taken by a majority of college students. As such, they are a powerful venue for advancing students' skills and attitudes toward mathematics. This article reports on the development and validation of the Quantitative Reasoning for College Science (QuaRCS) Assessment, a numeracy assessment instrument designed for college-level general education science students. It has been administered to more than four thousand students over eight semesters of refinement. We show that the QuaRCS is able to distinguish varying levels of quantitative literacy and present performance statistics for both individual items and the instrument as a whole. Responses from a survey of forty-eight Astronomy and Mathematics educators show that these two groups share views regarding which quantitative skills are most important in the contexts of science literacy and educated citizenship, and the skills assessed with the QuaRCS are drawn from these ran...

  13. Reliability and Validity of Quantitative Video Analysis of Baseball Pitching Motion.

    Science.gov (United States)

    Oyama, Sakiko; Sosa, Araceli; Campbell, Rebekah; Correa, Alexandra

    2017-02-01

    Video recordings are used to quantitatively analyze pitchers' techniques. However, reliability and validity of such analysis is unknown. The purpose of the study was to investigate the reliability and validity of joint and segment angles identified during a pitching motion using video analysis. Thirty high school baseball pitchers participated. The pitching motion was captured using 2 high-speed video cameras and a motion capture system. Two raters reviewed the videos to digitize the body segments to calculate 2-dimensional angles. The corresponding 3-dimensional angles were calculated from the motion capture data. Intrarater reliability, interrater reliability, and validity of the 2-dimensional angles were determined. The intrarater and interrater reliability of the 2-dimensional angles were high for most variables. The trunk contralateral flexion at maximum external rotation was the only variable with high validity. Trunk contralateral flexion at ball release, trunk forward flexion at foot contact and ball release, shoulder elevation angle at foot contact, and maximum shoulder external rotation had moderate validity. Two-dimensional angles at the shoulder, elbow, and trunk could be measured with high reliability. However, the angles are not necessarily anatomically correct, and thus use of quantitative video analysis should be limited to angles that can be measured with good validity.

  14. Validation and measurement uncertainty estimation in food microbiology: differences between quantitative and qualitative methods

    Directory of Open Access Journals (Sweden)

    Vesna Režić Dereani

    2010-09-01

    Full Text Available The aim of this research is to describe quality control procedures, procedures for validation and measurement uncertainty (MU determination as an important element of quality assurance in food microbiology laboratory for qualitative and quantitative type of analysis. Accreditation is conducted according to the standard ISO 17025:2007. General requirements for the competence of testing and calibration laboratories, which guarantees the compliance with standard operating procedures and the technical competence of the staff involved in the tests, recently are widely introduced in food microbiology laboratories in Croatia. In addition to quality manual introduction, and a lot of general documents, some of the most demanding procedures in routine microbiology laboratories are measurement uncertainty (MU procedures and validation experiment design establishment. Those procedures are not standardized yet even at international level, and they require practical microbiological knowledge, altogether with statistical competence. Differences between validation experiments design for quantitative and qualitative food microbiology analysis are discussed in this research, and practical solutions are shortly described. MU for quantitative determinations is more demanding issue than qualitative MU calculation. MU calculations are based on external proficiency testing data and internal validation data. In this paper, practical schematic descriptions for both procedures are shown.

  15. Histological and Quantitative Study of the Effect of Eruca Sativa Seed Oil on The Testis of Albino Rat

    Directory of Open Access Journals (Sweden)

    Mona A. R. Salem and Nehal A. Moustafa

    2001-06-01

    Full Text Available Eruca Sativa (E.S or Gargir seed oil is widely used in folk medicine. This study was conducted to investigate its possible effect on male rat fertility. Histological changes of the testis, level of testosterone hormone and sperm count were determined. The results revealed that administration of low dose of E.S. seed oil caused dilatation of the seminiferous tubules, proliferation of spermatogenic cells and increase of its mitotic activity. Increased number of sperms and epididymis weight, elevated level of testosterone hormone and hyperplasia of interstitial Leydig cells have also been noticed. DNA analysis revealed an increase of the percentage of haploid and decrease of diploid and tetraploid cells. Administration of E.S. seed oil at higher dose showed. decreased diameter of the seminiferous tubules, reduced spermatogenic activity and number of sperms . Also testosterone hormone level decreased and the interstitial cells appeared few. DNA analysis showed a reduction of the percentage of the haploid and increase of the percentage of diploid and tetraploid cells.

  16. Evaluation of the quantitative performances of supercritical fluid chromatography: from method development to validation.

    Science.gov (United States)

    Dispas, Amandine; Lebrun, Pierre; Ziemons, Eric; Marini, Roland; Rozet, Eric; Hubert, Philippe

    2014-08-01

    Recently, the number of papers about SFC increased drastically but scientists did not truly focus their work on quantitative performances of this technique. In order to prove the potential of UHPSFC, the present work discussed about the different steps of the analytical life cycle of a method: from development to validation and application. Moreover, the UHPSFC quantitative performances were evaluated in comparison with UHPLC, which is the main technique used for quality control in the pharmaceutical industry and then could be considered as a reference. The methods were developed using Design Space strategy, leading to the optimization of robust method. In this context, when the Design Space optimization shows guarantee of quality, no more robustness study is required prior to the validation. Then, the methods were geometrically transferred in order to reduce the analysis time. The UHPSFC and UHPLC methods were validated based on the total error approach using accuracy profile. Even if UHPLC showed better precision and sensitivity, UHPSFC method is able to give accurate results in a dosing range larger than the 80-120% range required by the European Medicines Agency. Consequently, UHPSFC results are valid and could be used for the control of active substance in a finished pharmaceutical product. Finally, UHPSFC validated method was used to analyse real samples and gave similar results than the reference method (UHPLC).

  17. Validation of In utero Tractography of Human Fetal Commissural and Internal Capsule Fibers with Histological Structure Tensor Analysis

    OpenAIRE

    Mitter, Christian; Jakab, András; Peter C Brugger; Ricken, Gerda; Gruber, Gerlinde M.; Bettelheim, Dieter; Scharrer, Anke; Langs, Georg; Hainfellner, Johannes A.; Prayer, Daniela; Kasprian, Gregor

    2015-01-01

    Diffusion tensor imaging (DTI) and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establish in utero DTI as a clinical imaging tool, an independent comparison between macroscopic imaging and microscopic histology data in the same subjec...

  18. Two- and three-dimensional quantitative image analysis of coronary arteries from high-resolution histological sections

    Science.gov (United States)

    Holmes, David R., III; Robb, Richard A.

    2000-05-01

    appropriate descriptions of these results must be displayed to clinicians in a clear way. Preliminary results are promising, but continued development of algorithms for processing histological data is needed.

  19. Quantitative US Elastography Can Be Used to Quantify Mechanical and Histologic Tendon Healing in a Rabbit Model of Achilles Tendon Transection.

    Science.gov (United States)

    Yamamoto, Yohei; Yamaguchi, Satoshi; Sasho, Takahisa; Fukawa, Taisuke; Akatsu, Yorikazu; Akagi, Ryuichiro; Yamaguchi, Tadashi; Takahashi, Kenji; Nagashima, Kengo; Takahashi, Kazuhisa

    2017-05-01

    Purpose To determine the time-dependent change in strain ratios (SRs) at the healing site of an Achilles tendon rupture in a rabbit model of tendon transection and to assess the correlation between SRs and the mechanical and histologic properties of the healing tissue. Materials and Methods Experimental methods were approved by the institutional animal care and use committee. The Achilles tendons of 24 New Zealand white rabbits (48 limbs) were surgically transected. The SRs of Achilles tendons were calculated by using compression-based quantitative ultrasonographic elastography measurements obtained 2, 4, 8, and 12 weeks after transection. After in vivo elastography, the left Achilles tendon was harvested for mechanical testing of ultimate load, ultimate stress, elastic modulus, and linear stiffness, and the right tendons were harvested for tissue histologic analysis with the Bonar scale. Time-dependent changes in SRs, mechanical parameters, and Bonar scale scores were evaluated by using repeated-measures analysis of variance. The correlation between SRs and each measured variable was evaluated by using the Spearman rank correlation coefficient. Results Mean SRs and Bonar scale values decreased as a function of time after transection, whereas mechanical parameters increased (P tendon. (©) RSNA, 2017 Online supplemental material is available for this article.

  20. Quantitative myocardial perfusion measurement using CT perfusion: a validation study in a porcine model of reperfused acute myocardial infarction.

    Science.gov (United States)

    So, Aaron; Hsieh, Jiang; Li, Jian-Ying; Hadway, Jennifer; Kong, Hua-Fu; Lee, Ting-Yim

    2012-06-01

    We validated a CT perfusion technique with beam hardening (BH) correction for quantitative measurement of myocardial blood flow (MBF). Acute myocardial infarction (AMI) was created in four pigs by occluding the distal LAD for 1 h followed by reperfusion. MBF was measured from dynamic contrast enhanced CT (DCE-CT) scanning of the heart, with correction of cardiac motion and BH, before ischemic insult and on day 7, 10 and 14 post. On day 14 post, radiolabeled microspheres were injected to measure MBF and the results were compared with those measured by CT perfusion. Excised hearts were stained with 2,3,5-triphenyltetrazolium chloride (TTC) to determine the relationship between MBF measured by CT Perfusion and myocardial viability. MBF measured by CT perfusion was strongly correlated with that by microspheres over a wide range of MBF values (R = 0.81, from 25 to 225 ml min(-1) 100 g(-1)). While MBF in the LAD territory decreased significantly from 98.4 ± 2.5 ml min(-1) 100 g(-1) at baseline to 32.2 ± 9.1 ml min(-1) 100 g(-1), P 0.05). TTC staining confirmed incomplete infarction in the LAD territory and no infarction in the LCx territory. Microvascular obstruction in infarcted tissue resulted in no-reflow and hence persistently low MBF in the reperfused LAD territory which contained a mixture of viable and non-viable tissue. CT perfusion measurement of MBF was accurate and correlated well with histology and microspheres measurements.

  1. Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation1[OPEN

    Science.gov (United States)

    Tiffin, Peter; Guhlin, Joseph; Atkins, Paul; Baltes, Nicholas J.; Denny, Roxanne

    2017-01-01

    Genome-wide association (GWA) studies offer the opportunity to identify genes that contribute to naturally occurring variation in quantitative traits. However, GWA relies exclusively on statistical association, so functional validation is necessary to make strong claims about gene function. We used a combination of gene-disruption platforms (Tnt1 retrotransposons, hairpin RNA-interference constructs, and CRISPR/Cas9 nucleases) together with randomized, well-replicated experiments to evaluate the function of genes that an earlier GWA study in Medicago truncatula had identified as candidates contributing to variation in the symbiosis between legumes and rhizobia. We evaluated ten candidate genes found in six clusters of strongly associated single nucleotide polymorphisms, selected on the basis of their strength of statistical association, proximity to annotated gene models, and root or nodule expression. We found statistically significant effects on nodule production for three candidate genes, each validated in two independent mutants. Annotated functions of these three genes suggest their contributions to quantitative variation in nodule production occur through processes not previously connected to nodulation, including phosphorous supply and salicylic acid-related defense response. These results demonstrate the utility of GWA combined with reverse mutagenesis technologies to discover and validate genes contributing to naturally occurring variation in quantitative traits. The results highlight the potential for GWA to complement forward genetics in identifying the genetic basis of ecologically and economically important traits. PMID:28057894

  2. Quantitative Image Analysis of Epithelial and Stromal Area in Histological Sections of Colorectal Cancer: An Emerging Diagnostic Tool

    Directory of Open Access Journals (Sweden)

    R. Rogojanu

    2015-01-01

    Full Text Available In colorectal cancer (CRC, an increase in the stromal (S area with the reduction of the epithelial (E parts has been suggested as an indication of tumor progression. Therefore, an automated image method capable of discriminating E and S areas would allow an improved diagnosis. Immunofluorescence staining was performed on paraffin-embedded sections from colorectal tumors (16 samples from patients with liver metastasis and 18 without. Noncancerous tumor adjacent mucosa (n=5 and normal mucosa (n=4 were taken as controls. Epithelial cells were identified by an anti-keratin 8 (K8 antibody. Large tissue areas (5–63 mm2/slide including tumor center, tumor front, and adjacent mucosa were scanned using an automated microscopy system (TissueFAXS. With our newly developed algorithms, we showed that there is more K8-immunoreactive E in the tumor center than in tumor adjacent and normal mucosa. Comparing patients with and without metastasis, the E/S ratio decreased by 20% in the tumor center and by 40% at tumor front in metastatic samples. The reduction of E might be due to a more aggressive phenotype in metastasis patients. The novel software allowed a detailed morphometric analysis of cancer tissue compartments as tools for objective quantitative measurements, reduced analysis time, and increased reproducibility of the data.

  3. Quantitative imaging of D-2-hydroxyglutarate (D2HG in selected histological tissue areas by a novel bioluminescence technique

    Directory of Open Access Journals (Sweden)

    Nadine Fabienne Voelxen

    2016-03-01

    Full Text Available AbstractPatients with malignant gliomas have a poor prognosis with average survival of less than one year. Whereas in other tumor entities the characteristics of tumor metabolism are successfully used for therapeutic approaches, such developments are very rare in brain tumors, notably in gliomas. One metabolic feature characteristic of gliomas, in particular diffuse astrocytomas and oligodendroglial tumors, is the variable content of D-2-hydroxyglutarate (D2HG, a metabolite, which was discovered first in this tumor entity. D2HG is generated in large amounts due to various gain-of–function mutations in the isocitrate dehydrogenases IDH-1 and IDH-2. Meanwhile, D2HG has been detected in several other tumor entities including intrahepatic bile-duct cancer, chondrosarcoma, acute myeloid leukemia, and angioimmunoblastic T-cell lymphoma. D2HG is barely detectable in healthy tissue (< 0.1 mM, but its concentration increases up to 35 mM in malignant tumor tissues. Consequently, the oncometabolite D2HG has gained increasing interest in the field of tumor metabolism. To facilitate its quantitative measurement without loss of spatial resolution at a microscopical level, we have developed a novel bioluminescence assay for determining D2HG in sections of snap-frozen tissue. The assay was verified independently by photometric tests and liquid chromatography / mass spectrometry (LC/MS. The novel technique allows the microscopically resolved determination of D2HG in a concentration range of 0 – 10 µmol/g tissue (wet weight. In combination with the already established bioluminescence imaging techniques for ATP, glucose, pyruvate, and lactate, the novel D2HG assay enables a comparative characterization of the metabolic profile of individual tumors in a further dimension.

  4. Validation of PCR methods for quantitation of genetically modified plants in food.

    Science.gov (United States)

    Hübner, P; Waiblinger, H U; Pietsch, K; Brodmann, P

    2001-01-01

    For enforcement of the recently introduced labeling threshold for genetically modified organisms (GMOs) in food ingredients, quantitative detection methods such as quantitative competitive (QC-PCR) and real-time PCR are applied by official food control laboratories. The experiences of 3 European food control laboratories in validating such methods were compared to describe realistic performance characteristics of quantitative PCR detection methods. The limit of quantitation (LOQ) of GMO-specific, real-time PCR was experimentally determined to reach 30-50 target molecules, which is close to theoretical prediction. Starting PCR with 200 ng genomic plant DNA, the LOQ depends primarily on the genome size of the target plant and ranges from 0.02% for rice to 0.7% for wheat. The precision of quantitative PCR detection methods, expressed as relative standard deviation (RSD), varied from 10 to 30%. Using Bt176 corn containing test samples and applying Bt176 specific QC-PCR, mean values deviated from true values by -7to 18%, with an average of 2+/-10%. Ruggedness of real-time PCR detection methods was assessed in an interlaboratory study analyzing commercial, homogeneous food samples. Roundup Ready soybean DNA contents were determined in the range of 0.3 to 36%, relative to soybean DNA, with RSDs of about 25%. Taking the precision of quantitative PCR detection methods into account, suitable sample plans and sample sizes for GMO analysis are suggested. Because quantitative GMO detection methods measure GMO contents of samples in relation to reference material (calibrants), high priority must be given to international agreements and standardization on certified reference materials.

  5. Validation procedures for quantitative gluten ELISA methods: AOAC allergen community guidance and best practices.

    Science.gov (United States)

    Koerner, Terry B; Abbott, Michael; Godefroy, Samuel Benrejeb; Popping, Bert; Yeung, Jupiter M; Diaz-Amigo, Carmen; Roberts, James; Taylor, Steve L; Baumert, Joseph L; Ulberth, Franz; Wehling, Paul; Koehler, Peter

    2013-01-01

    The food allergen analytical community is endeavoring to create harmonized guidelines for the validation of food allergen ELISA methodologies to help protect food-sensitive individuals and promote consumer confidence. This document provides additional guidance to existing method validation publications for quantitative food allergen ELISA methods. The gluten-specific criterion provided in this document is divided into sections for information required by the method developer about the assay and information for the implementation of the multilaboratory validation study. Many of these recommendations and guidance are built upon the widely accepted Codex Alimentarius definitions and recommendations for gluten-free foods. The information in this document can be used as the basis of a harmonized validation protocol for any ELISA method for gluten, whether proprietary or nonproprietary, that will be submitted to AOAC andlor regulatory authorities or other bodies for status recognition. Future work is planned for the implementation of this guidance document for the validation of gluten methods and the creation of gluten reference materials.

  6. Validity of a quantitative clinical measurement tool of trunk posture in idiopathic scoliosis.

    Science.gov (United States)

    Fortin, Carole; Feldman, Debbie E; Cheriet, Farida; Labelle, Hubert

    2010-09-01

    Concurrent validity between postural indices obtained from digital photographs (two-dimensional [2D]), surface topography imaging (three-dimensional [3D]), and radiographs. To assess the validity of a quantitative clinical postural assessment tool of the trunk based on photographs (2D) as compared to a surface topography system (3D) as well as indices calculated from radiographs. To monitor progression of scoliosis or change in posture over time in young persons with idiopathic scoliosis (IS), noninvasive and nonionizing methods are recommended. In a clinical setting, posture can be quite easily assessed by calculating key postural indices from photographs. Quantitative postural indices of 70 subjects aged 10 to 20 years old with IS (Cobb angle, 15 degrees -60 degrees) were measured from photographs and from 3D trunk surface images taken in the standing position. Shoulder, scapula, trunk list, pelvis, scoliosis, and waist angles indices were calculated with specially designed software. Frontal and sagittal Cobb angles and trunk list were also calculated on radiographs. The Pearson correlation coefficients (r) was used to estimate concurrent validity of the 2D clinical postural tool of the trunk with indices extracted from the 3D system and with those obtained from radiographs. The correlation between 2D and 3D indices was good to excellent for shoulder, pelvis, trunk list, and thoracic scoliosis (0.81>rrposture among persons with IS. Further, it may contribute to a reduction in the use of radiographs to monitor scoliosis progression.

  7. A quantitative evaluation of gross versus histologic neuroma formation in a rabbit forelimb amputation model: potential implications for the operative treatment and study of neuromas

    Directory of Open Access Journals (Sweden)

    Kuiken Todd A

    2011-10-01

    Full Text Available Abstract Background Surgical treatment of neuromas involves excision of neuromas proximally to the level of grossly "normal" fascicles; however, proximal changes at the axonal level may have both functional and therapeutic implications with regard to amputated nerves. In order to better understand the retrograde "zone of injury" that occurs after nerve transection, we investigated the gross and histologic changes in transected nerves using a rabbit forelimb amputation model. Methods Four New Zealand White rabbits underwent a forelimb amputation with transection and preservation of the median, radial, and ulnar nerves. After 8 weeks, serial sections of the amputated nerves were then obtained in a distal-to-proximal direction toward the brachial plexus. Quantitative histomorphometric analysis was performed on all nerve specimens. Results All nerves demonstrated statistically significant increases in nerve cross-sectional area between treatment and control limbs at the distal nerve end, but these differences were not observed 10 mm more proximal to the neuroma bulb. At the axonal level, an increased number of myelinated fibers were seen at the distal end of all amputated nerves. The number of myelinated fibers progressively decreased in proximal sections, normalizing at 15 mm proximally, or the level of the brachial plexus. The cross-sectional area of myelinated fibers was significantly decreased in all sections of the treatment nerves, indicating that atrophic axonal changes proceed proximally at least to the level of the brachial plexus. Conclusions Morphologic changes at the axonal level extend beyond the region of gross neuroma formation in a distal-to-proximal fashion after nerve transection. This discrepancy between gross and histologic neuromas signifies the need for improved standardization among neuroma models, while also providing a fresh perspective on how we should view neuromas during peripheral nerve surgery.

  8. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions*

    Science.gov (United States)

    Shatsky, Maxim; Dong, Ming; Liu, Haichuan; Yang, Lee Lisheng; Choi, Megan; Singer, Mary E.; Geller, Jil T.; Fisher, Susan J.; Hall, Steven C.; Hazen, Terry C.; Brenner, Steven E.; Butland, Gareth; Jin, Jian; Witkowska, H. Ewa; Chandonia, John-Marc; Biggin, Mark D.

    2016-01-01

    Identifying protein-protein interactions (PPIs) at an acceptable false discovery rate (FDR) is challenging. Previously we identified several hundred PPIs from affinity purification - mass spectrometry (AP-MS) data for the bacteria Escherichia coli and Desulfovibrio vulgaris. These two interactomes have lower FDRs than any of the nine interactomes proposed previously for bacteria and are more enriched in PPIs validated by other data than the nine earlier interactomes. To more thoroughly determine the accuracy of ours or other interactomes and to discover further PPIs de novo, here we present a quantitative tagless method that employs iTRAQ MS to measure the copurification of endogenous proteins through orthogonal chromatography steps. 5273 fractions from a four-step fractionation of a D. vulgaris protein extract were assayed, resulting in the detection of 1242 proteins. Protein partners from our D. vulgaris and E. coli AP-MS interactomes copurify as frequently as pairs belonging to three benchmark data sets of well-characterized PPIs. In contrast, the protein pairs from the nine other bacterial interactomes copurify two- to 20-fold less often. We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome. These PPIs are as strongly validated by other data as our AP-MS interactomes and overlap with our AP-MS interactome for D.vulgaris within 3% of expectation, once FDRs and false negative rates are taken into account. Finally, we reanalyzed data from two quantitative tagless screens of human cell extracts. We estimate that the novel PPIs reported in these studies have an FDR of at least 85% and find that less than 7% of the novel PPIs identified in each screen overlap. Our results establish that a quantitative tagless method can be used to validate and identify PPIs, but that such data must be analyzed carefully to minimize the FDR. PMID:27099342

  9. Segmentation of histological structures for fractal analysis

    Science.gov (United States)

    Dixon, Vanessa; Kouznetsov, Alexei; Tambasco, Mauro

    2009-02-01

    Pathologists examine histology sections to make diagnostic and prognostic assessments regarding cancer based on deviations in cellular and/or glandular structures. However, these assessments are subjective and exhibit some degree of observer variability. Recent studies have shown that fractal dimension (a quantitative measure of structural complexity) has proven useful for characterizing structural deviations and exhibits great potential for automated cancer diagnosis and prognosis. Computing fractal dimension relies on accurate image segmentation to capture the architectural complexity of the histology specimen. For this purpose, previous studies have used techniques such as intensity histogram analysis and edge detection algorithms. However, care must be taken when segmenting pathologically relevant structures since improper edge detection can result in an inaccurate estimation of fractal dimension. In this study, we established a reliable method for segmenting edges from grayscale images. We used a Koch snowflake, an object of known fractal dimension, to investigate the accuracy of various edge detection algorithms and selected the most appropriate algorithm to extract the outline structures. Next, we created validation objects ranging in fractal dimension from 1.3 to 1.9 imitating the size, structural complexity, and spatial pixel intensity distribution of stained histology section images. We applied increasing intensity thresholds to the validation objects to extract the outline structures and observe the effects on the corresponding segmentation and fractal dimension. The intensity threshold yielding the maximum fractal dimension provided the most accurate fractal dimension and segmentation, indicating that this quantitative method could be used in an automated classification system for histology specimens.

  10. Exploring discrepancies between quantitative validation results and the geomorphic plausibility of statistical landslide susceptibility maps

    Science.gov (United States)

    Steger, Stefan; Brenning, Alexander; Bell, Rainer; Petschko, Helene; Glade, Thomas

    2016-06-01

    Empirical models are frequently applied to produce landslide susceptibility maps for large areas. Subsequent quantitative validation results are routinely used as the primary criteria to infer the validity and applicability of the final maps or to select one of several models. This study hypothesizes that such direct deductions can be misleading. The main objective was to explore discrepancies between the predictive performance of a landslide susceptibility model and the geomorphic plausibility of subsequent landslide susceptibility maps while a particular emphasis was placed on the influence of incomplete landslide inventories on modelling and validation results. The study was conducted within the Flysch Zone of Lower Austria (1,354 km2) which is known to be highly susceptible to landslides of the slide-type movement. Sixteen susceptibility models were generated by applying two statistical classifiers (logistic regression and generalized additive model) and two machine learning techniques (random forest and support vector machine) separately for two landslide inventories of differing completeness and two predictor sets. The results were validated quantitatively by estimating the area under the receiver operating characteristic curve (AUROC) with single holdout and spatial cross-validation technique. The heuristic evaluation of the geomorphic plausibility of the final results was supported by findings of an exploratory data analysis, an estimation of odds ratios and an evaluation of the spatial structure of the final maps. The results showed that maps generated by different inventories, classifiers and predictors appeared differently while holdout validation revealed similar high predictive performances. Spatial cross-validation proved useful to expose spatially varying inconsistencies of the modelling results while additionally providing evidence for slightly overfitted machine learning-based models. However, the highest predictive performances were obtained for

  11. A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance

    Directory of Open Access Journals (Sweden)

    Wang Xiaowei

    2008-12-01

    Full Text Available Abstract Background Quantitative polymerase chain reaction (QPCR is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specific amplification of non-target genes has frequently been a problem. Although several online databases have been created for the storage and retrieval of experimentally validated primers, only a few thousand primer pairs are currently present in existing databases and the primers are not designed for use under a common PCR thermal profile. Results We previously reported the implementation of an algorithm to predict PCR primers for most known human and mouse genes. We now report the use of that resource to identify 17483 pairs of primers that have been experimentally verified to amplify unique sequences corresponding to distinct murine transcripts. The primer pairs have been validated by gel electrophoresis, DNA sequence analysis and thermal denaturation profile. In addition to the validation studies, we have determined the uniformity of amplification using the primers and the technical reproducibility of the QPCR reaction using the popular and inexpensive SYBR Green I detection method. Conclusion We have identified an experimentally validated collection of murine primer pairs for PCR and QPCR which can be used under a common PCR thermal profile, allowing the evaluation of transcript abundance of a large number of genes in parallel. This feature is increasingly attractive for confirming and/or making more precise data trends observed from experiments performed with DNA microarrays.

  12. Validating Quantitative Measurement Using Qualitative Data: Combining Rasch Scaling and Latent Semantic Analysis in Psychiatry

    Science.gov (United States)

    Lange, Rense

    2015-02-01

    An extension of concurrent validity is proposed that uses qualitative data for the purpose of validating quantitative measures. The approach relies on Latent Semantic Analysis (LSA) which places verbal (written) statements in a high dimensional semantic space. Using data from a medical / psychiatric domain as a case study - Near Death Experiences, or NDE - we established concurrent validity by connecting NDErs qualitative (written) experiential accounts with their locations on a Rasch scalable measure of NDE intensity. Concurrent validity received strong empirical support since the variance in the Rasch measures could be predicted reliably from the coordinates of their accounts in the LSA derived semantic space (R2 = 0.33). These coordinates also predicted NDErs age with considerable precision (R2 = 0.25). Both estimates are probably artificially low due to the small available data samples (n = 588). It appears that Rasch scalability of NDE intensity is a prerequisite for these findings, as each intensity level is associated (at least probabilistically) with a well- defined pattern of item endorsements.

  13. Definitions and validation criteria for biomarkers and surrogate endpoints: development and testing of a quantitative hierarchical levels of evidence schema

    DEFF Research Database (Denmark)

    Lassere, Marissa N; Johnson, Kent R; Boers, Maarten

    2007-01-01

    of the National Institutes of Health definitions of biomarker, surrogate endpoint, and clinical endpoint was useful. CONCLUSION: Further development and application of this schema provides incentives and guidance for effective biomarker and surrogate endpoint research, and more efficient drug discovery...... endpoints, and leading indicators, a quantitative surrogate validation schema was developed and subsequently evaluated at a stakeholder workshop. RESULTS: The search identified several classification schema and definitions. Components of these were incorporated into a new quantitative surrogate validation...

  14. Validation of quantitative and qualitative methods for detecting allergenic ingredients in processed foods in Japan.

    Science.gov (United States)

    Sakai, Shinobu; Adachi, Reiko; Akiyama, Hiroshi; Teshima, Reiko

    2013-06-19

    A labeling system for food allergenic ingredients was established in Japan in April 2002. To monitor the labeling, the Japanese government announced official methods for detecting allergens in processed foods in November 2002. The official methods consist of quantitative screening tests using enzyme-linked immunosorbent assays (ELISAs) and qualitative confirmation tests using Western blotting or polymerase chain reactions (PCR). In addition, the Japanese government designated 10 μg protein/g food (the corresponding allergenic ingredient soluble protein weight/food weight), determined by ELISA, as the labeling threshold. To standardize the official methods, the criteria for the validation protocol were described in the official guidelines. This paper, which was presented at the Advances in Food Allergen Detection Symposium, ACS National Meeting and Expo, San Diego, CA, Spring 2012, describes the validation protocol outlined in the official Japanese guidelines, the results of interlaboratory studies for the quantitative detection method (ELISA for crustacean proteins) and the qualitative detection method (PCR for shrimp and crab DNAs), and the reliability of the detection methods.

  15. Quantitative regional validation of the visual rating scale for posterior cortical atrophy

    Energy Technology Data Exchange (ETDEWEB)

    Moeller, Christiane; Benedictus, Marije R.; Koedam, Esther L.G.M.; Scheltens, Philip [VU University Medical Center, Alzheimer Center and Department of Neurology, Neuroscience Campus Amsterdam, P.O. Box 7057, Amsterdam (Netherlands); Flier, Wiesje M. van der [VU University Medical Center, Alzheimer Center and Department of Neurology, Neuroscience Campus Amsterdam, P.O. Box 7057, Amsterdam (Netherlands); VU University Medical Center, Department of Epidemiology and Biostatistics, Neuroscience Campus Amsterdam, P.O. Box 7057, Amsterdam (Netherlands); Versteeg, Adriaan; Wattjes, Mike P.; Barkhof, Frederik [VU University Medical Center, Department of Radiology and Nuclear Medicine, Neuroscience Campus Amsterdam, P.O. Box 7057, Amsterdam (Netherlands); Vrenken, Hugo [VU University Medical Center, Department of Radiology and Nuclear Medicine, Neuroscience Campus Amsterdam, P.O. Box 7057, Amsterdam (Netherlands); VU University Medical Center, Department of Physics and Medical Technology, Neuroscience Campus Amsterdam, P.O. Box 7057, Amsterdam (Netherlands)

    2014-02-15

    Validate the four-point visual rating scale for posterior cortical atrophy (PCA) on magnetic resonance images (MRI) through quantitative grey matter (GM) volumetry and voxel-based morphometry (VBM) to justify its use in clinical practice. Two hundred twenty-nine patients with probable Alzheimer's disease and 128 with subjective memory complaints underwent 3T MRI. PCA was rated according to the visual rating scale. GM volumes of six posterior structures and the total posterior region were extracted using IBASPM and compared among PCA groups. To determine which anatomical regions contributed most to the visual scores, we used binary logistic regression. VBM compared local GM density among groups. Patients were categorised according to their PCA scores: PCA-0 (n = 122), PCA-1 (n = 143), PCA-2 (n = 79), and PCA-3 (n = 13). All structures except the posterior cingulate differed significantly among groups. The inferior parietal gyrus volume discriminated the most between rating scale levels. VBM showed that PCA-1 had a lower GM volume than PCA-0 in the parietal region and other brain regions, whereas between PCA-1 and PCA-2/3 GM atrophy was mostly restricted to posterior regions. The visual PCA rating scale is quantitatively validated and reliably reflects GM atrophy in parietal regions, making it a valuable tool for the daily radiological assessment of dementia. (orig.)

  16. An automatic framework for quantitative validation of voxel based morphometry measures of anatomical brain asymmetry.

    Science.gov (United States)

    Pepe, Antonietta; Dinov, Ivo; Tohka, Jussi

    2014-10-15

    The study of anatomical brain asymmetries has been a topic of great interest in the neuroimaging community in the past decades. However, the accuracy of brain asymmetry measurements has been rarely investigated. In this study, we propose a fully automatic methodology for the quantitative validation of brain tissue asymmetries as measured by Voxel Based Morphometry (VBM) from structural magnetic resonance (MR) images. Starting from a real MR image, the methodology generates simulated 3D MR images with a known and realistic pattern of inter-hemispheric asymmetry that models the left-occipital right-frontal petalia of a normal brain and the related rightward bending of the inter-hemispheric fissure. As an example, we generated a dataset of 64 simulated MR images and applied this dataset for the quantitative validation of optimized VBM measures of asymmetries in brain tissue composition. Our results suggested that VBM analysis strongly depended on the spatial normalization of the individual brain images, the selected template space, and the amount of spatial smoothing applied. The most accurate asymmetry detections were achieved by 9-degrees of freedom registration to the symmetrical template space with 4 to 8mm spatial smoothing.

  17. Validating quantitative precipitation forecast for the Flood Meteorological Office, Patna region during 2011-2014

    Science.gov (United States)

    Giri, R. K.; Panda, Jagabandhu; Rath, Sudhansu S.; Kumar, Ravindra

    2016-06-01

    In order to issue an accurate warning for flood, a better or appropriate quantitative forecasting of precipitation is required. In view of this, the present study intends to validate the quantitative precipitation forecast (QPF) issued during southwest monsoon season for six river catchments (basin) under the flood meteorological office, Patna region. The forecast is analysed statistically by computing various skill scores of six different precipitation ranges during the years 2011-2014. The analysis of QPF validation indicates that the multi-model ensemble (MME) based forecasting is more reliable in the precipitation ranges of 1-10 and 11-25 mm. However, the reliability decreases for higher ranges of rainfall and also for the lowest range, i.e., below 1 mm. In order to testify synoptic analogue method based MME forecasting for QPF during an extreme weather event, a case study of tropical cyclone Phailin is performed. It is realized that in case of extreme events like cyclonic storms, the MME forecasting is qualitatively useful for issue of warning for the occurrence of floods, though it may not be reliable for the QPF. However, QPF may be improved using satellite and radar products.

  18. Chronic Antibody-Mediated Rejection in Nonhuman Primate Renal Allografts: Validation of Human Histological and Molecular Phenotypes.

    Science.gov (United States)

    Adam, B A; Smith, R N; Rosales, I A; Matsunami, M; Afzali, B; Oura, T; Cosimi, A B; Kawai, T; Colvin, R B; Mengel, M

    2017-04-26

    Molecular testing represents a promising adjunct for the diagnosis of antibody-mediated rejection (AMR). Here, we apply a novel gene expression platform in sequential formalin-fixed paraffin-embedded samples from nonhuman primate (NHP) renal transplants. We analyzed 34 previously described gene transcripts related to AMR in humans in 197 archival NHP samples, including 102 from recipients that developed chronic AMR, 80 from recipients without AMR, and 15 normal native nephrectomies. Three endothelial genes (VWF, DARC, and CAV1), derived from 10-fold cross-validation receiver operating characteristic curve analysis, demonstrated excellent discrimination between AMR and non-AMR samples (area under the curve = 0.92). This three-gene set correlated with classic features of AMR, including glomerulitis, capillaritis, glomerulopathy, C4d deposition, and DSAs (r = 0.39-0.63, p < 0.001). Principal component analysis confirmed the association between three-gene set expression and AMR and highlighted the ambiguity of v lesions and ptc lesions between AMR and T cell-mediated rejection (TCMR). Elevated three-gene set expression corresponded with the development of immunopathological evidence of rejection and often preceded it. Many recipients demonstrated mixed AMR and TCMR, suggesting that this represents the natural pattern of rejection. These data provide NHP animal model validation of recent updates to the Banff classification including the assessment of molecular markers for diagnosing AMR. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

  19. [Development and validation of event-specific quantitative PCR method for genetically modified maize LY038].

    Science.gov (United States)

    Mano, Junichi; Masubuchi, Tomoko; Hatano, Shuko; Futo, Satoshi; Koiwa, Tomohiro; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Akiyama, Hiroshi; Teshima, Reiko; Kurashima, Takeyo; Takabatake, Reona; Kitta, Kazumi

    2013-01-01

    In this article, we report a novel real-time PCR-based analytical method for quantitation of the GM maize event LY038. We designed LY038-specific and maize endogenous reference DNA-specific PCR amplifications. After confirming the specificity and linearity of the LY038-specific PCR amplification, we determined the conversion factor required to calculate the weight-based content of GM organism (GMO) in a multilaboratory evaluation. Finally, in order to validate the developed method, an interlaboratory collaborative trial according to the internationally harmonized guidelines was performed with blind DNA samples containing LY038 at the mixing levels of 0, 0.5, 1.0, 5.0 and 10.0%. The precision of the method was evaluated as the RSD of reproducibility (RSDR), and the values obtained were all less than 25%. The limit of quantitation of the method was judged to be 0.5% based on the definition of ISO 24276 guideline. The results from the collaborative trial suggested that the developed quantitative method would be suitable for practical testing of LY038 maize.

  20. Quantitative Validation of a Human Body Finite Element Model Using Rigid Body Impacts.

    Science.gov (United States)

    Vavalle, Nicholas A; Davis, Matthew L; Stitzel, Joel D; Gayzik, F Scott

    2015-09-01

    Validation is a critical step in finite element model (FEM) development. This study focuses on the validation of the Global Human Body Models Consortium full body average male occupant FEM in five localized loading regimes-a chest impact, a shoulder impact, a thoracoabdominal impact, an abdominal impact, and a pelvic impact. Force and deflection outputs from the model were compared to experimental traces and corridors scaled to the 50th percentile male. Predicted fractures and injury severity measures were compared to evaluate the model's injury prediction capabilities. The methods of ISO/TS 18571 were used to quantitatively assess the fit of model outputs to experimental force and deflection traces. The model produced peak chest, shoulder, thoracoabdominal, abdominal, and pelvis forces of 4.8, 3.3, 4.5, 5.1, and 13.0 kN compared to 4.3, 3.2, 4.0, 4.0, and 10.3 kN in the experiments, respectively. The model predicted rib and pelvic fractures related to Abbreviated Injury Scale scores within the ranges found experimentally all cases except the abdominal impact. ISO/TS 18571 scores for the impacts studied had a mean score of 0.73 with a range of 0.57-0.83. Well-validated FEMs are important tools used by engineers in advancing occupant safety.

  1. Validating quantitative precipitation forecast for the Flood Meteorological Office, Patna region during 2011–2014

    Indian Academy of Sciences (India)

    R K Giri; Jagabandhu Panda; Sudhansu S Rath; Ravindra Kumar

    2016-06-01

    In order to issue an accurate warning for flood, a better or appropriate quantitative forecasting of precipitationis required. In view of this, the present study intends to validate the quantitative precipitationforecast (QPF) issued during southwest monsoon season for six river catchments (basin) under theflood meteorological office, Patna region. The forecast is analysed statistically by computing various skillscores of six different precipitation ranges during the years 2011–2014. The analysis of QPF validationindicates that the multi-model ensemble (MME) based forecasting is more reliable in the precipitationranges of 1–10 and 11–25 mm. However, the reliability decreases for higher ranges of rainfall and also forthe lowest range, i.e., below 1 mm. In order to testify synoptic analogue method based MME forecastingfor QPF during an extreme weather event, a case study of tropical cyclone Phailin is performed. It isrealized that in case of extreme events like cyclonic storms, the MME forecasting is qualitatively usefulfor issue of warning for the occurrence of floods, though it may not be reliable for the QPF. However,QPF may be improved using satellite and radar products.

  2. Development and validation of HPLC method for quantitative analysis of triamcinolone in biodegradable microparticles

    Directory of Open Access Journals (Sweden)

    A. A. Silva-Júnior

    2009-01-01

    Full Text Available

    A simple, rapid, selective and specific high performance liquid chromatographic (HPLC method for quantitative analysis of the triamcinolone in polylactide-co-glycolide acid (PLGA microparticles was developed. The chromatographic parameters were reversed-phase C18 column, 250mm x 4.6mm, with particle size 5 m. The column oven was thermostated at 35 ºC ± 2 ºC. The mobile phase was methanol/water 45:55 (v/v and elution was isocratic at a flow-rate of 1mL.mL-1. The determinations were performed using a UV-Vis detector at 239 nm. The injected sample volume was 10 µL. The standard curve was linear (r2 > 0.999 in the concentration range 100-2500 ng.mL-1. The method showed adequate precision, with a relative standard deviation (RSD was smaller than 3%. The accuracy was analyzed by adding a standard drug and good recovery values were obtained for all drug concentrations used. The method showed specificity and selectivity with linearity in the working range and good precision and accuracy, making it very suitable for quantitation of triamcinolone in PLGA microparticles. Keywords: triamcinolone; HPLC analytical method; PLGA microparticles; analytical method validation.

  3. Selective detection of histologically aggressive prostate cancer: an Early Detection Research Network Prediction model to reduce unnecessary prostate biopsies with validation in the Prostate Cancer Prevention Trial.

    Science.gov (United States)

    Williams, Stephen B; Salami, Simpa; Regan, Meredith M; Ankerst, Donna P; Wei, John T; Rubin, Mark A; Thompson, Ian M; Sanda, Martin G

    2012-05-15

    Limited survival benefit and excess treatment because of prostate-specific antigen (PSA) screening in randomized trials suggests a need for more restricted selection of prostate biopsy candidates by discerning risk of histologically aggressive versus indolent cancer before biopsy. Subjects undergoing first prostate biopsy enrolled in a multicenter, prospective cohort of the National Cancer Institute Early Detection Research Network (N = 635) were analyzed to develop a model for predicting histologically aggressive prostate cancers. The control arm of the Prostate Cancer Prevention Trial (N = 3833) was used to validate the generalization of the predictive model. The Early Detection Research Network cohort was comprised of men among whom 57% had no cancer, 14% had indolent cancer, and 29% had aggressive cancer. Age, body mass index, family history of prostate cancer, abnormal digital rectal examination (DRE), and PSA density (PSAD) were associated with aggressive cancer (all P cancer (area under the curve [AUC] = 0.81 vs 0.71, P Prostate Cancer Prevention Trial cohort accurately identified men at low (cancer for whom biopsy could be averted (AUC = 0.78; 95% confidence interval, 0.75-0.80). Under criteria from the Early Detection Research Network model, prostate biopsy can be restricted to men with PSAD >0.1 ng/mL/cc or abnormal DRE. When PSAD is obesity can identify biopsy candidates. A predictive model incorporating age, family history, obesity, PSAD, and DRE elucidates criteria whereby ¼ of prostate biopsies can be averted while retaining high sensitivity in detecting aggressive prostate cancer. Copyright © 2011 American Cancer Society.

  4. Validation of absolute quantitative real-time PCR for the diagnosis of Streptococcus agalactiae in fish.

    Science.gov (United States)

    Sebastião, Fernanda de A; Lemos, Eliana G M; Pilarski, Fabiana

    2015-12-01

    Streptococcus agalactiae (GBS) are Gram-positive cocci responsible for substantial losses in tilapia fish farms in Brazil and worldwide. It causes septicemia, meningoencephalitis and mortality of whole shoals that can occur within 72 h. Thus, diagnostic methods are needed that are rapid, specific and sensitive. In this study, a pair of specific primers for GBS was generated based on the cfb gene sequence and initially evaluated by conventional PCR. The protocols for absolute quantitative real-time PCR (qPCR) were then adapted to validate the technique for the identification and quantification of GBS isolated by real-time detection of amplicons using fluorescence measurements. Finally, an infectivity test was conducted in tilapia infected with GBS strains. Total DNA from the host brain was subjected to the same technique, and the strains were re-isolated to validate Koch's postulates. The assay showed 100% specificity for the other bacterial species evaluated and a sensitivity of 367 gene copies per 20 mg of brain tissue within 4 h, making this test a valuable tool for health monitoring programs.

  5. Reliability and validity of quantitative sensory testing in persons with spinal cord injury and neuropathic pain.

    Science.gov (United States)

    Felix, Elizabeth R; Widerström-Noga, Eva G

    2009-01-01

    Quantitative sensory testing (QST) has been used to assess neurological function in various chronic pain patient populations. In the present study, we investigated the ability of QST to reliably characterize somatosensory dysfunction in subjects with spinal cord injury (SCI) and neuropathic pain by measuring mechanical, vibration, and thermal detection and pain thresholds. Test-retest reliability was determined based on data collected from 10 subjects with SCI and neuropathic pain who underwent QST on two occasions approximately 3 weeks apart. The intraclass correlation coefficients for mechanical, vibration, warm, and cool detection thresholds were in the "substantial" range, while thresholds for cold pain and hot pain demonstrated "fair" stability in this sample of patients. To determine the validity of QST in persons with SCI-related neuropathic pain, we evaluated the relationship between somatosensory thresholds and severity of neuropathic pain symptoms with multiple linear regression analysis. Thermal pain threshold was the only QST variable significantly related to the severity of neuropathic pain symptoms. The present study provides preliminary evidence that QST is a reliable and valid adjunct measurement strategy for quantifying the neurological dysfunction associated with neuropathic pain in persons with SCI.

  6. Validation of reference genes for real-time quantitative RT-PCR studies in Talaromyces marneffei.

    Science.gov (United States)

    Dankai, Wiyada; Pongpom, Monsicha; Vanittanakom, Nongnuch

    2015-11-01

    Talaromyces marneffei (or Penicillium marneffei) is an opportunistic pathogen that can cause disseminated disease in human immunodeficiency virus (HIV)-infected patients, especially in Southeast Asia. T. marneffei is a thermally dimorphic fungus. Typically, T. marneffei has an adaptive morphology. It grows in a filamentous form (mould) at 25°C and can differentiate to produce asexual spores (conidia). In contrast, at 37°C, it grows as yeast cells that divide by fission. This study aimed to validate a quantitative reverse-transcription polymerase chain reaction (qRT-PCR) for gene expression analysis in T. marneffei. Analysis of relative gene expression by qRT-PCR requires normalization of data using a proper reference gene. However, suitable reference genes have not been identified in gene expression studies across different cell types or under different experimental conditions in T. marneffei. In this study, four housekeeping genes were selected for analysis: β-actin (act); glyceraldehyde-3-phosphate dehydrogenase (gapdh); β-tubulin (benA) and 18S rRNA. Two analysis programs; BestKeeper and geNorm software tools were used to validate the expression of the candidate normalized genes. The results indicated that the actin gene was the one which was most stably expressed and was recommended for use as the endogenous control for gene expression analysis of all growth forms in T. marneffei by qRT-PCR under normal and stress conditions.

  7. Validation of Zebrafish (Danio rerio) Reference Genes for Quantitative Real-time RT-PCR Normalization

    Institute of Scientific and Technical Information of China (English)

    Rongying TANG; Andrew DODD; Daniel LAI; Warren C.MCNABB; Donald R.LOVE

    2007-01-01

    The normalization of quantitative real time RT-PCR (qRT-PCR) is important to obtain accurate gene expression data. The most common method for qRT-PCR normalization is to use reference, or housekeeping genes. However, there is emerging evidence that even reference genes can be regulated under different conditions, qRT-PCR has only recently been used in terms of zebrafish gene expression studies and there is no validated set of reference genes. This study characterizes the expression of nine possible reference genes during zebrafish embryonic development and in a zebrafish tissue panel. All nine reference genes exhibited variable expression. The β-actin, EF1α and Rpl13α genes comprise a validated reference gene panel for zebrafish developmental time course studies, and the EF1α, Rpl13α and 18S rRNA genes are more suitable as a reference gene panel for zebrafish tissue analysis. Importantly, the zebrafish GAPDH gene appears unsuitable as reference gene for both types of studies.

  8. Quantitative Determination of Synthesized Genotoxic Impurities in Nifuroxazide Capsules by Validated Chromatographic Methods.

    Science.gov (United States)

    Abdelwahab, Nada S; Ali, Nouruddin W; Zaki, Marco M; Abdelkawy, M; El-Saadi, Mohammed T

    2017-07-31

    Two accurate, selective, and precise chromatographic methods, namely TLC-densitometric and reversed-phase (RP)-HPLC, were developed and validated for the simultaneous determination of nifuroxazide (NIF) and its four synthesized impurities, which are also reported to be its related substances in the range of 10–100 μg/band and 10–100 μg/mL for NIF in the TLC and RP-HPLC methods, respectively. The developed TLC-densitometric method depended on the separation and quantitation of the studied components on silica gel 60 F254 TLC plates. Ethyl acetate–acetone–methanol–ammonia (85 + 25 + 5 + 0.5, v/v/v/v) was used as the developing system, and the separated bands were UV-scanned at 230 nm. On the other hand, the developed RP-HPLC method depended on chromatographic separation using a C8 column at 25°C and an aqueous solution of 0.1% sodium lauryl sulfate–acetonitrile as the mobile phase delivered according to the gradient elution program. Factors affecting the developed methods were studied and optimized. Also, method validation was carried out according to International Conference on Harmonization guidelines. The proposed methods were successfully applied for the determination of the studied drug in its bulk powder and in its pharmaceutical formulation. The developed methods showed no significant difference when compared with the reported RP-HPLC one. Their advantage is being the first stability-indicating methods for NIF and its genotoxic impurities.

  9. Stereological Analysis of Liver Biopsy Histology Sections as a Reference Standard for Validating Non-Invasive Liver Fat Fraction Measurements by MRI

    Science.gov (United States)

    St. Pierre, Tim G.; House, Michael J.; Bangma, Sander J.; Pang, Wenjie; Bathgate, Andrew; Gan, Eng K.; Ayonrinde, Oyekoya T.; Bhathal, Prithi S.; Clouston, Andrew; Olynyk, John K.; Adams, Leon A.

    2016-01-01

    Background and Aims Validation of non-invasive methods of liver fat quantification requires a reference standard. However, using standard histopathology assessment of liver biopsies is problematical because of poor repeatability. We aimed to assess a stereological method of measuring volumetric liver fat fraction (VLFF) in liver biopsies and to use the method to validate a magnetic resonance imaging method for measurement of VLFF. Methods VLFFs were measured in 59 subjects (1) by three independent analysts using a stereological point counting technique combined with the Delesse principle on liver biopsy histological sections and (2) by three independent analysts using the HepaFat-Scan® technique on magnetic resonance images of the liver. Bland Altman statistics and intraclass correlation (IC) were used to assess the repeatability of each method and the bias between the methods of liver fat fraction measurement. Results Inter-analyst repeatability coefficients for the stereology and HepaFat-Scan® methods were 8.2 (95% CI 7.7–8.8)% and 2.4 (95% CI 2.2–2.5)% VLFF respectively. IC coefficients were 0.86 (95% CI 0.69–0.93) and 0.990 (95% CI 0.985–0.994) respectively. Small biases (≤3.4%) were observable between two pairs of analysts using stereology while no significant biases were observable between any of the three pairs of analysts using HepaFat-Scan®. A bias of 1.4±0.5% VLFF was observed between the HepaFat-Scan® method and the stereological method. Conclusions Repeatability of the stereological method is superior to the previously reported performance of assessment of hepatic steatosis by histopathologists and is a suitable reference standard for validating non-invasive methods of measurement of VLFF. PMID:27501242

  10. Cross-method validation as a solution to the problem of excessive simplification of measurement in quantitative IR research

    DEFF Research Database (Denmark)

    Beach, Derek

    2007-01-01

    The purpose of this article is to make IR scholars more aware of the costs of choosing quantitative methods. The article first shows that quantification can have analytical ‘costs’ when the measures created are too simple to capture the essence of the systematized concept that was supposed...... detail based upon a review of the democratic peace literature. I then offer two positive suggestions for a way forward. First, I argue that quantitative scholars should spend more time validating their measures, and in particular should engage in multi-method partnerships with qualitative scholars...... that have a deep understanding of particular cases in order to exploit the comparative advantages of qualitative methodology, using the more accurate qualitative measures to validate their own quantitative measures. Secondly, quantitative scholars should lower their level of ambition given the often poor...

  11. Enhanced characterization of calcified areas in intravascular ultrasound virtual histology images by quantification of the acoustic shadow: validation against computed tomography coronary angiography.

    Science.gov (United States)

    Broersen, Alexander; de Graaf, Michiel A; Eggermont, Jeroen; Wolterbeek, Ron; Kitslaar, Pieter H; Dijkstra, Jouke; Bax, Jeroen J; Reiber, Johan H C; Scholte, Arthur J

    2016-04-01

    We enhance intravascular ultrasound virtual histology (VH) tissue characterization by fully automatic quantification of the acoustic shadow behind calcified plaque. VH is unable to characterize atherosclerosis located behind calcifications. In this study, the quantified acoustic shadows are considered calcified to approximate the real dense calcium (DC) plaque volume. In total, 57 patients with 108 coronary lesions were included. A novel post-processing step is applied on the VH images to quantify the acoustic shadow and enhance the VH results. The VH and enhanced VH results are compared to quantitative computed tomography angiography (QTA) plaque characterization as reference standard. The correlation of the plaque types between enhanced VH and QTA differs significantly from the correlation with unenhanced VH. For DC, the correlation improved from 0.733 to 0.818. Instead of an underestimation of DC in VH with a bias of 8.5 mm(3), there was a smaller overestimation of 1.1 mm(3) in the enhanced VH. Although tissue characterization within the acoustic shadow in VH is difficult, the novel algorithm improved the DC tissue characterization. This algorithm contributes to accurate assessment of calcium on VH and could be applied in clinical studies.

  12. Selection of Valid Reference Genes for Reverse Transcription Quantitative PCR Analysis in Heliconius numata (Lepidoptera: Nymphalidae)

    Science.gov (United States)

    Chouteau, Mathieu; Whibley, Annabel; Joron, Mathieu; Llaurens, Violaine

    2016-01-01

    Identifying the genetic basis of adaptive variation is challenging in non-model organisms and quantitative real time PCR. is a useful tool for validating predictions regarding the expression of candidate genes. However, comparing expression levels in different conditions requires rigorous experimental design and statistical analyses. Here, we focused on the neotropical passion-vine butterflies Heliconius, non-model species studied in evolutionary biology for their adaptive variation in wing color patterns involved in mimicry and in the signaling of their toxicity to predators. We aimed at selecting stable reference genes to be used for normalization of gene expression data in RT-qPCR analyses from developing wing discs according to the minimal guidelines described in Minimum Information for publication of Quantitative Real-Time PCR Experiments (MIQE). To design internal RT-qPCR controls, we studied the stability of expression of nine candidate reference genes (actin, annexin, eF1α, FK506BP, PolyABP, PolyUBQ, RpL3, RPS3A, and tubulin) at two developmental stages (prepupal and pupal) using three widely used programs (GeNorm, NormFinder and BestKeeper). Results showed that, despite differences in statistical methods, genes RpL3, eF1α, polyABP, and annexin were stably expressed in wing discs in late larval and pupal stages of Heliconius numata. This combination of genes may be used as a reference for a reliable study of differential expression in wings for instance for genes involved in important phenotypic variation, such as wing color pattern variation. Through this example, we provide general useful technical recommendations as well as relevant statistical strategies for evolutionary biologists aiming to identify candidate-genes involved adaptive variation in non-model organisms. PMID:27271971

  13. Selection of Valid Reference Genes for Reverse Transcription Quantitative PCR Analysis in Heliconius numata (Lepidoptera: Nymphalidae).

    Science.gov (United States)

    Piron Prunier, Florence; Chouteau, Mathieu; Whibley, Annabel; Joron, Mathieu; Llaurens, Violaine

    2016-01-01

    Identifying the genetic basis of adaptive variation is challenging in non-model organisms and quantitative real time PCR. is a useful tool for validating predictions regarding the expression of candidate genes. However, comparing expression levels in different conditions requires rigorous experimental design and statistical analyses. Here, we focused on the neotropical passion-vine butterflies Heliconius, non-model species studied in evolutionary biology for their adaptive variation in wing color patterns involved in mimicry and in the signaling of their toxicity to predators. We aimed at selecting stable reference genes to be used for normalization of gene expression data in RT-qPCR analyses from developing wing discs according to the minimal guidelines described in Minimum Information for publication of Quantitative Real-Time PCR Experiments (MIQE). To design internal RT-qPCR controls, we studied the stability of expression of nine candidate reference genes (actin, annexin, eF1α, FK506BP, PolyABP, PolyUBQ, RpL3, RPS3A, and tubulin) at two developmental stages (prepupal and pupal) using three widely used programs (GeNorm, NormFinder and BestKeeper). Results showed that, despite differences in statistical methods, genes RpL3, eF1α, polyABP, and annexin were stably expressed in wing discs in late larval and pupal stages of Heliconius numata This combination of genes may be used as a reference for a reliable study of differential expression in wings for instance for genes involved in important phenotypic variation, such as wing color pattern variation. Through this example, we provide general useful technical recommendations as well as relevant statistical strategies for evolutionary biologists aiming to identify candidate-genes involved adaptive variation in non-model organisms.

  14. New Magnetic Resonance Imaging Index for Renal Fibrosis Assessment: A Comparison between Diffusion-Weighted Imaging and T1 Mapping with Histological Validation

    Science.gov (United States)

    Friedli, I.; Crowe, L. A.; Berchtold, L.; Moll, S.; Hadaya, K.; de Perrot, T.; Vesin, C.; Martin, P.-Y.; de Seigneux, S.; Vallée, J.-P.

    2016-01-01

    A need exists to noninvasively assess renal interstitial fibrosis, a common process to all kidney diseases and predictive of renal prognosis. In this translational study, Magnetic Resonance Imaging (MRI) T1 mapping and a new segmented Diffusion-Weighted Imaging (DWI) technique, for Apparent Diffusion Coefficient (ADC), were first compared to renal fibrosis in two well-controlled animal models to assess detection limits. Validation against biopsy was then performed in 33 kidney allograft recipients (KARs). Predictive MRI indices, ΔT1 and ΔADC (defined as the cortico-medullary differences), were compared to histology. In rats, both T1 and ADC correlated well with fibrosis and inflammation showing a difference between normal and diseased kidneys. In KARs, MRI indices were not sensitive to interstitial inflammation. By contrast, ΔADC outperformed ΔT1 with a stronger negative correlation to fibrosis (R2 = 0.64 against R2 = 0.29 p < 0.001). ΔADC tends to negative values in KARs harboring cortical fibrosis of more than 40%. Using a discriminant analysis method, the ΔADC, as a marker to detect such level of fibrosis or higher, led to a specificity and sensitivity of 100% and 71%, respectively. This new index has potential for noninvasive assessment of fibrosis in the clinical setting. PMID:27439482

  15. Correction for FDG PET dose extravasations: Monte Carlo validation and quantitative evaluation of patient studies

    Energy Technology Data Exchange (ETDEWEB)

    Silva-Rodríguez, Jesús, E-mail: jesus.silva.rodriguez@sergas.es; Aguiar, Pablo, E-mail: pablo.aguiar.fernandez@sergas.es [Fundación Ramón Domínguez, Santiago de Compostela, Galicia (Spain); Servicio de Medicina Nuclear, Complexo Hospitalario Universidade de Santiago de Compostela (USC), 15782, Galicia (Spain); Grupo de Imaxe Molecular, Instituto de Investigación Sanitarias (IDIS), Santiago de Compostela, 15706, Galicia (Spain); Sánchez, Manuel; Mosquera, Javier; Luna-Vega, Víctor [Servicio de Radiofísica y Protección Radiológica, Complexo Hospitalario Universidade de Santiago de Compostela (USC), 15782, Galicia (Spain); Cortés, Julia; Garrido, Miguel [Servicio de Medicina Nuclear, Complexo Hospitalario Universitario de Santiago de Compostela, 15706, Galicia, Spain and Grupo de Imaxe Molecular, Instituto de Investigación Sanitarias (IDIS), Santiago de Compostela, 15706, Galicia (Spain); Pombar, Miguel [Servicio de Radiofísica y Protección Radiológica, Complexo Hospitalario Universitario de Santiago de Compostela, 15706, Galicia (Spain); Ruibal, Álvaro [Servicio de Medicina Nuclear, Complexo Hospitalario Universidade de Santiago de Compostela (USC), 15782, Galicia (Spain); Grupo de Imaxe Molecular, Instituto de Investigación Sanitarias (IDIS), Santiago de Compostela, 15706, Galicia (Spain); Fundación Tejerina, 28003, Madrid (Spain)

    2014-05-15

    Purpose: Current procedure guidelines for whole body [18F]fluoro-2-deoxy-D-glucose (FDG)-positron emission tomography (PET) state that studies with visible dose extravasations should be rejected for quantification protocols. Our work is focused on the development and validation of methods for estimating extravasated doses in order to correct standard uptake value (SUV) values for this effect in clinical routine. Methods: One thousand three hundred sixty-seven consecutive whole body FDG-PET studies were visually inspected looking for extravasation cases. Two methods for estimating the extravasated dose were proposed and validated in different scenarios using Monte Carlo simulations. All visible extravasations were retrospectively evaluated using a manual ROI based method. In addition, the 50 patients with higher extravasated doses were also evaluated using a threshold-based method. Results: Simulation studies showed that the proposed methods for estimating extravasated doses allow us to compensate the impact of extravasations on SUV values with an error below 5%. The quantitative evaluation of patient studies revealed that paravenous injection is a relatively frequent effect (18%) with a small fraction of patients presenting considerable extravasations ranging from 1% to a maximum of 22% of the injected dose. A criterion based on the extravasated volume and maximum concentration was established in order to identify this fraction of patients that might be corrected for paravenous injection effect. Conclusions: The authors propose the use of a manual ROI based method for estimating the effectively administered FDG dose and then correct SUV quantification in those patients fulfilling the proposed criterion.

  16. Quantitative analysis of gene expression in fixed colorectal carcinoma samples as a method for biomarker validation

    Science.gov (United States)

    OSTASIEWICZ, BEATA; OSTASIEWICZ, PAWEŁ; DUŚ-SZACHNIEWICZ, KAMILA; OSTASIEWICZ, KATARZYNA; ZIÓŁKOWSKI, PIOTR

    2016-01-01

    Biomarkers have been described as the future of oncology. Modern proteomics provide an invaluable tool for the near-whole proteome screening for proteins expressed differently in neoplastic vs. healthy tissues. However, in order to select the most promising biomarkers, an independent method of validation is required. The aim of the current study was to propose a methodology for the validation of biomarkers. Due to material availability the majority of large scale biomarker studies are performed using formalin-fixed paraffin-embedded (FFPE) tissues, therefore these were selected for use in the current study. A total of 10 genes were selected from what have been previously described as the most promising candidate biomarkers, and the expression levels were analyzed with reverse transcription-quantitative polymerase chain reaction (RT-qPCR) using calibrator normalized relative quantification with the efficiency correction. For 6/10 analyzed genes, the results were consistent with the proteomic data; for the remaining four genes, the results were inconclusive. The upregulation of karyopherin α 2 (KPNA2) and chromosome segregation 1-like (CSE1L) in colorectal carcinoma, in addition to downregulation of chloride channel accessory 1 (CLCA1), fatty acid binding protein 1 (FABP1), sodium channel, voltage gated, type VII α subunit (SCN7A) and solute carrier family 26 (anion exchanger), member 3 (SLC26A3) was confirmed. With the combined use of proteomic and genetic tools, it was reported, for the first time to the best of our knowledge, that SCN7A was downregulated in colorectal carcinoma at mRNA and protein levels. It had been previously suggested that the remaining five genes served an important role in colorectal carcinogenesis, however the current study provided strong evidence to support their use as biomarkers. Thus, it was concluded that combination of RT-qPCR with proteomics offers a powerful methodology for biomarker identification, which can be used to analyze

  17. Validation of Reference Genes for Quantitative Real-Time PCR in Laodelphax striatellus

    Institute of Scientific and Technical Information of China (English)

    HE Xiu-ting; LIU Cheng-cheng; LI Zhao-qun; ZHANG Zan; LI Guo-qing; LI Fei; DONG Shuang-lin

    2014-01-01

    The normalization of quantitative real-time PCR (qPCR) is important to obtain accurate gene expression data, and the most common method for qPCR normalization is to use reference genes. However, reference genes can be regulated under different conditions. qPCR has recently been used for gene expression study in Laodelphax striatellus, but there is no study on validation of the reference genes. In this study, ifve new housekeeping genes (LstrTUB1, LstrTUB2, LstrTUB3, LstrARF and LstrRPL9) in L. striatellus were cloned and deposited in the GenBank with accession numbers of JF728809, JF728810, JF728811, JF728807 and JF728806, respectively. Furthermore, mRNA expressions of the five genes and β-actin were measured by qPCR with insect samples of different instar at nymph stage, and the expression stabilities were determined by the software geNorm and NormFinder. As a result, ARF and RPL9 were consistently more stable thanβ-actin, while three TUB genes were less stable than β-actin. To determine the optimal number of reference genes used in qPCR, a pairwise variations analysis by geNorm indicated that two references ARF and RPL9 were required to obtain the accurate quantiifcation. These results were further conifrmed by the validation qPCR experiment with chitinase gene as the target gene, in which the standard error of the mRNA quantiifcation by using binary reference ARF-RPL9 was much lower than those by ARF, RPL9 orβ-actin alone. Taken together, our study suggested that the combination of ARF-RPL9 could replaceβ-actin as the reference genes for qPCR in L. striatellus.

  18. Gamma camera calibration and validation for quantitative SPECT imaging with (177)Lu.

    Science.gov (United States)

    D'Arienzo, M; Cazzato, M; Cozzella, M L; Cox, M; D'Andrea, M; Fazio, A; Fenwick, A; Iaccarino, G; Johansson, L; Strigari, L; Ungania, S; De Felice, P

    2016-06-01

    Over the last years (177)Lu has received considerable attention from the clinical nuclear medicine community thanks to its wide range of applications in molecular radiotherapy, especially in peptide-receptor radionuclide therapy (PRRT). In addition to short-range beta particles, (177)Lu emits low energy gamma radiation of 113keV and 208keV that allows gamma camera quantitative imaging. Despite quantitative cancer imaging in molecular radiotherapy having been proven to be a key instrument for the assessment of therapeutic response, at present no general clinically accepted quantitative imaging protocol exists and absolute quantification studies are usually based on individual initiatives. The aim of this work was to develop and evaluate an approach to gamma camera calibration for absolute quantification in tomographic imaging with (177)Lu. We assessed the gamma camera calibration factors for a Philips IRIX and Philips AXIS gamma camera system using various reference geometries, both in air and in water. Images were corrected for the major effects that contribute to image degradation, i.e. attenuation, scatter and dead- time. We validated our method in non-reference geometry using an anthropomorphic torso phantom provided with the liver cavity uniformly filled with (177)LuCl3. Our results showed that calibration factors depend on the particular reference condition. In general, acquisitions performed with the IRIX gamma camera provided good results at 208keV, with agreement within 5% for all geometries. The use of a Jaszczak 16mL hollow sphere in water provided calibration factors capable of recovering the activity in anthropomorphic geometry within 1% for the 208keV peak, for both gamma cameras. The point source provided the poorest results, most likely because scatter and attenuation correction are not incorporated in the calibration factor. However, for both gamma cameras all geometries provided calibration factors capable of recovering the activity in

  19. Development and validation of a direct homologous quantitative sandwich ELISA for fathead minnow (Pimephales promelas) vitellogenin.

    Science.gov (United States)

    Eidem, Janne K; Kleivdal, Hans; Kroll, Kevin; Denslow, Nancy; van Aerle, Ronny; Tyler, Charles; Panter, Grace; Hutchinson, Tom; Goksøyr, Anders

    2006-06-15

    Vitellogenin (Vtg) is an established and sensitive endpoint for analysis of exposure to (anti-)oestrogens and their mimics in fish [Sumpter, J.P., 1995. Feminized responses in fish to environmental estrogens. Toxicol. Lett. 82, 737-742; Arukwe, A., Goksøyr, A., 2003. Eggshell and egg yolk proteins in fish: hepatic proteins for the next generation: oogenetic, population, and evolutionary implications of endocrine disruption. Comp. Hepatol. 2, 4. ]. In some instances, links have been drawn between high level induction of Vtg and adverse health effects in fish [Herman, R.L., Kincaide, H.L., 1988. Pathological effects of orally administered estradiol to rainbow trout. Aquaculture 72, 165-172; Schwaiger, J., Spieser, O.H., Bauer, C., Ferling, H., Mallow, U., Kalbfus, W., Negele, R.D., 2000. Chronic toxicity of nonylphenol and ethinyloestraiol: haematological and histopathological effects in juvenile common carp (Cyprinus carpio). Aquat. Toxicol. 51, 69-78]. The widespread use of Vtg as a biomarker has led to the development of a variety of assays to quantitatively measure Vtg concentrations in tissue samples from fish, and hence a need for a standardization of the performance criteria and validation of such assays [Goksøyr, A., Eidem, J.K., Kristiansen, S.I., Nilsen, B.M., 2003. On the need for a standardized set-up for validation studies of fish vitellogenin assays as an endpoint in endocrine disruptor testing and screening-a proposal. ]. One of the most popular test fish species for assessing chemical effects is the fathead minnow (Pimephales promelas), which is now used widely for studies into endocrine disruption [Panter, G.H., Hutchinson, T.H., Lange, R., Lye, C.M., Sumpter, J.P., Zerulla, M., Tyler, C.R., 2002. Utility of a juvenile fathead minnow screening assay for detecting (anti)estrogenic substances. Environ. Toxicol. Chem. 21, 319-326; Hutchinson, T.H., Yokota, H., Hagino, S., Ozato, K., 2003. Development of fish tests for endocrine disruptors. Pure Appl

  20. Principles and methods for the validation of quantitative remote sensing products

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    We first discuss the relativity of "true value and homogeneity" for quantitative remote sensing products (QRSPs), and then propose the definitions of "eigenaccuracy" and "eigenhomogeneity" under practical conditions. The eigenaccuracy and eigenhomogeneity for land surface crucial parameters such as albedo, leaf area index (LAI), and surface temperature are analyzed based on a series of experiments. Secondly, we point out the differences and similarities between the scale-free phenomena of the QRSPs and the measurements of the coastline length (1-dimensional) and the curved surface area (2-dimensional). An information fractal algorithm for the QRSPs is presented. In a case study for the LAI, when the fractal dimension is 2.16, the ratio of the LAI retrieval values obtained respectively from remote sensing data of 30 m and 6 km pixel resolution can actually reach as high as 2.86 for the same 6 km pixel using the same retrieval model. Finally, we propose an operational validation method "one test and two matches" and multipoint observation when the real situation does not allow carrying out scanning measurement without gap and overlap on the ground surface.

  1. Prediction of prostate cancer recurrence using quantitative phase imaging: Validation on a general population

    Science.gov (United States)

    Sridharan, Shamira; Macias, Virgilia; Tangella, Krishnarao; Melamed, Jonathan; Dube, Emily; Kong, Max Xiangtian; Kajdacsy-Balla, André; Popescu, Gabriel

    2016-09-01

    Prediction of biochemical recurrence risk of prostate cancer following radical prostatectomy is critical for determining whether the patient would benefit from adjuvant treatments. Various nomograms exist today for identifying individuals at higher risk for recurrence; however, an optimistic under-estimation of recurrence risk is a common problem associated with these methods. We previously showed that anisotropy of light scattering measured using quantitative phase imaging, in the stromal layer adjacent to cancerous glands, is predictive of recurrence. That nested-case controlled study consisted of specimens specifically chosen such that the current prognostic methods fail. Here we report on validating the utility of optical anisotropy for prediction of prostate cancer recurrence in a general population of 192 patients, with 17% probability of recurrence. Our results show that our method can identify recurrent cases with 73% sensitivity and 72% specificity, which is comparable to that of CAPRA-S, a current state of the art method, in the same population. However, our results show that optical anisotropy outperforms CAPRA-S for patients with Gleason grades 7–10. In essence, we demonstrate that anisotropy is a better biomarker for identifying high-risk cases, while Gleason grade is better suited for selecting non-recurrence. Therefore, we propose that anisotropy and current techniques be used together to maximize prediction accuracy.

  2. Polymorphism in nimodipine raw materials: development and validation of a quantitative method through differential scanning calorimetry.

    Science.gov (United States)

    Riekes, Manoela Klüppel; Pereira, Rafael Nicolay; Rauber, Gabriela Schneider; Cuffini, Silvia Lucia; de Campos, Carlos Eduardo Maduro; Silva, Marcos Antonio Segatto; Stulzer, Hellen Karine

    2012-11-01

    Due to the physical-chemical and therapeutic impacts of polymorphism, its monitoring in raw materials is necessary. The purpose of this study was to develop and validate a quantitative method to determine the polymorphic content of nimodipine (NMP) raw materials based on differential scanning calorimetry (DSC). The polymorphs required for the development of the method were characterized through DSC, X-ray powder diffraction (XRPD) and Raman spectroscopy and their polymorphic identity was confirmed. The developed method was found to be linear, robust, precise, accurate and specific. Three different samples obtained from distinct suppliers (NMP 1, NMP 2 and NMP 3) were firstly characterized through XRPD and DSC as polymorphic mixtures. The determination of their polymorphic identity revealed that all samples presented the Modification I (Mod I) or metastable form in greatest proportion. Since the commercial polymorph is Mod I, the polymorphic characteristic of the samples analyzed needs to be investigated. Thus, the proposed method provides a useful tool for the monitoring of the polymorphic content of NMP raw materials. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Prognostic impact of proliferation for resected early stage 'pure' invasive lobular breast cancer: Cut-off analysis of Ki67 according to histology and clinical validation.

    Science.gov (United States)

    Carbognin, Luisa; Sperduti, Isabella; Fabi, Alessandra; Dieci, Maria Vittoria; Kadrija, Dzenete; Griguolo, Gaia; Pilotto, Sara; Guarneri, Valentina; Zampiva, Ilaria; Brunelli, Matteo; Orvieto, Enrico; Nortilli, Rolando; Fiorio, Elena; Parolin, Veronica; Manfrin, Erminia; Caliò, Anna; Nisticò, Cecilia; Pellini, Francesca; Scarpa, Aldo; Pollini, Giovanni Paolo; Conte, Pierfranco; Tortora, Giampaolo; Bria, Emilio

    2017-10-01

    The intent of this analysis was to investigate and validate the prognostic potential of Ki67 in a multi-center series of patients affected by early stage 'pure' invasive lobular carcinoma (ILC). Clinical-pathological data of patients affected by ILC were correlated with overall survival and disease-free survival (OS/DFS); data from a parallel invasive ductal carcinoma (IDC) patients' cohort were gathered as well. The maximally selected Log-Rank statistics analysis was applied to Ki67 continuous variable to estimate the appropriate cut-off. The Subpopulation Treatment Effect Pattern Plot (STEPP) analysis was performed as well. Data from overall 1097 (457/222 ILC: training/validation set; 418 IDC) patients were gathered. The identified optimal Ki67 cut-offs were 4% and 14% for DFS in ILC and IDC cohort, respectively. In ILC patients, the Ki67 cut-off was an independent OS predictor. Ten-years OS and DFS were 89.9% and 77.2% (p = 0.007) and 79.4% and 69.2% (p = 0.03) for patients with Ki67 ≤ 4% and >4%, respectively. In IDC patients, 10-years OS was 93.8% and 71.7%, p = 0.02, DFS was 84.0% and 52.6%, p = 0.0003, for patients with Ki67 ≤ 14% and >14%, respectively. In the validation set, the optimal Ki67 OS cut-off was 5%. The STEPP analysis showed that in the presence of low Ki67 values, IDC patients have a better DFS than ILC patients, while with the increase of values the prognosis tends to overlap. Despite the retrospective design of the study, the prognostic relevance of Ki67 (as well as its optimal cut-off) seems to significantly differ according to breast cancer histology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Assessment of Scientific Literacy: Development and Validation of the Quantitative Assessment of Socio-Scientific Reasoning (QuASSR)

    Science.gov (United States)

    Romine, William L.; Sadler, Troy D.; Kinslow, Andrew T.

    2017-01-01

    We describe the development and validation of the Quantitative Assessment of Socio-scientific Reasoning (QuASSR) in a college context. The QuASSR contains 10 polytomous, two-tiered items crossed between two scenarios, and is based on theory suggesting a four-pronged structure for SSR (complexity, perspective taking, inquiry, and skepticism). In…

  5. Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

    Science.gov (United States)

    Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

    2017-01-01

    Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

  6. Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method.

    Science.gov (United States)

    Yu, Chen; Zhang, Qian; Xu, Peng-Yao; Bai, Yin; Shen, Wen-Bin; Di, Bin; Su, Meng-Xiang

    2017-09-15

    Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated (1) H-qNMR method for assay of octreotide acetate, a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard. Experimental conditions, including relaxation delay time, the numbers of scans, and pulse angle, were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision, and robustness. The assay result was compared with that by means of high performance liquid chromatography, which is provided by Chinese Pharmacopoeia. The statistical F test, Student's t test, and nonparametric test at 95% confidence level indicate that there was no significant difference between these two methods. qNMR is a simple and accurate quantitative tool with no need for specific corresponding reference standards. It has the potential of the quantitative analysis of other peptide drugs and standardization of the corresponding reference standards. Copyright © 2017 John Wiley & Sons, Ltd.

  7. Expanding the Framework of Internal and External Validity in Quantitative Research.

    Science.gov (United States)

    Onwuegbuzie, Anthony J.

    An experiment is deemed to be valid, inasmuch as valid cause-effect relationships are established, if the results are due only to the manipulated independent variable (possess internal validity) and are generalizable to groups, environments, and contexts outside of the experimental settings (possess external validity). Consequently, all…

  8. Exploring valid reference genes for quantitative real-time PCR analysis in Sesamia inferens (Lepidoptera: Noctuidae.

    Directory of Open Access Journals (Sweden)

    Meng Sun

    Full Text Available The pink stem borer, Sesamia inferens, which is endemic in China and other parts of Asia, is a major pest of rice and causes significant yield loss in this host plant. Very few studies have addressed gene expression in S. inferens. Quantitative real-time PCR (qRT-PCR is currently the most accurate and sensitive method for gene expression analysis. In qRT-PCR, data are normalized using reference genes, which help control for internal differences and reduce error between samples. In this study, seven candidate reference genes, 18S ribosomal RNA (18S rRNA, elongation factor 1 (EF1, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, ribosomal protein S13 (RPS13, ribosomal protein S20 (RPS20, tubulin (TUB, and β-actin (ACTB were evaluated for their suitability in normalizing gene expression under different experimental conditions. The results indicated that three genes (RPS13, RPS20, and EF1 were optimal for normalizing gene expression in different insect tissues (head, epidermis, fat body, foregut, midgut, hindgut, Malpighian tubules, haemocytes, and salivary glands. 18S rRNA, EF1, and GAPDH were best for normalizing expression with respect to developmental stages and sex (egg masses; first, second, third, fourth, fifth, and sixth instar larvae; male and female pupae; and one-day-old male and female adults. 18S rRNA, RPS20, and TUB were optimal for fifth instars exposed to different temperatures (-8, -6, -4, -2, 0, and 27°C. To validate this recommendation, the expression profile of a target gene heat shock protein 83 gene (hsp83 was investigated, and results showed the selection was necessary and effective. In conclusion, this study describes reference gene sets that can be used to accurately measure gene expression in S. inferens.

  9. Exploring valid reference genes for quantitative real-time PCR analysis in Sesamia inferens (Lepidoptera: Noctuidae).

    Science.gov (United States)

    Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

    2015-01-01

    The pink stem borer, Sesamia inferens, which is endemic in China and other parts of Asia, is a major pest of rice and causes significant yield loss in this host plant. Very few studies have addressed gene expression in S. inferens. Quantitative real-time PCR (qRT-PCR) is currently the most accurate and sensitive method for gene expression analysis. In qRT-PCR, data are normalized using reference genes, which help control for internal differences and reduce error between samples. In this study, seven candidate reference genes, 18S ribosomal RNA (18S rRNA), elongation factor 1 (EF1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein S13 (RPS13), ribosomal protein S20 (RPS20), tubulin (TUB), and β-actin (ACTB) were evaluated for their suitability in normalizing gene expression under different experimental conditions. The results indicated that three genes (RPS13, RPS20, and EF1) were optimal for normalizing gene expression in different insect tissues (head, epidermis, fat body, foregut, midgut, hindgut, Malpighian tubules, haemocytes, and salivary glands). 18S rRNA, EF1, and GAPDH were best for normalizing expression with respect to developmental stages and sex (egg masses; first, second, third, fourth, fifth, and sixth instar larvae; male and female pupae; and one-day-old male and female adults). 18S rRNA, RPS20, and TUB were optimal for fifth instars exposed to different temperatures (-8, -6, -4, -2, 0, and 27°C). To validate this recommendation, the expression profile of a target gene heat shock protein 83 gene (hsp83) was investigated, and results showed the selection was necessary and effective. In conclusion, this study describes reference gene sets that can be used to accurately measure gene expression in S. inferens.

  10. Examining the Content Validity of the WHOQOL-BRF from Respondents' Perspective by Quantitative Methods

    Science.gov (United States)

    Yao, Grace; Wu, Chia-Huei; Yang, Cheng-Ta

    2008-01-01

    Content validity, the extent to which a measurement reflects the specific intended domain of content, is a basic type of validity for a valid measurement. It was usually examined qualitatively and relied on experts' subjective judgments, not on respondents' responses. Therefore, the purpose of this study was to introduce and demonstrate how to use…

  11. Histology protocols

    Directory of Open Access Journals (Sweden)

    CarloAlberto Redi

    2010-06-01

    Full Text Available Tim D. Hewitson & Ian A. Darby (Eds Humana press, Totowa, New Jersey (USA Series: Springer Protocols Methods in Molecular Biology, Volume 611, 2010 Pages: 230; € 83.15 ISBN: 978-1-60327-344-2 Impressive as it can sounds in the era that Biology see a clear dominance of reductionism with the idea that complexity can be disentagled more and more thanks to the use of molecular tools, the reader will remain fascinated by this slim and agile volume devoted to bring together what apparently are two separeted words: molecular biology and histology. Simply remembering to the youngest scientists.....

  12. Validation of quantitative analysis method for triamcinolone in ternary complexes by UV-Vis spectrophotometry

    Directory of Open Access Journals (Sweden)

    GEORGE DARLOS A. AQUINO

    2011-06-01

    Full Text Available Triamcinolone (TRI, a drug widely used in the treatment of ocular inflammatory diseases, is practically insoluble in water, which limits its use in eye drops. Cyclodextrins (CDs have been used to increase the solubility or dissolution rate of drugs. The purpose of the present study was to validate a UV-Vis spectrophotometric method for quantitative analysis of TRI in inclusion complexes with beta-cyclodextrin (B-CD associated with triethanolamine (TEA (ternary complex. The proposed analytical method was validated with respect to the parameters established by the Brazilian regulatory National Agency of Sanitary Monitoring (ANVISA. The analytical measurements of absorbance were made at 242nm, at room temperature, in a 1-cm path-length cuvette. The precision and accuracy studies were performed at five concentration levels (4, 8, 12, 18 and 20μg.mL-1. The B-CD associated with TEA did not provoke any alteration in the photochemical behavior of TRI. The results for the measured analytical parameters showed the success of the method. The standard curve was linear (r2 > 0.999 in the concentration range from 2 to 24 μg.mL-1. The method achieved good precision levels in the inter-day (relative standard deviation-RSD <3.4% and reproducibility (RSD <3.8% tests. The accuracy was about 80% and the pH changes introduced in the robustness study did not reveal any relevant interference at any of the studied concentrations. The experimental results demonstrate a simple, rapid and affordable UV-Vis spectrophotometric method that could be applied to the quantitation of TRI in this ternary complex. Keywords: Validation. Triamcinolone. Beta-cyclodextrin. UV- Vis spectrophotometry. Ternary complexes. RESUMO Validação de método de análise quantitativa para a triancinolona a partir de complexo ternário por espectrofotometria de UV-Vis A triancinolona (TRI é um fármaco amplamente utilizado no tratamento de doenças inflamatórias do globo ocular e

  13. Preliminary evaluation of a fully automated quantitative framework for characterizing general breast tissue histology via color histogram and color texture analysis

    Science.gov (United States)

    Keller, Brad M.; Gastounioti, Aimilia; Batiste, Rebecca C.; Kontos, Despina; Feldman, Michael D.

    2016-03-01

    Visual characterization of histologic specimens is known to suffer from intra- and inter-observer variability. To help address this, we developed an automated framework for characterizing digitized histology specimens based on a novel application of color histogram and color texture analysis. We perform a preliminary evaluation of this framework using a set of 73 trichrome-stained, digitized slides of normal breast tissue which were visually assessed by an expert pathologist in terms of the percentage of collagenous stroma, stromal collagen density, duct-lobular unit density and the presence of elastosis. For each slide, our algorithm automatically segments the tissue region based on the lightness channel in CIELAB colorspace. Within each tissue region, a color histogram feature vector is extracted using a common color palette for trichrome images generated with a previously described method. Then, using a whole-slide, lattice-based methodology, color texture maps are generated using a set of color co-occurrence matrix statistics: contrast, correlation, energy and homogeneity. The extracted features sets are compared to the visually assessed tissue characteristics. Overall, the extracted texture features have high correlations to both the percentage of collagenous stroma (r=0.95, phistological processes in digitized histology specimens.

  14. Definitions and validation criteria for biomarkers and surrogate endpoints: development and testing of a quantitative hierarchical levels of evidence schema

    DEFF Research Database (Denmark)

    Lassere, Marissa N; Johnson, Kent R; Boers, Maarten

    2007-01-01

    to develop a hierarchical schema that systematically evaluates and ranks the surrogacy status of biomarkers and surrogates; and to obtain feedback from stakeholders. METHODS: After a systematic search of Medline and Embase on biomarkers, surrogate (outcomes, endpoints, markers, indicators), intermediate...... endpoints, and leading indicators, a quantitative surrogate validation schema was developed and subsequently evaluated at a stakeholder workshop. RESULTS: The search identified several classification schema and definitions. Components of these were incorporated into a new quantitative surrogate validation...... of the National Institutes of Health definitions of biomarker, surrogate endpoint, and clinical endpoint was useful. CONCLUSION: Further development and application of this schema provides incentives and guidance for effective biomarker and surrogate endpoint research, and more efficient drug discovery...

  15. Validation of high-performance liquid chromatography (HPLC method for quantitative analysis of histamine in fish and fishery products

    Directory of Open Access Journals (Sweden)

    B.K.K.K. Jinadasa

    2016-12-01

    Full Text Available A high-performance liquid chromatography method is described for quantitative determination and validation of histamine in fish and fishery product samples. Histamine is extracted from fish/fishery products by homogenizing with tri-chloro acetic acid, separated with Amberlite CG-50 resin and C18-ODS Hypersil reversed phase column at ambient temperature (25°C. Linear standard curves with high correlation coefficients were obtained. An isocratic elution program was used; the total elution time was 10 min. The method was validated by assessing the following aspects; specificity, repeatability, reproducibility, linearity, recovery, limits of detection, limit of quantification and uncertainty. The validated parameters are in good agreement with method and it is a useful tool for determining histamine in fish and fishery products.

  16. Consensus strategy to quantitate malignant cells in myeloma patients is validated in a multicenter study

    NARCIS (Netherlands)

    Willems, P; Verhagen, O; Segeren, C; Veenhuizen, P; Guikema, J; Wiemer, E; Groothuis, L; Buitenweg-de Jong, T; Kok, H; Bloem, A; Bos, N; Vellenga, E; Mensink, E; Sonneveld, P; van der Schoot, HLE; Raymakers, R

    2000-01-01

    Recently the Belgium-Dutch Hematology-Oncology group initiated a multicenter study to evaluate whether myeloma patients treated with intensive chemotherapy benefit from additional peripheral stem cell transplantation. To determine treatment response accurately, we decided to quantitate malignant cel

  17. Validity of a Semi-Quantitative Food Frequency Questionnaire for Collegiate Athletes

    Directory of Open Access Journals (Sweden)

    Ayaka Sunam

    2016-06-01

    Full Text Available Background: Food frequency questionnaires (FFQs have been developed and validated for various populations. To our knowledge, however, no FFQ has been validated for young athletes. Here, we investigated whether an FFQ that was developed and validated to estimate dietary intake in middle-aged persons was also valid for estimating that in young athletes. Methods: We applied an FFQ that had been developed for the Japan Public Health Center-based Prospective Cohort Study with modification to the duration of recollection. A total of 156 participants (92 males completed the FFQ and a 3-day non-consecutive 24-hour dietary recall (24hDR. Validity of the mean estimates was evaluated by calculating the percentage differences between the 24hDR and FFQ. Ranking estimation was validated using Spearman’s correlation coefficient (CC, and the degree of miscategorization was determined by joint classification. Results: The FFQ underestimated energy intake by approximately 10% for both males and females. For 35 nutrients, the median (range deattenuated CC was 0.30 (0.10 to 0.57 for males and 0.32 (−0.08 to 0.62 for females. For 19 food groups, the median (range deattenuated CC was 0.32 (0.17 to 0.72 for males and 0.34 (−0.11 to 0.58 for females. For both nutrient and food group intakes, cross-classification analysis indicated extreme miscategorization rates of 3% to 5%. Conclusions: An FFQ developed and validated for middle-aged persons had comparable validity among young athletes. This FFQ might be useful for assessing habitual dietary intake in collegiate athletes, especially for calcium, vitamin C, vegetables, fruits, and milk and dairy products.

  18. Development, validation and quantitative assessment of an enzymatic assay suitable for small molecule screening and profiling: A case-study

    Directory of Open Access Journals (Sweden)

    Vicente Sancenon

    2015-06-01

    Full Text Available The successful discovery and subsequent development of small molecule inhibitors of drug targets relies on the establishment of robust, cost-effective, quantitative, and physiologically relevant in vitro assays that can support prolonged screening and optimization campaigns. The current study illustrates the process of developing and validating an enzymatic assay for the discovery of small molecule inhibitors using alkaline phosphatase from bovine intestine as model target. The assay development workflow includes an initial phase of optimization of assay materials, reagents, and conditions, continues with a process of miniaturization and automation, and concludes with validation by quantitative measurement of assay performance and signal variability. The assay is further evaluated for dose–response and mechanism-of-action studies required to support structure–activity-relationship studies. Emphasis is placed on the most critical aspects of assay optimization and other relevant considerations, including the technology, assay materials, buffer constituents, reaction conditions, liquid handling equipment, analytical instrumentation, and quantitative assessments. Examples of bottlenecks encountered during assay development and strategies to address them are provided.

  19. A validated UHPLC-tandem mass spectrometry method for quantitative analysis of flavonolignans in milk thistle (Silybum marianum) extracts.

    Science.gov (United States)

    Graf, Tyler N; Cech, Nadja B; Polyak, Stephen J; Oberlies, Nicholas H

    2016-07-15

    Validated methods are needed for the analysis of natural product secondary metabolites. These methods are particularly important to translate in vitro observations to in vivo studies. Herein, a method is reported for the analysis of the key secondary metabolites, a series of flavonolignans and a flavonoid, from an extract prepared from the seeds of milk thistle [Silybum marianum (L.) Gaertn. (Asteraceae)]. This report represents the first UHPLC MS-MS method validated for quantitative analysis of these compounds. The method takes advantage of the excellent resolution achievable with UHPLC to provide a complete analysis in less than 7min. The method is validated using both UV and MS detectors, making it applicable in laboratories with different types of analytical instrumentation available. Lower limits of quantitation achieved with this method range from 0.0400μM to 0.160μM with UV and from 0.0800μM to 0.160μM with MS. The new method is employed to evaluate variability in constituent composition in various commercial S. marianum extracts, and to show that storage of the milk thistle compounds in DMSO leads to degradation.

  20. Cross-method validation as a solution to the problem of excessive simplification of measurement in quantitative IR research

    DEFF Research Database (Denmark)

    Beach, Derek

    2007-01-01

    The purpose of this article is to make IR scholars more aware of the costs of choosing quantitative methods. The article first shows that quantification can have analytical ‘costs’ when the measures created are too simple to capture the essence of the systematized concept that was supposed...... to be measured. If we create measures that do not accurately map the structure of the systematized concept, we are left with inaccurate and misleading measures that result in biased inferences. This is illustrated by replicating a recent article published in International Organization, and then discussed in more...... detail based upon a review of the democratic peace literature. I then offer two positive suggestions for a way forward. First, I argue that quantitative scholars should spend more time validating their measures, and in particular should engage in multi-method partnerships with qualitative scholars...

  1. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    DEFF Research Database (Denmark)

    Zhu, Mingyao; Bzdusek, Karl; Brink, Carsten

    2013-01-01

    Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE).......Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE)....

  2. Tumor Delineation and Quantitative Assessment of Glucose Metabolic Rate within Histologic Subtypes of Non-Small Cell Lung Cancer by Using Dynamic (18)F Fluorodeoxyglucose PET.

    Science.gov (United States)

    Meijer, Tineke W H; de Geus-Oei, Lioe-Fee; Visser, Eric P; Oyen, Wim J G; Looijen-Salamon, Monika G; Visvikis, Dimitris; Verhagen, Ad F T M; Bussink, Johan; Vriens, Dennis

    2016-11-15

    Purpose To assess whether dynamic fluorine 18 ((18)F) fluorodeoxyglucose (FDG) positron emission tomography (PET) has added value over static (18)F-FDG PET for tumor delineation in non-small cell lung cancer (NSCLC) radiation therapy planning by using pathology volumes as the reference standard and to compare pharmacokinetic rate constants of (18)F-FDG metabolism, including regional variation, between NSCLC histologic subtypes. Materials and Methods The study was approved by the institutional review board. Patients gave written informed consent. In this prospective observational study, 1-hour dynamic (18)F-FDG PET/computed tomographic examinations were performed in 35 patients (36 resectable NSCLCs) between 2009 and 2014. Static and parametric images of glucose metabolic rate were obtained to determine lesion volumes by using three delineation strategies. Pathology volume was calculated from three orthogonal dimensions (n = 32). Whole tumor and regional rate constants and blood volume fraction (VB) were computed by using compartment modeling. Results Pathology volumes were larger than PET volumes (median difference, 8.7-25.2 cm(3); Wilcoxon signed rank test, P segmentation on static (18)F-FDG PET images is in best agreement with pathology volume and could be useful for NSCLC autocontouring. Differences in glycolytic rate and VB between SCC and AC are relevant for research in targeting agents and radiation therapy dose escalation. (©) RSNA, 2016 Online supplemental material is available for this article.

  3. Moroccan colloquial Arabic version of the Mini International Neuropsychiatric Interview (MINI): qualitative and quantitative validation.

    Science.gov (United States)

    Kadri, N; Agoub, M; El Gnaoui, S; Alami, Kh Mchichi; Hergueta, T; Moussaoui, D

    2005-03-01

    The validation of mini international neuropsychiatric interview (MINI) into Moroccan Colloquial Arabic language demonstrated good psychometric properties. The concordance between translated MINI's and expert diagnoses was good with kappa values greater than 0.80. The reliability inter-rater and test-retest were excellent with kappa values above 0.80 and 0.90, respectively.

  4. Development and validation of X-ray diffraction method for quantitative determination of crystallinity in warfarin sodium products.

    Science.gov (United States)

    Siddiqui, Akhtar; Rahman, Ziyaur; Korang-Yeboah, Maxwell; Khan, Mansoor A

    2015-09-30

    The objective of this study was to develop and validate XRPD analytical method for the estimation of percent crystalline warfarin sodium present in drug products. Warfarin sodium (WS) is a clathrate containing Isopropyl alcohol entrapped in the crystalline structure. Four types of WS-excipient mixtures were prepared and used to make four formulations: M1 containing lactose monohydrate (WS: excipient 1:9), M2 containing anhydrous lactose (WS: excipient 1:9), M3 containing lactose monohydrate (WS: excipient 1:21.5), M4 containing lactose anhydrous (WS: excipient 1:21.5). Thoroughly mixed powders were packed in the XRD sample holders and diffractogram were collected. Diffractogram in the 7-9 2θ were found to be distinctive as the peak intensity grows with increasing percent crystalline WS. This peak region was, therefore, used to validate the XRPD method. Validation parameters were evaluated for accuracy, precision, linearity, limit of detection (LOD), and limit of quantitation (LOQ). LOD and LOQ for M1, M2, M3, and M4 were 3.04, 3.17, 4.17, 4.49% and 9.21, 9.62, 12.65, 13.30%, respectively. The method was found to be linear with R(2)>0.99. With changing scan speed, X-ray power output, and type of sample holder, the method was found to be robust. Prediction of the % crystalline content of the WS sample with known crystallinity showed close agreement between actual and predicted value. In summary, XRPD method was validated, which can be used as a quantitative method for the estimation of % crystalline WS present in a drug product.

  5. Selection and validation of reference genes for quantitative gene expression studies in Erythroxylum coca

    OpenAIRE

    2013-01-01

    Real-time quantitative PCR is a powerful technique for the investigation of comparative gene expression, but its accuracy and reliability depend on the reference genes used as internal standards. Only genes that show a high level of expression stability are suitable for use as reference genes, and these must be identified on a case-by-case basis. Erythroxylum coca produces and accumulates high amounts of the pharmacologically active tropane alkaloid cocaine (especially in the leaves), and is ...

  6. Repeatability and relative validity of a quantitative food-frequency questionnaire among French adults

    Directory of Open Access Journals (Sweden)

    Emmanuel Barrat

    2012-10-01

    Full Text Available Background: A 50-item self-administered food frequency questionnaire (FFQ was developed for French adults, to assess the intake of energy, 10 macronutrients, 11 vitamins, and 11 minerals, and to be used in the context of a medical consultation. Objective: To assess the repeatability and relative validity of this FFQ compared to a 7-day diet record (7-DR. Design: A total of 54 and 100 French adults were included in the repeatability and validation studies, respectively. Repeatability was assessed using two FFQs, the second carried out 3 weeks after the first. In the validation study, subjects first completed the FFQ, then the 7-DR the following week. Energy and nutrient intakes were compared using Pearson correlation. The degree of misclassification by the FFQ, compared to the 7-DR, was calculated by a contingency table of quintiles. Bland–Altman plots assessed the correlation between FFQ and 7-DR across the intake range. Results: Repeatability for intake, explored by Pearson correlation, was 0.62–0.90 (median: 0.81. Relative validity, as determined by Pearson correlation for the nutrient intake derived from the FFQ and 7-DR, was 0.36–0.80 (0.64. The FFQ tended to report higher fiber and micronutrient intake than 7-DR. Misclassification into opposite quintiles ranged 0–6% (1%, whereas classification into same or adjacent quintiles ranged 59–83% (74%. Bland–Altman plots showed good agreement for most nutrients across the range of intake. Conclusion: This new FFQ showed a high repeatability and good relative validity, and thanks to its short length, should be a useful tool for rapidly evaluating the nutrient intake of French adults.

  7. Identification and validation of quantitative trait loci (QTL for canine hip dysplasia (CHD in German Shepherd Dogs.

    Directory of Open Access Journals (Sweden)

    Lena Fels

    Full Text Available Canine hip dysplasia (CHD is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20-32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL and a novel QTL for CHD in German Shepherd Dogs.

  8. Quantitative [18F]fluorodopa/PET and histology of fetal mesencephalic dopaminergic grafts to the striatum of MPTP-poisoned minipigs

    DEFF Research Database (Denmark)

    Dall, Annette Møller; Danielsen, Erik Hvid; Sørensen, Jens Christian

    2002-01-01

    , and again at 3 and 6 months postsurgery, all animals were subjected to quantitative [18F]fluorodopa PET scans and testing for motor impairment. At the end of 6 months, tyrosine hydroxylase (TH)-containing neurons were counted in the grafts by stereological methods. The MPTP poisoning persistently reduced......The functional restoration of the dopamine innervation of striatum in MPTP-poisoned Göttingen minipigs was assessed for 6 months following grafting of fetal pig mesencephalic neurons. Pigs were assigned to a normal control group and a MPTP-poisoned group, members of which received no further...

  9. A validated new method for nevirapine quantitation in human plasma via high-performance liquid chromatography.

    Science.gov (United States)

    Silverthorn, Courtney F; Parsons, Teresa L

    2006-01-01

    A fully validated and clinically relevant assay was developed for the assessment of nevirapine concentrations in neonate blood plasma samples. Solid-phase extraction with an acid-base wash series was used to prepare subject samples for analysis. Samples were separated by high performance liquid chromatography and detected at 280 nm on a C8 reverse-phase column in an isocratic mobile phase. The retention times of nevirapine and its internal standard were 5.0 and 6.9 min, respectively. The method was validated by assessment of accuracy and precision (statistical values 0.996) and the average recovery was 93% (n = 18). The lower limit of quantification (relative standard deviation <20%) was determined to be 25 ng/mL for 50 microL of plasma, allowing detection of as little as 1.25 ng of nevirapine in a sample. This value represents an increase in sensitivity of up to 30-fold over previously published methods.

  10. Quantitative analysis of toxic and essential elements in human hair. Clinical validity of results.

    Science.gov (United States)

    Kosanovic, Melita; Jokanovic, Milan

    2011-03-01

    Over the last three decades, there has been an increasing awareness of environmental and occupational exposures to toxic or potentially toxic trace elements. The evolution of biological monitoring includes knowledge of kinetics of toxic and/or essential elements and adverse health effects related to their exposure. The debate whether a hair is a valid sample for biomonitoring or not is still attracting the attention of analysts, health care professionals, and environmentalists. Although researchers have found many correlations of essential elements to diseases, metabolic disorders, environmental exposures, and nutritional status, opponents of the concept of hair analysis object that hair samples are unreliable due to the influence of external factors. This review discusses validity of hair as a sample for biomonitoring of essential and toxic elements, with emphasis on pre-analytical, analytical, and post-analytical factors influencing results.

  11. Relative validity and reliability of a quantitative food frequency questionnaire for adults in Guam

    Directory of Open Access Journals (Sweden)

    Rachael T. Leon Guerrero

    2015-05-01

    Full Text Available Background: Guam is a US territory in the western Pacific with a diverse population that includes understudied ethnic groups such as Chamorros and Filipinos. A food frequency questionnaire (FFQ to estimate dietary intake was needed to facilitate studies of diet and health among adults living in Guam. Objective: To develop and validate an FFQ to assess dietary intake over a 1-year period among adult Guam residents. Design: A three-part study was conducted: 1 an initial cross-sectional study using 24-h recalls to identify a food and beverage list for the FFQ and resulting in a final FFQ containing 142 food and drink items; 2 to test reliability, 56 different individuals completed the FFQ twice; and 3 to test relative validity, self-administered FFQs and up to 2 days of food record data from an additional 109 individuals were collected, and daily nutrient intake from the two methods was compared. Results: The reliability of the FFQ was very good (ρ range=0.65–0.75, and the relative validity of the FFQ was good for women (median Spearman's correlation [ρ] between instruments of 0.45 across 20 nutrients and an interquartile range [IQR] of 0.42–0.58 and generally adequate for men (median ρ=0.31, IQR=0.23–0.55. Validity was also good for Chamorros (median ρ=0.47, IQR=0.38–0.53 and generally adequate for Filipinos (median ρ=0.42, IQR=0.20–0.62. Correlations after energy adjustment were lower (overall median ρ=0.20, IQR=0.14–0.26. Conclusions: The FFQ can be used to rank nutrient intake for adults in Guam and may be helpful in the analysis of relationships between diet and chronic disease in Guam.

  12. Evaluating the validity of spectral calibration models for quantitative analysis following signal preprocessing.

    Science.gov (United States)

    Chen, Da; Grant, Edward

    2012-11-01

    When paired with high-powered chemometric analysis, spectrometric methods offer great promise for the high-throughput analysis of complex systems. Effective classification or quantification often relies on signal preprocessing to reduce spectral interference and optimize the apparent performance of a calibration model. However, less frequently addressed by systematic research is the affect of preprocessing on the statistical accuracy of a calibration result. The present work demonstrates the effectiveness of two criteria for validating the performance of signal preprocessing in multivariate models in the important dimensions of bias and precision. To assess the extent of bias, we explore the applicability of the elliptic joint confidence region (EJCR) test and devise a new means to evaluate precision by a bias-corrected root mean square error of prediction. We show how these criteria can effectively gauge the success of signal pretreatments in suppressing spectral interference while providing a straightforward means to determine the optimal level of model complexity. This methodology offers a graphical diagnostic by which to visualize the consequences of pretreatment on complex multivariate models, enabling optimization with greater confidence. To demonstrate the application of the EJCR criterion in this context, we evaluate the validity of representative calibration models using standard pretreatment strategies on three spectral data sets. The results indicate that the proposed methodology facilitates the reliable optimization of a well-validated calibration model, thus improving the capability of spectrophotometric analysis.

  13. Daphnia and fish toxicity of (benzo)triazoles: validated QSAR models, and interspecies quantitative activity-activity modelling.

    Science.gov (United States)

    Cassani, Stefano; Kovarich, Simona; Papa, Ester; Roy, Partha Pratim; van der Wal, Leon; Gramatica, Paola

    2013-08-15

    Due to their chemical properties synthetic triazoles and benzo-triazoles ((B)TAZs) are mainly distributed to the water compartments in the environment, and because of their wide use the potential effects on aquatic organisms are cause of concern. Non testing approaches like those based on quantitative structure-activity relationships (QSARs) are valuable tools to maximize the information contained in existing experimental data and predict missing information while minimizing animal testing. In the present study, externally validated QSAR models for the prediction of acute (B)TAZs toxicity in Daphnia magna and Oncorhynchus mykiss have been developed according to the principles for the validation of QSARs and their acceptability for regulatory purposes, proposed by the Organization for Economic Co-operation and Development (OECD). These models are based on theoretical molecular descriptors, and are statistically robust, externally predictive and characterized by a verifiable structural applicability domain. They have been applied to predict acute toxicity for over 300 (B)TAZs without experimental data, many of which are in the pre-registration list of the REACH regulation. Additionally, a model based on quantitative activity-activity relationships (QAAR) has been developed, which allows for interspecies extrapolation from daphnids to fish. The importance of QSAR/QAAR, especially when dealing with specific chemical classes like (B)TAZs, for screening and prioritization of pollutants under REACH, has been highlighted. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. QUANTITATIVE HISTOLOGICAL OBSERVATION OF THE DISGESTIVE TRACTS OF XINGJING ANGORA RABBITS%荥经长毛兔消化道计量组织学观察

    Institute of Scientific and Technical Information of China (English)

    吴雪; 何敏; 杨本康; 叶萌玲; 张卫华

    2012-01-01

    本文采用大体解剖、石蜡组织切片技术和Spot321图像分析系统对荥经长毛兔消化道各段进行了观察研究.结果显示:荥经长毛兔消化道具典型草食动物结构特性,口腔内具发达的牙齿,上蜃纵向开裂;食道粗短,黏膜表皮角质化;胃囊状膨大,黏膜皱褶发达;小肠长,肠绒毛发达;大肠较长,无肠绒毛.各段管腔壁由内向外依次分为黏膜、粘膜下层、肌层、浆膜(外膜)四层结构,各部位的主要区别在于黏膜层,此外,粘膜下层、肌层的相对厚度等也存在差异.荥经长毛兔消化道的解剖学和组织学结构与其食草性功能密切相关.%This article tries to analyze and research the alimentary canals of Xingjing Angora rabbits by the methods of groee'anatomy,paraffin tissue section and Spot321 image dissector system. Results show that the Xingjing Angora rabbits are typical herbivores. There are developed teeth in their mouths, and their upper b'ps crack vertically. The esophagus, whose mucous epidermals keratinizate, are short and thick. The stomachs are voluminous like bags and the mucosas are abundant. There are lots of intestinal villus in their small intestines, which are very long. The large intestines are relatively long and in particular caecums are thick and big. Paragraphs cavity walls can be divided into four layer structures;mucosa; submucosa;muscle layer and serosal from the inside out,and their main differences lie in mucous layers, submucosas as well as muscular layers. This study shows that Xingjing Angora rabbits'anatomical and histologic structural characteristics of digestive tracts are similar to those of the ordinary rabbits,and structural characteristics of the entire digestive tract are closely connected with functions of eating grass.

  15. Classification tool for the systematic histological assessment of hepatocellular carcinoma, macroregenerative nodules, and dysplastic nodules in cirrhotic liver

    Institute of Scientific and Technical Information of China (English)

    A Quaglia; MA Jutand; A Dhillon; A Godfrey; R Togni; P Bioulac-Sage; C Balabaud; M Winnock; AP Dhillon

    2005-01-01

    AIM: To design a classification tool for the histological assessment of hepatocellular carcinoma (HCC), dysplastic nodules (DN), and macroregenerative nodules (MRN) in cirrhotic liver.METHODS: Two hundred and twelve hepatocellular nodules (106 HCC;74 MRN;32 DN) were assessed systematically, quantitatively, and semiquantitatively as appropriate for 10 histological features that have been described as helpful in distinguishing small HCC, DN, and MRN in cirrhotic livers. The data were analyzed by multiple correspondence analysis (MCA).RESULTS: MCA distributed HCC, DN, and MRN as defined by traditional histological evaluation as well as the individual histological variables, in a "malignancy scale".Based on the MCA data representation, we created a classification tool, which categorizes an individual nodular lesion as MRN, DN, or HCC based on the balance of all histological features (i.e., vascular invasion, capsular invasion, tumor necrosis, tumor heterogeneity, reticulin loss,capillarization of sinusoids, trabecular thickness, nuclear atypia, and mitotic activity). The classification tool dassified most (83%) of a validation set of 47 nodules in the same way as the routine histological assessment. No discrepandes were present for DN and MRN between the routine histological assignment and the classification tool. Of 25 HCC assigned by routine assessment in the validation set, 8were assigned to the DN category by the classification tool.CONCLUSION: We have designed a classification tool for the histological assessment of HCC and its putative precursors in cirrhotic liver. Application of this tool systematically records histological features of diagnostic importance in the evaluation of small HCC.

  16. Fairness is not validity or cultural bias in racial-group assessment: a quantitative perspective.

    Science.gov (United States)

    Helms, Janet E

    2006-11-01

    When test scores that differ by racial groups are used for assessment purposes, resulting decisions regarding members of the lower scoring group are potentially unfair. Fairness is defined as the removal from test scores of systematic variance attributable to experiences of racial or cultural socialization, and it is differentiated from test-score validity and cultural bias. Two fairness models for identifying, quantifying, and removing from test scores construct-irrelevant variance attributable to racial or cultural psychological attributes are presented. ((c) 2006 APA, all rights reserved).

  17. AMS method validation for quantitation in pharmacokinetic studies with concomitant extravascular and intravenous administration.

    Science.gov (United States)

    Lappin, Graham; Seymour, Mark; Young, Graeme; Higton, David; Hill, Howard M

    2011-02-01

    A technique has emerged in the past few years that has enabled a drug's intravenous pharmacokinetics to be readily obtained in humans without having to conduct extensive toxicology studies by this route of administration or expand protracted effort in formulation. The technique involves the intravenous administration of a low dose of (14)C-labelled drug (termed a tracer dose) concomitantly with a non-labelled extravascular dose given at therapeutically levels. Plasma samples collected over time are analysed to determine the total parent drug concentration by LC-MS (which essentially measures that arising from the oral dose) and by LC followed by accelerator mass spectrometry (AMS) to determine the (14)C-drug concentration (i.e., that arising from the intravenous dose). There are currently no published accounts of how the principles of bioanalytical validation might be applied to intravenous studies using AMS as an analytical technique. The authors describe the primary elements of AMS when used with LC separation and how this off-line technique differs from LC-MS. They then discuss how the principles of bioanalytical validation might be applied to determine selectivity, accuracy, precision and stability of methods involving LC followed by AMS analysis.

  18. A Quantitative Structure Activity Relationship for acute oral toxicity of pesticides on rats: Validation, domain of application and prediction.

    Science.gov (United States)

    Hamadache, Mabrouk; Benkortbi, Othmane; Hanini, Salah; Amrane, Abdeltif; Khaouane, Latifa; Si Moussa, Cherif

    2016-02-13

    Quantitative Structure Activity Relationship (QSAR) models are expected to play an important role in the risk assessment of chemicals on humans and the environment. In this study, we developed a validated QSAR model to predict acute oral toxicity of 329 pesticides to rats because a few QSAR models have been devoted to predict the Lethal Dose 50 (LD50) of pesticides on rats. This QSAR model is based on 17 molecular descriptors, and is robust, externally predictive and characterized by a good applicability domain. The best results were obtained with a 17/9/1 Artificial Neural Network model trained with the Quasi Newton back propagation (BFGS) algorithm. The prediction accuracy for the external validation set was estimated by the Q(2)ext and the root mean square error (RMS) which are equal to 0.948 and 0.201, respectively. 98.6% of external validation set is correctly predicted and the present model proved to be superior to models previously published. Accordingly, the model developed in this study provides excellent predictions and can be used to predict the acute oral toxicity of pesticides, particularly for those that have not been tested as well as new pesticides.

  19. Validity and reliability of a dish-based, semi-quantitative food frequency questionnaire for Korean diet and cancer research.

    Science.gov (United States)

    Park, Min Kyung; Noh, Hwa Young; Song, Na Yeun; Paik, Hee Young; Park, Sohee; Joung, Hyojee; Song, Won O; Kim, Jeongseon

    2012-01-01

    This study evaluated the validity and reliability of applying a newly developed dish-based, semi-quantitative food frequency questionnaire (FFQ) for Korean diet and cancer research. The subjects in the present study were 288 Korean adults over 30 years of age who had completed two FFQs and four 3-day diet records (DRs) from May 2008 to February 2009. Student's t-tests, Chi-square tests, and Spearman's rank correlation coefficients were used to estimate and compare intakes from different dietary assessment tools. Agreement in quintiles was calculated to validate agreement between the results of the second FFQ (FFQ-2) conducted in February 2009 and the DRs. Median Spearman's correlation coefficients between the intake of nutrients and foods assessed by the FFQ-1 and FFQ-2 were 0.59 and 0.57, respectively, and the coefficients between the intake of nutrients and foods assessed by the FFQ-2 and the DRs were 0.31 and 0.29, respectively. The quintile classifications of same or adjacent quintile for intake of nutrients and foods were 64% and 65%, respectively. Misclassification into opposite quintiles occurred in less than 5% for all dietary factors. Thus this newly-developed, Korean dish-based FFQ demonstrated moderate correspondence with the four 3-day DRs. Its reliability and validity are comparable to those reported in other studies.

  20. Validation of Cross-calibration Schemes for Quantitative Bone SPECT/CT Using Different Sources under Various Geometric Conditions.

    Science.gov (United States)

    Miyaji, Noriaki; Miwa, Kenta; Motegi, Kazuki; Umeda, Takuro; Wagatsuma, Kei; Fukai, Shohei; Takiguchi, Tomohiro; Terauchi, Takashi; Koizumi, Mitsuru

    Several cross-calibration schemes have been proposed to produce quantitative values in bone SPECT imaging. Differences in the radionuclide sources and geometric conditions can decrease the accuracy of cross-calibration factor (CCF). The present study aimed to validate the effects of calibration schemes using different sources under various geometric conditions. Temporal variations as well as variations in acquisition counts and the shapes of (57)Co standard and (99m)Tc point sources and a (99m)Tc disk source were determined. The effects of the geometric conditions of the source-to-camera distance (SCD) and lateral distance on the CCF were investigated by moving the camera or source away from the origin. The system planar sensitivity of NEMA incorporated into a Symbia Intevo SPECT/CT device (Siemens®) was defined as reference values. The temporal variation in CCF using the (57)Co source was relatively stable within the range of 0.7% to 2.3%, whereas the (99m)Tc source ranged from 2.7% to 7.3%. In terms of source shape, the (57)Co standard point source was the most stable. Both SCD and lateral distance decreased as a function of distance from the origin. Errors in the geometric condition were higher for the (57)Co standard point source than the (99m)Tc disk source. Different calibration schemes influenced the reliability of quantitative values. The (57)Co standard point source was stable over a long period, and this helped to maintain the quality of quantitative SPECT/CT imaging data. The CCF accuracy of the (99m)Tc source decreased depending on the preparative method. The method of calibration for quantitative SPECT should be immediately standardized to eliminate uncertainty.

  1. Validation of an analytical methodology for the quantitative analysis of petroleum hydrocarbons in marine sediment samples

    Directory of Open Access Journals (Sweden)

    Eloy Yordad Companioni Damas

    2009-01-01

    Full Text Available This work describes a validation of an analytical procedure for the analysis of petroleum hydrocarbons in marine sediment samples. The proposed protocol is able to measure n-alkanes and polycyclic aromatic hydrocarbons (PAH in samples at concentrations as low as 30 ng/g, with a precision better than 15% for most of analytes. The extraction efficiency of fortified sediments varied from 65.1 to 105.6% and 59.7 to 97.8%, for n-alkanes and PAH in the ranges: C16 - C32 and fluoranthene - benzo(apyrene, respectively. The analytical protocol was applied to determine petroleum hydrocarbons in sediments collected from a marine coastal zone.

  2. RP-HPLC Method Development and Its Validation for Quantitative Determination of Rimonabant in Human Plasma

    Directory of Open Access Journals (Sweden)

    Shravan Bankey

    2012-01-01

    Full Text Available A simple, accurate, and precise HPLC method was developed and validated for determination of rimonabant in human plasma. Following liquid-liquid extraction, chromatographic separation was accomplished using C18 column with mobile phase consisting of acetonitrile : water (90 : 10, v/v, drug was detected at 260 nm using UVdetector. The LOD and LOQ were 3.0 and 10.0 μg/L, respectively. The method is linear in the interval 50.0–1000.0 μg/L. The average extraction recovery of drug from plasma was found to be 92.2%. The percent CV of the method was found to be less than 10.8%, and accuracy was found between 94.5 and 106.7%. The assay may be applied to a pharmacokinetic and bioequivalence study of rimonabant.

  3. [Quantitative evaluation of 123I-FP-CIT SPECT: validation of a semiautomated method].

    Science.gov (United States)

    Lorenzo Bosquet, C; Cuberas Borrós, G; Miquel Rodríguez, F; Caresia, P; Aguadé Bruix, S; Castell Conesa, J

    2005-01-01

    To assess the utility of a quantification of the 123I-FP-CIT uptake by the definition of some reference values, normal range values and interobserver variation. Fifty patients with a 123I-FP-CIT SPECT: 25 patients had a pathological SPECT with the diagnosis of Parkinson's disease and the remaining had a qualitative normal SPET, with the diagnosis of 14 drug-induced Parkinsonism and 11 with psychogenic Parkinsonism. In the transversal slices, the best central slice that showed the nuclei of the base best was selected and standard ROIs (Region Of Interest) were applied. Specific (caudate and putamen) versus non specific (occipital) and laterality ratios were calculated. A normal statistical analysis for independent quantitative samples was used (mean, standard deviation and range) as well as variation coefficient and correlation coefficient of two observers and the 10th and 90th percentile. The variation coefficient interobserver was 3.24-5.61 and the correlation coefficient was 0.89-0.99. Cut-off values between both populations were established at 2.10 in the right putamen and at 2.05 in the left. Cut-off values definition in caudate were not assessable due to overlapping of ratios of both populations. This quantification method is highly reproducible. It makes it possible to obtain reference values and to define normal range.

  4. The overall impact of testing on medical student learning: quantitative estimation of consequential validity.

    Science.gov (United States)

    Kreiter, Clarence D; Green, Joseph; Lenoch, Susan; Saiki, Takuya

    2013-10-01

    Given medical education's longstanding emphasis on assessment, it seems prudent to evaluate whether our current research and development focus on testing makes sense. Since any intervention within medical education must ultimately be evaluated based upon its impact on student learning, this report seeks to provide a quantitative accounting of the learning gains attained through educational assessments. To approach this question, we estimate achieved learning within a medical school environment that optimally utilizes educational assessments. We compare this estimate to learning that might be expected in a medical school that employs no educational assessments. Effect sizes are used to estimate testing's total impact on learning by summarizing three effects; the direct effect, the indirect effect, and the selection effect. The literature is far from complete, but the available evidence strongly suggests that each of these effects is large and the net cumulative impact on learning in medical education is over two standard deviations. While additional evidence is required, the current literature shows that testing within medical education makes a strong positive contribution to learning.

  5. Selection and validation of reference genes for quantitative gene expression studies in Erythroxylum coca.

    Science.gov (United States)

    Docimo, Teresa; Schmidt, Gregor W; Luck, Katrin; Delaney, Sven K; D'Auria, John C

    2013-01-01

    Real-time quantitative PCR is a powerful technique for the investigation of comparative gene expression, but its accuracy and reliability depend on the reference genes used as internal standards. Only genes that show a high level of expression stability are suitable for use as reference genes, and these must be identified on a case-by-case basis. Erythroxylum coca produces and accumulates high amounts of the pharmacologically active tropane alkaloid cocaine (especially in the leaves), and is an emerging model for the investigation of tropane alkaloid biosynthesis. The identification of stable internal reference genes for this species is important for its development as a model species, and would enable comparative analysis of candidate biosynthetic genes in the different tissues of the coca plant. In this study, we evaluated the expression stability of nine candidate reference genes in E. coca ( Ec6409, Ec10131, Ec11142, Actin, APT2, EF1α, TPB1, Pex4, Pp2aa3). The expression of these genes was measured in seven tissues (flowers, stems, roots and four developmental leaf stages) and the stability of expression was assessed using three algorithms (geNorm, NormFinder and BestKeeper). From our results we conclude that Ec10131 and TPB1 are the most appropriate internal reference genes in leaves (where the majority of cocaine is produced), while Ec10131 and Ec6409 are the most suitable internal reference genes across all of the tissues tested.

  6. Intracranial aneurysm segmentation in 3D CT angiography: method and quantitative validation

    Science.gov (United States)

    Firouzian, Azadeh; Manniesing, R.; Flach, Z. H.; Risselada, R.; van Kooten, F.; Sturkenboom, M. C. J. M.; van der Lugt, A.; Niessen, W. J.

    2010-03-01

    Accurately quantifying aneurysm shape parameters is of clinical importance, as it is an important factor in choosing the right treatment modality (i.e. coiling or clipping), in predicting rupture risk and operative risk and for pre-surgical planning. The first step in aneurysm quantification is to segment it from other structures that are present in the image. As manual segmentation is a tedious procedure and prone to inter- and intra-observer variability, there is a need for an automated method which is accurate and reproducible. In this paper a novel semi-automated method for segmenting aneurysms in Computed Tomography Angiography (CTA) data based on Geodesic Active Contours is presented and quantitatively evaluated. Three different image features are used to steer the level set to the boundary of the aneurysm, namely intensity, gradient magnitude and variance in intensity. The method requires minimum user interaction, i.e. clicking a single seed point inside the aneurysm which is used to estimate the vessel intensity distribution and to initialize the level set. The results show that the developed method is reproducible, and performs in the range of interobserver variability in terms of accuracy.

  7. Sperm counts in enzymatically liquefied cervical mucus: quantitative validation using donor cervical mucus.

    Science.gov (United States)

    de Agostini, A; Campana, A

    1996-02-01

    The post-coital test evaluates the penetration of spermatozoa into cervical mucus; it relies on subjective measurements and therefore lacks precision. Enzymatic liquefaction of cervical mucus allows sperm concentration to be measured in post-coital test samples, but the reliability of such measurements is not known. Donor cervical mucus was used as a model to test the accuracy and sensitivity of sperm quantification in liquefied cervical mucus. Donor cervical mucus was dissolved by enzymatic treatments in the presence of known numbers of spermatozoa and the recovery of sperm cells was assessed after liquefaction of the samples. Enzymatic treatment of cervical mucus with a combination of bromelin and glycosidases resulted in reliable and fast liquefaction of the samples. The accuracy of sperm concentration measurements was 89 +/- 10% (mean +/- SD, n = 50), and the sensitivity limits were 1 x 10(6) and 0.2 x 10(6) spermatozoa/ml for quantitative concentration measurement and qualitative sperm detection respectively. This study demonstrates that liquefaction of cervical mucus by combined protease and glycosidases allows accurate and sensitive determination of sperm concentration in the sample. Therefore we believe that valuable data can be obtained for sperm concentration and total sperm counts in post-coital tests, that should help to improve the reliability of the post-coital test.

  8. Validation of Quantitative HPLC Method for Bacosides in KeenMind.

    Science.gov (United States)

    Dowell, Ashley; Davidson, George; Ghosh, Dilip

    2015-01-01

    Brahmi (Bacopa monnieri) has been used by Ayurvedic medical practitioners in India for almost 3000 years. The pharmacological properties of Bacopa monnieri were studied extensively and the activities were attributed mainly due to the presence of characteristic saponins called "bacosides." Bacosides are complex mixture of structurally closely related compounds, glycosides of either jujubogenin or pseudojujubogenin. The popularity of herbal medicines and increasing clinical evidence to support associated health claims require standardisation of the phytochemical actives contained in these products. However, unlike allopathic medicines which typically contain a single active compound, herbal medicines are typically complex mixtures of various phytochemicals. The assay for bacosides in the British Pharmacopoeia monograph for Bacopa monnieri exemplifies that only a subset of bacosides present are included in the calculation of total bacosides. These results in calculated bacoside values are significantly lower than those attained for the same material using more inclusive techniques such as UV spectroscopy. This study illustrates some of the problems encountered when applying chemical analysis for standardisation of herbal medicines, particularly in relation to the new method development and validation of bacosides from KeenMind.

  9. Validation of Quantitative HPLC Method for Bacosides in KeenMind

    Directory of Open Access Journals (Sweden)

    Ashley Dowell

    2015-01-01

    Full Text Available Brahmi (Bacopa monnieri has been used by Ayurvedic medical practitioners in India for almost 3000 years. The pharmacological properties of Bacopa monnieri were studied extensively and the activities were attributed mainly due to the presence of characteristic saponins called “bacosides.” Bacosides are complex mixture of structurally closely related compounds, glycosides of either jujubogenin or pseudojujubogenin. The popularity of herbal medicines and increasing clinical evidence to support associated health claims require standardisation of the phytochemical actives contained in these products. However, unlike allopathic medicines which typically contain a single active compound, herbal medicines are typically complex mixtures of various phytochemicals. The assay for bacosides in the British Pharmacopoeia monograph for Bacopa monnieri exemplifies that only a subset of bacosides present are included in the calculation of total bacosides. These results in calculated bacoside values are significantly lower than those attained for the same material using more inclusive techniques such as UV spectroscopy. This study illustrates some of the problems encountered when applying chemical analysis for standardisation of herbal medicines, particularly in relation to the new method development and validation of bacosides from KeenMind.

  10. Semiautomatic, Quantitative Measurement of Aortic Valve Area Using CTA: Validation and Comparison with Transthoracic Echocardiography

    Directory of Open Access Journals (Sweden)

    V. Tuncay

    2015-01-01

    Full Text Available Objective. The aim of this work was to develop a fast and robust (semiautomatic segmentation technique of the aortic valve area (AVA MDCT datasets. Methods. The algorithm starts with detection and cropping of Sinus of Valsalva on MPR image. The cropped image is then binarized and seed points are manually selected to create an initial contour. The contour moves automatically towards the edge of aortic AVA to obtain a segmentation of the AVA. AVA was segmented semiautomatically and manually by two observers in multiphase cardiac CT scans of 25 patients. Validation of the algorithm was obtained by comparing to Transthoracic Echocardiography (TTE. Intra- and interobserver variability were calculated by relative differences. Differences between TTE and MDCT manual and semiautomatic measurements were assessed by Bland-Altman analysis. Time required for manual and semiautomatic segmentations was recorded. Results. Mean differences from TTE were −0.19 (95% CI: −0.74 to 0.34 cm2 for manual and −0.10 (95% CI: −0.45 to 0.25 cm2 for semiautomatic measurements. Intra- and interobserver variability were 8.4 ± 7.1% and 27.6 ± 16.0% for manual, and 5.8 ± 4.5% and 16.8 ± 12.7% for semiautomatic measurements, respectively. Conclusion. Newly developed semiautomatic segmentation provides an accurate, more reproducible, and faster AVA segmentation result.

  11. Validities of three multislice algorithms for quantitative low-energy transmission electron microscopy.

    Science.gov (United States)

    Ming, W Q; Chen, J H

    2013-11-01

    Three different types of multislice algorithms, namely the conventional multislice (CMS) algorithm, the propagator-corrected multislice (PCMS) algorithm and the fully-corrected multislice (FCMS) algorithm, have been evaluated in comparison with respect to the accelerating voltages in transmission electron microscopy. Detailed numerical calculations have been performed to test their validities. The results show that the three algorithms are equivalent for accelerating voltage above 100kV. However, below 100 kV, the CMS algorithm will introduce significant errors, not only for higher-order Laue zone (HOLZ) reflections but also for zero-order Laue zone (ZOLZ) reflections. The differences between the PCMS and FCMS algorithms are negligible and mainly appear in HOLZ reflections. Nonetheless, when the accelerating voltage is further lowered to 20 kV or below, the PCMS algorithm will also yield results deviating from the FCMS results. The present study demonstrates that the propagation of the electron wave from one slice to the next slice is actually cross-correlated with the crystal potential in a complex manner, such that when the accelerating voltage is lowered to 10 kV, the accuracy of the algorithms is dependent of the scattering power of the specimen. © 2013 Elsevier B.V. All rights reserved.

  12. Quantitative endoscopic imaging elastic scattering spectroscopy: model system/tissue phantom validation

    Science.gov (United States)

    Lindsley, E. H.; Farkas, D. L.

    2008-02-01

    We have designed and built an imaging elastic scattering spectroscopy endoscopic instrument for the purpose of detecting cancer in vivo. As part of our testing and validation of the system, known targets representing potential disease states of interest were constructed using polystyrene beads of known average diameter and TiO II crystals embedded in a two-layer agarose gel. Final construction geometry was verified using a dissection microscope. The phantoms were then imaged using the endoscopic probe at a known incident angle, and the results compared to model predictions. The mathematical model that was used combines classic ray-tracing optics with Mie scattering to predict the images that would be observed by the probe at a given physical distance from a Mie-regime scattering media. This model was used generate the expected observed response for a broad range of parameter values, and these results were then used as a library to fit the observed data from the phantoms. Compared against the theoretical library, the best matching signal correlated well with known phantom material dimensions. These results lead us to believe that imaging elastic scattering can be useful in detection/diagnosis, but further refinement of the device will be necessary to detect the weak signals in a real clinical setting.

  13. Validation of a quantitative food frequency questionnaire developed to under graduate students.

    Science.gov (United States)

    Komatsu, Tiemy Rosana; Oku, Simone Kimie; Gimeno, Suely Godoy Agostinho; Asakura, Leiko; Coelho, Luciola de Castro; Silva, Clarissa Viana Demezio da; Akutsu, Rita de Cassia Coelho Almeida; Sachs, Anita

    2013-12-01

    A validity test of a Food Frequency Questionnaire was carried out using 50 students of health occupation in São Paulo, Brazil. Therefore, a three day dietary record was used as reference method and variables such as energy, macronutrients and dietary fiber were analyzed. The accordance between the Food Frequency Questionnaire and average data from dietary record was tested with kappa statistics and intra-class correlation coefficients (ICC). Limits of agreement were estimated by the Bland-Altman's method. Better results were found for calories (ICC 0.43; 95%CI 0.17 - 0.63) and non-energy-adjusted nutrients, except dietary fiber (ICC 0.34; 95%CI 0.07 - 0.56). The percentage of individuals classified in the same category of consumption was nearly half (49.8%), while only 16% of them were classified in opposite categories. With the exception of lipids, other analyzed variables tended to be overestimated by the Food Frequency Questionnaire. The Food Frequency Questionnaire is recommended as a method of assessing food intake of university students in studies which focus on calorie estimates and also intend to classify groups into intake categories.

  14. Statistical inference for the within-device precision of quantitative measurements in assay validation.

    Science.gov (United States)

    Liu, Jen-Pei; Lu, Li-Tien; Liao, C T

    2009-09-01

    Intermediate precision is one of the most important characteristics for evaluation of precision in assay validation. The current methods for evaluation of within-device precision recommended by the Clinical Laboratory Standard Institute (CLSI) guideline EP5-A2 are based on the point estimator. On the other hand, in addition to point estimators, confidence intervals can provide a range for the within-device precision with a probability statement. Therefore, we suggest a confidence interval approach for assessment of the within-device precision. Furthermore, under the two-stage nested random-effects model recommended by the approved CLSI guideline EP5-A2, in addition to the current Satterthwaite's approximation and the modified large sample (MLS) methods, we apply the technique of generalized pivotal quantities (GPQ) to derive the confidence interval for the within-device precision. The data from the approved CLSI guideline EP5-A2 illustrate the applications of the confidence interval approach and comparison of results between the three methods. Results of a simulation study on the coverage probability and expected length of the three methods are reported. The proposed method of the GPQ-based confidence intervals is also extended to consider the between-laboratories variation for precision assessment.

  15. Development and validation of a RP–HPLC method for the quantitation studies of fipronil in Parakill suspensions

    Directory of Open Access Journals (Sweden)

    Elena Gabriela Oltean

    2011-12-01

    Full Text Available An isocratic high-performance liquid chromatography (HPLC procedure was developed for the quantitative determination of fipronil in suspensions of Parakill. HPLC separation was carried out by reversed phase chromatography on Betasil C18 (250 mm x 4.6 mm i.d.; 5 μm particle size, held in thermostat at 25°C. The mobile phase consisted of Acetonitrile/ Distilled water (60/ 40 v/ v, with a flow rate of 1 ml/ min and with UV detection at 220 nm. In order to validate the method, the following parameters have been investigated linearity (r2=0.9999, range, precision, accuracy, specificity, limit of detection and limit of quantification. The described method can be successfully applied for the analysis of the active pharmaceutical compound in PARAKILL suspensions.

  16. Development and validation of a RP- HPLC method for the quantitation studies of bromadiolone in Ratitox F

    Directory of Open Access Journals (Sweden)

    Elena Gabriela Oltean

    2011-12-01

    Full Text Available An isocratic high-performance liquid chromatography (HPLC procedure was developed for the quantitative determination of bromadiolone (hydroxycoumarins in Ratitox F product – rodenticide. HPLC separation was carried out by reversed phase chromatography ODS 2 Hypersil C18 (250 mm x 4.6 mm i.e.; 5 ìm particle size, held in thermostat at 25°C. The mobile phase consisted of methanol/0.1% aqueous solution phosphoric acid (90/10v/v, with a flow rate of 1 ml/min and with UV detection at 265 nm. In order to validate the method, the following parameters have been investigated- linearity (r2 = 0.9999, range, precision, accuracy, specificity, limit of detection and limit of quantification. The described method can be successfully applied for the analysis of Ratitox F – rodenticide.

  17. UPDATE February 2012 - The Food Crises: Predictive validation of a quantitative model of food prices including speculators and ethanol conversion

    CERN Document Server

    Lagi, Marco; Bertrand, Karla Z; Bar-Yam, Yaneer

    2012-01-01

    Increases in global food prices have led to widespread hunger and social unrest---and an imperative to understand their causes. In a previous paper published in September 2011, we constructed for the first time a dynamic model that quantitatively agreed with food prices. Specifically, the model fit the FAO Food Price Index time series from January 2004 to March 2011, inclusive. The results showed that the dominant causes of price increases during this period were investor speculation and ethanol conversion. The model included investor trend following as well as shifting between commodities, equities and bonds to take advantage of increased expected returns. Here, we extend the food prices model to January 2012, without modifying the model but simply continuing its dynamics. The agreement is still precise, validating both the descriptive and predictive abilities of the analysis. Policy actions are needed to avoid a third speculative bubble that would cause prices to rise above recent peaks by the end of 2012.

  18. Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.

    Directory of Open Access Journals (Sweden)

    Alexandre Filipe Borges

    Full Text Available Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gene expression analysis plays a fundamental role. Quantitative reverse transcription polymerase chain reaction (qRT-PCR is currently amongst the most powerful techniques to perform gene expression studies. Nevertheless, accurate gene expression quantification strongly relies on appropriate reference gene selection for sample normalization. Concerning V. vinifera, limited information still exists as for which genes are the most suitable to be used as reference under particular experimental conditions. In this work, seven candidate genes were investigated for their stability in grapevine samples referring to four distinct stresses (Erysiphe necator, wounding and UV-C irradiation in leaves and Phaeomoniella chlamydospora colonization in wood. The expression stability was evaluated using geNorm, NormFinder and BestKeeper. In all cases, full agreement was not observed for the three methods. To provide comprehensive rankings integrating the three different programs, for each treatment, a consensus ranking was created using a non-weighted unsupervised rank aggregation method. According to the last, the three most suitable reference genes to be used in grapevine leaves, regardless of the stress, are UBC, VAG and PEP. For the P. chlamydospora treatment, EF1, CYP and UBC were the best scoring genes. Acquaintance of the most suitable reference genes to be used in grapevine samples can contribute for accurate gene expression quantification in forthcoming studies.

  19. Reference gene validation for quantitative RT-PCR during biotic and abiotic stresses in Vitis vinifera.

    Science.gov (United States)

    Borges, Alexandre Filipe; Fonseca, Catarina; Ferreira, Ricardo Boavida; Lourenço, Ana Maria; Monteiro, Sara

    2014-01-01

    Grapevine is one of the most cultivated fruit crop worldwide with Vitis vinifera being the species with the highest economical importance. Being highly susceptible to fungal pathogens and increasingly affected by environmental factors, it has become an important agricultural research area, where gene expression analysis plays a fundamental role. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is currently amongst the most powerful techniques to perform gene expression studies. Nevertheless, accurate gene expression quantification strongly relies on appropriate reference gene selection for sample normalization. Concerning V. vinifera, limited information still exists as for which genes are the most suitable to be used as reference under particular experimental conditions. In this work, seven candidate genes were investigated for their stability in grapevine samples referring to four distinct stresses (Erysiphe necator, wounding and UV-C irradiation in leaves and Phaeomoniella chlamydospora colonization in wood). The expression stability was evaluated using geNorm, NormFinder and BestKeeper. In all cases, full agreement was not observed for the three methods. To provide comprehensive rankings integrating the three different programs, for each treatment, a consensus ranking was created using a non-weighted unsupervised rank aggregation method. According to the last, the three most suitable reference genes to be used in grapevine leaves, regardless of the stress, are UBC, VAG and PEP. For the P. chlamydospora treatment, EF1, CYP and UBC were the best scoring genes. Acquaintance of the most suitable reference genes to be used in grapevine samples can contribute for accurate gene expression quantification in forthcoming studies.

  20. Validation of a simple and inexpensive method for the quantitation of infarct in the rat brain

    Directory of Open Access Journals (Sweden)

    Schilichting C.L.R.

    2004-01-01

    Full Text Available A gravimetric method was evaluated as a simple, sensitive, reproducible, low-cost alternative to quantify the extent of brain infarct after occlusion of the medial cerebral artery in rats. In ether-anesthetized rats, the left medial cerebral artery was occluded for 1, 1.5 or 2 h by inserting a 4-0 nylon monofilament suture into the internal carotid artery. Twenty-four hours later, the brains were processed for histochemical triphenyltetrazolium chloride (TTC staining and quantitation of the schemic infarct. In each TTC-stained brain section, the ischemic tissue was dissected with a scalpel and fixed in 10% formalin at 0ºC until its total mass could be estimated. The mass (mg of the ischemic tissue was weighed on an analytical balance and compared to its volume (mm³, estimated either by plethysmometry using platinum electrodes or by computer-assisted image analysis. Infarct size as measured by the weighing method (mg, and reported as a percent (% of the affected (left hemisphere, correlated closely with volume (mm³, also reported as % estimated by computerized image analysis (r = 0.88; P < 0.001; N = 10 or by plethysmography (r = 0.97-0.98; P < 0.0001; N = 41. This degree of correlation was maintained between different experimenters. The method was also sensitive for detecting the effect of different ischemia durations on infarct size (P < 0.005; N = 23, and the effect of drug treatments in reducing the extent of brain damage (P < 0.005; N = 24. The data suggest that, in addition to being simple and low cost, the weighing method is a reliable alternative for quantifying brain infarct in animal models of stroke.

  1. Quantitative validation of sensory mapping in persistent postherniorrhaphy inguinal pain patients undergoing triple neurectomy.

    Science.gov (United States)

    Bjurström, M F; Álvarez, R; Nicol, A L; Olmstead, R; Amid, P K; Chen, D C

    2017-04-01

    Neurectomy of the inguinal nerves may be considered for selected refractory cases of chronic postherniorrhaphy inguinal pain (CPIP). There is to date a paucity of easily applicable clinical tools to identify neuropathic pain and examine the neurosensory effects of remedial surgery. The present quantitative sensory testing (QST) pilot study evaluates a sensory mapping technique. Longitudinal (preoperative, immediate postoperative, and late postoperative) dermatomal sensory mapping and a comprehensive QST protocol were conducted in CPIP patients with unilateral, predominantly neuropathic inguinodynia presenting for triple neurectomy (n = 13). QST was conducted in four areas on the affected, painful side and in one contralateral comparison site. QST variables were compared according to sensory mapping outcomes: (o)/normal sensation, (+)/pain, and (-)/numbness. Diagnostic ability of the sensory mapping outcomes to detect QST-assessed allodynia or hypoesthesia was estimated through calculation of specificity and sensitivity values. Preoperatively, patients exhibited mechanical hypoesthesia and allodynia and pressure allodynia and hyperalgesia in painful areas mapped (+) (p mapping outcome (+) demonstrated high ability to detect mechanical allodynia [sensitivity 0.74 (95% CI 0.61-0.86), specificity 0.94 (0.84-1.00)] and pressure allodynia [sensitivity 0.96 (0.89-1.00), specificity 1.00 (1.00-1.00)], but not thermal allodynia. Postoperatively, mapped areas of numbness (-) were associated with mechanical and thermal hypoesthesia (p mapping provides an accurate clinical neuropathic assessment with strong correlation to QST findings of preoperative mechanical and pressure allodynia, and postoperative mechanical and thermal hypoesthesia in CPIP patients undergoing neurectomy.

  2. Quantitative analysis of concrete using portable x-ray fluorescence: Method development and validation

    Energy Technology Data Exchange (ETDEWEB)

    Washington, Aaron L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Narrows, William [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Christian, Jonathan H. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Msgwood, Leroy [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-07-27

    During Decommissioning and Demolition (D&D) activities at SRS, it is important that the building be screened for radionuclides and heavy metals to ensure that the proper safety and disposal metrics are in place. A major source of contamination at DOE facilities is the accumulation of mercury contamination, from nuclear material processing and Liquid Waste System (LWS). This buildup of mercury could possibly cause harm to any demolition crew or the environment should this material be released. The current standard method is to take core samples in various places in the facility and use X-ray fluorescence (XRF) to detect the contamination. This standard method comes with a high financial value due to the security levels of these sample facilities with unknown contamination levels. Here in we propose the use of portable XRF units to detect for this contamination on-site. To validate this method, the instrument has to be calibrated to detect the heavy metal contamination, be both precise with the known elemental concentrations and consistent with its actual results of a sample concrete and pristine contaminant, and be able to detect changes in the sample concrete’s composition. After receiving the various concrete samples with their compositions found by a XRF wave-dispersive method, the calibration factor’s linear regressions were adjusted to give the baseline concentration of the concrete with no contamination. Samples of both concrete and concrete/flyash were evaluated; their standard deviations revealed that the measurements were consistent with the known composition. Finally, the samples were contaminated with different concentrations of sodium tungsten dihydrate, allowed to air dry, and measured. When the contaminated samples were analyzed, the heavy metal contamination was seen within the spectrum of the instrument, but there was not a trend of quantification based on the concentration of the solution.

  3. A Validated Reverse Phase HPLC Analytical Method for Quantitation of Glycoalkaloids in Solanum lycocarpum and Its Extracts

    Directory of Open Access Journals (Sweden)

    Renata Fabiane Jorge Tiossi

    2012-01-01

    Full Text Available Solanum lycocarpum (Solanaceae is native to the Brazilian Cerrado. Fruits of this species contain the glycoalkaloids solasonine (SN and solamargine (SM, which display antiparasitic and anticancer properties. A method has been developed for the extraction and HPLC-UV analysis of the SN and SM in different parts of S. lycocarpum, mainly comprising ripe and unripe fruits, leaf, and stem. This analytical method was validated and gave good detection response with linearity over a dynamic range of 0.77–1000.00 μg mL−1 and recovery in the range of 80.92–91.71%, allowing a reliable quantitation of the target compounds. Unripe fruits displayed higher concentrations of glycoalkaloids (1.04% ± 0.01 of SN and 0.69% ± 0.00 of SM than the ripe fruits (0.83% ± 0.02 of SN and 0.60% ± 0.01 of SM. Quantitation of glycoalkaloids in the alkaloidic extract gave 45.09% ± 1.14 of SN and 44.37% ± 0.60 of SM, respectively.

  4. Interlaboratory validation of quantitative duplex real-time PCR method for screening analysis of genetically modified maize.

    Science.gov (United States)

    Takabatake, Reona; Koiwa, Tomohiro; Kasahara, Masaki; Takashima, Kaori; Futo, Satoshi; Minegishi, Yasutaka; Akiyama, Hiroshi; Teshima, Reiko; Oguchi, Taichi; Mano, Junichi; Furui, Satoshi; Kitta, Kazumi

    2011-01-01

    To reduce the cost and time required to routinely perform the genetically modified organism (GMO) test, we developed a duplex quantitative real-time PCR method for a screening analysis simultaneously targeting an event-specific segment for GA21 and Cauliflower Mosaic Virus 35S promoter (P35S) segment [Oguchi et al., J. Food Hyg. Soc. Japan, 50, 117-125 (2009)]. To confirm the validity of the method, an interlaboratory collaborative study was conducted. In the collaborative study, conversion factors (Cfs), which are required to calculate the GMO amount (%), were first determined for two real-time PCR instruments, the ABI PRISM 7900HT and the ABI PRISM 7500. A blind test was then conducted. The limit of quantitation for both GA21 and P35S was estimated to be 0.5% or less. The trueness and precision were evaluated as the bias and reproducibility of the relative standard deviation (RSD(R)). The determined bias and RSD(R) were each less than 25%. We believe the developed method would be useful for the practical screening analysis of GM maize.

  5. Simultaneous quantitation and validation of method for the quality evaluation of Eucommiae cortex by HPLC/UV.

    Science.gov (United States)

    Zhao, Bing Tian; Jeong, Su Yang; Kim, Tae In; Seo, Eun Kyoung; Min, Byung Sun; Son, Jong Keun; Woo, Mi Hee

    2015-12-01

    A new HPLC/UV method has been developed for the simultaneous quantitative determination of four major components in Eucommiae cortex, namely geniposidic acid (1), geniposide (2), pinoresinol di-O-β-D-glucopyranoside (3), and liriodendrin (4). Simultaneous separations of these four components were achieved on a J'sphere ODS C(18) column (250 × 4.6 mm, 4 µm). The elution was done using water with 0.1% phosphoric acid (A) and acetonitrile with 0.1% phosphoric acid (B) in a two-step elution of the mobile phase at a flow rate of 1.0 mL/min and a wavelength of 230 nm. The method was validated for linearity, recovery, precision, accuracy, stability and robustness. All calibration curves showed good linear regression (r(2) > 0.999) within the test ranges. This method showed good recovery and reproducibility for the quantification of these four components in 85 species of Eucommiae cortex. The intra-day and inter-day precisions were lower than 0.53% (as a relative standard deviation, RSD) and accuracies between 93.00 and 106.28% for all standards. The results indicate that the established HPLC/UV method is suitable for quantitation and quality evaluation of Eucommiae cortex.

  6. Development and validation of a GC-FID method for quantitative analysis of oleic acid and related fatty acids☆

    Institute of Scientific and Technical Information of China (English)

    Honggen Zhang; Zhenyu Wang; Oscar Liu

    2015-01-01

    Oleic acid is a common pharmaceutical excipient that has been widely used in various dosage forms. Gas chromatography (GC) has often been used as the quantitation method for fatty acids normally requiring a derivatization step. The aim of this study was to develop a simple, robust, and derivatization-free GC method that is suitable for routine analysis of all the major components in oleic acid USP-NF (United States Pharmacopeia-National Formulary) material. A gas chromatography-flame ionization detection (GC-FID) method was developed for direct quantitative analysis of oleic acid and related fatty acids in oleic acid USP-NF material. Fifteen fatty acids were separated using a DB-FFAP (nitroterephthalic acid modified polyethylene glycol) capillary GC column (30 m × 0.32 mm i.d.) with a total run time of 20 min. The method was validated in terms of specificity, linearity, precision, accuracy, sensitivity, and robustness. The method can be routinely used for the purpose of oleic acid USP-NF material analysis.

  7. Development and Validation of RP-HPLC Method for Quantitative Estimation of Vinpocetine in Pure and Pharmaceutical Dosage Forms

    Directory of Open Access Journals (Sweden)

    Subrata Bhadra

    2011-01-01

    Full Text Available A simple, precise, specific, and accurate reversed phase high performance liquid chromatographic (RP-HPLC method was developed and validated for determination of vinpocetine in pure and pharmaceutical dosage forms. The different analytical performance parameters such as linearity, accuracy, specificity, precision, and sensitivity (limit of detection and limit of quantitation were determined according to International Conference on Harmonization ICH Q2 (R1 guidelines. RP-HPLC was conducted on Zorbax C18 (150 mm length × 4.6 mm ID, 5 μm column. The mobile phase was consisting of buffer (containing 1.54% w/v ammonium acetate solution and acetonitrile in the ratio (40 : 60, v/v, and the flow rate was maintained at 1.0 mLmin−1. Vinpocetine was monitored using Agilent 1200 series equipped with photo diode array detector (λ = 280 nm. Linearity was observed in concentration range of 160–240 μgmL−1, and correlation coefficient was found excellent (R2 = 0.999. All the system suitability parameters were found within the range. The proposed method is rapid, cost-effective and can be used as a quality-control tool for routine quantitative analysis of vinpocetine in pure and pharmaceutical dosage forms.

  8. Trace-Level Volatile Quantitation by DART-MS following Headspace Extraction - Optimization and Validation in Grapes.

    Science.gov (United States)

    Jastrzembski, Jillian A; Bee, Madeleine Y; Sacks, Gavin L

    2017-10-02

    Ambient Ionization - Mass Spectrometry (AI-MS) techniques like Direct Analysis in Real Time (DART) offer the potential for rapid quantitative analyses of trace volatiles in food matrices, but performance is generally limited by the lack of pre-concentration and extraction steps. The sensitivity and selectivity of AI-MS approaches can be improved through solid-phase microextraction (SPME) with appropriate thin-film geometries, e.g. solid phase mesh enhanced sorption from headspace (SPMESH). This work improves the SPMESH-DART-MS approach for use in food analyses, and validates the approach for trace volatile analysis for two compounds in real samples (grape macerates). SPMESH units prepared with different sorbent coatings were evaluated for their ability to extract a range of odor-active volatiles, with polydimethylsiloxane/divinylbenzene giving the most satisfactory results. In combination with high-resolution mass spectrometry (HRMS), detection limits for SPMESH-DART-MS under 4 ng/L in less than 30 s acquisition times could be achieved for some volatiles (3-isobutyl-2-methoxypyrazine (IBMP), β-damascenone). A comparison of SPMESH-DART-MS and SPME-GC-MS quantitation of linalool and IBMP demonstrates excellent agreement between the two methods using real grape samples (r2≥0.90), although linalool measurements appeared to also include isobaric interferences.

  9. Construction of measurement uncertainty profiles for quantitative analysis of genetically modified organisms based on interlaboratory validation data.

    Science.gov (United States)

    Macarthur, Roy; Feinberg, Max; Bertheau, Yves

    2010-01-01

    A method is presented for estimating the size of uncertainty associated with the measurement of products derived from genetically modified organisms (GMOs). The method is based on the uncertainty profile, which is an extension, for the estimation of uncertainty, of a recent graphical statistical tool called an accuracy profile that was developed for the validation of quantitative analytical methods. The application of uncertainty profiles as an aid to decision making and assessment of fitness for purpose is also presented. Results of the measurement of the quantity of GMOs in flour by PCR-based methods collected through a number of interlaboratory studies followed the log-normal distribution. Uncertainty profiles built using the results generally give an expected range for measurement results of 50-200% of reference concentrations for materials that contain at least 1% GMO. This range is consistent with European Network of GM Laboratories and the European Union (EU) Community Reference Laboratory validation criteria and can be used as a fitness for purpose criterion for measurement methods. The effect on the enforcement of EU labeling regulations is that, in general, an individual analytical result needs to be 1.8% to demonstrate noncompliance with a labeling threshold of 0.9%.

  10. Identification and validation of reference genes for quantitative real-time polymerase chain reaction in Cimex lectularius.

    Science.gov (United States)

    Mamidala, Praveen; Rajarapu, Swapna P; Jones, Susan C; Mittapalli, Omprakash

    2011-07-01

    Quantitative real-time polymerase chain reaction (qRT-PCR) has emerged as robust methodology for gene expression studies, but reference genes are crucial for accurate normalization. Commonly used reference genes are housekeeping genes that are thought to be nonregulated; however, their expression can be unstable across different experimental conditions. We report the identification and validation of suitable reference genes in the bed bug, Cimex lectularius, by using qRT-PCR. The expression stability of eight reference genes in different tissues (abdominal cuticle, midgut, Malpighian tubules, and ovary) and developmental stages (early instar nymphs, late instar nymphs, and adults) of pesticide-susceptible and pesticide-exposed C. lectularius were analyzed using geNorm, NormFinder, and BestKeeper. Overall expression analysis of the eight reference genes revealed significant variation among samples, indicating the necessity of validating suitable reference genes for accurate quantification of mRNA transcripts. Ribosomal protein (RPL18) exhibited the most stable gene expression across all the tissue and developmental-stage samples; a-tubulin revealed the least stability across all of the samples examined. Thus, we recommend RPL18 as a suitable reference gene for normalization in gene expression studies of C. lectularius.

  11. Modernization of Physical Appearance and Solution Color Tests Using Quantitative Tristimulus Colorimetry: Advantages, Harmonization, and Validation Strategies.

    Science.gov (United States)

    Pack, Brian W; Montgomery, Laura L; Hetrick, Evan M

    2015-10-01

    Color measurements, including physical appearance, are important yet often misunderstood and underappreciated aspects of a control strategy for drug substances and drug products. From a patient safety perspective, color can be an important control point for detecting contamination, impurities, and degradation products, with human visual acuity often more sensitive for colored impurities than instrumental techniques such as HPLC. Physical appearance tests and solution color tests can also serve an important role in ensuring that appropriate steps are taken such that clinical trials do not become unblinded when the active material is compared with another product or a placebo. Despite the importance of color tests, compendial visual tests are not harmonized across the major pharmacopoeias, which results in ambiguous specifications of little value, difficult communication of true sample color, and significant extra work required for global registration. Some pharmacopoeias have not yet recognized or adopted technical advances in the instrumental measurement of color and appearance, whereas others begin to acknowledge the advantage of instrumental colorimetry, yet leave implementation of the technology ambiguous. This commentary will highlight the above-mentioned inconsistencies, provide an avenue toward harmonization and modernization, and outline a scientifically sound approach for implementing quantitative technologies for improved measurement, communication, and control of color and appearance for both solutions and solids. Importantly, this manuscript, for the first time, outlines a color method validation approach that is consistent with the International Conference on Harmonization's guidance on the topic of method validation.

  12. A Vision of Quantitative Imaging Technology for Validation of Advanced Flight Technologies

    Science.gov (United States)

    Horvath, Thomas J.; Kerns, Robert V.; Jones, Kenneth M.; Grinstead, Jay H.; Schwartz, Richard J.; Gibson, David M.; Taylor, Jeff C.; Tack, Steve; Dantowitz, Ronald F.

    2011-01-01

    Flight-testing is traditionally an expensive but critical element in the development and ultimate validation and certification of technologies destined for future operational capabilities. Measurements obtained in relevant flight environments also provide unique opportunities to observe flow phenomenon that are often beyond the capabilities of ground testing facilities and computational tools to simulate or duplicate. However, the challenges of minimizing vehicle weight and internal complexity as well as instrumentation bandwidth limitations often restrict the ability to make high-density, in-situ measurements with discrete sensors. Remote imaging offers a potential opportunity to noninvasively obtain such flight data in a complementary fashion. The NASA Hypersonic Thermodynamic Infrared Measurements Project has demonstrated such a capability to obtain calibrated thermal imagery on a hypersonic vehicle in flight. Through the application of existing and accessible technologies, the acreage surface temperature of the Shuttle lower surface was measured during reentry. Future hypersonic cruise vehicles, launcher configurations and reentry vehicles will, however, challenge current remote imaging capability. As NASA embarks on the design and deployment of a new Space Launch System architecture for access beyond earth orbit (and the commercial sector focused on low earth orbit), an opportunity exists to implement an imagery system and its supporting infrastructure that provides sufficient flexibility to incorporate changing technology to address the future needs of the flight test community. A long term vision is offered that supports the application of advanced multi-waveband sensing technology to aid in the development of future aerospace systems and critical technologies to enable highly responsive vehicle operations across the aerospace continuum, spanning launch, reusable space access and global reach. Motivations for development of an Agency level imagery

  13. Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

    Directory of Open Access Journals (Sweden)

    Porceddu Enrico

    2009-02-01

    Full Text Available Abstract Background Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR. Results The expression stability of 32 genes was assessed by qRT-PCR using a set of cDNAs from 24 different plant samples, which included different tissues, developmental stages and temperature stresses. The selected sequences included 12 well-known HKGs representing different functional classes and 20 genes novel with reference to the normalization issue. The expression stability of the 32 candidate genes was tested by the computer programs geNorm and NormFinder using five different data-sets. Some discrepancies were detected in the ranking of the candidate reference genes, but there was substantial agreement between the groups of genes with the most and least stable expression. Three new identified reference genes appear more effective than the well-known and frequently used HKGs to normalize gene expression in wheat. Finally, the expression study of a gene encoding a PDI-like protein showed that its correct evaluation relies on the adoption of suitable normalization genes and can be negatively affected by the use of traditional HKGs with unstable expression, such as actin and α-tubulin. Conclusion The present research represents the first wide screening aimed to the identification of reference genes and of the corresponding primer pairs specifically designed for gene expression studies in wheat, in particular for qRT-PCR analyses. Several of the new identified reference genes outperformed the traditional HKGs in terms of expression stability

  14. Experimental validation of the AVIVET trap, a tool to quantitatively monitor the dynamics of Dermanyssus gallinae populations in laying hens.

    Science.gov (United States)

    Lammers, G A; Bronneberg, R G G; Vernooij, J C M; Stegeman, J A

    2016-12-05

    Dermanyssus gallinae (D.gallinae) infestation causes economic losses due to impaired health and production of hens and costs of parasite control across the world. Moreover, infestations are associated with reduced welfare of hens and may cause itching in humans. To effectively implement control methods it is crucially important to have high quality information about the D.gallinae populations in poultry houses in space and time. At present no validated tool is available to quantitatively monitor the dynamics of all four stages of D.gallinae (i.e., eggs, larvae, nymphs, and adults) in poultry houses.This article describes the experimental validation of the AVIVET trap, a device to quantitatively monitor dynamics of D.gallinae infestations. We used the device to study D.gallinae in fully equipped cages with two white specific pathogen free Leghorn laying hens experimentally exposed to three different infestation levels of D.gallinae (low to high).The AVIVET trap was successfully able to detect D.gallinae at high (5,000 D.gallinae), medium (2,500 D.gallinae), and low (50 D.gallinae) level of D.gallinae infestation. The linear equation Y = 10(∧)10(∧)(0.47 + 1.21X) with Y = log10 (Total number of D.gallinae nymphs and adults) in the cage and X = log10 (Total number of D.gallinae nymphs and adults) in the AVIVET trap explained 93.8% of the variation.The weight of D.gallinae in the AVIVET trap also appears to be a reliable parameter for quantifying D.gallinae infestation in a poultry house. The weight of D.gallinae in the AVIVET trap correlates 99.6% (P gallinae in the trap (i.e., eggs, larvae, nymphs, and adults) indicating that the trap is highly specific.From this experiment it can be concluded that the AVIVET trap is promising as quantitative tool for monitoring D.gallinae dynamics in a poultry house.

  15. Successful Validation of Sample Processing and Quantitative Real-Time PCR Capabilities on the International Space Station

    Science.gov (United States)

    Parra, Macarena; Jung, Jimmy; Almeida, Eduardo; Boone, Travis; Schonfeld, Julie; Tran, Luan

    2016-01-01

    The WetLab-2 system was developed by NASA Ames Research Center to offer new capabilities to researchers. The system can lyse cells and extract RNA (Ribonucleic Acid) on-orbit from different sample types ranging from microbial cultures to animal tissues. The purified RNA can then either be stabilized for return to Earth or can be used to conduct on-orbit quantitative Reverse Transcriptase PCR (Polymerase Chain Reaction) (qRT-PCR) analysis without the need for sample return. The qRT-PCR results can be downlinked to the ground a few hours after the completion of the run. The validation flight of the WetLab-2 system launched on SpaceX-8 on April 8, 2016. On orbit operations started on April 15th with system setup and was followed by three quantitative PCR runs using an E. coli genomic DNA template pre-loaded at three different concentrations. These runs were designed to discern if quantitative PCR functions correctly in microgravity and if the data is comparable to that from the ground control runs. The flight data showed no significant differences compared to the ground data though there was more variability in the values, this was likely due to the numerous small bubbles observed. The capability of the system to process samples and purify RNA was then validated using frozen samples prepared on the ground. The flight data for both E. coli and mouse liver clearly shows that RNA was successfully purified by our system. The E. coli qRT-PCR run showed successful singleplex, duplex and triplex capability. Data showed high variability in the resulting Cts (Cycle Thresholds [for the PCR]) likely due to bubble formation and insufficient mixing during the procedure run. The mouse liver qRT-PCR run had successful singleplex and duplex reactions and the variability was slightly better as the mixing operation was improved. The ability to purify and stabilize RNA and to conduct qRT-PCR on-orbit is an important step towards utilizing the ISS as a National Laboratory facility. The

  16. Evaluation and validation of candidate endogenous control genes for real-time quantitative PCR studies of breast cancer

    Directory of Open Access Journals (Sweden)

    Miller Nicola

    2007-11-01

    Full Text Available Abstract Background Real-time quantitative PCR (RQ-PCR forms the basis of many breast cancer biomarker studies and novel prognostic assays, paving the way towards personalised cancer treatments. Normalisation of relative RQ-PCR data is required to control for non-biological variation introduced during sample preparation. Endogenous control (EC genes, used in this context, should ideally be expressed constitutively and uniformly across treatments in all test samples. Despite widespread recognition that the accuracy of the normalised data is largely dependent on the reliability of the EC, there are no reports of the systematic validation of genes commonly used for this purpose in the analysis of gene expression by RQ-PCR in primary breast cancer tissues. The aim of this study was to identify the most suitable endogenous control genes for RQ-PCR analysis of primary breast tissue from a panel of eleven candidates in current use. Oestrogen receptor alpha (ESR1 was used a target gene to compare the effect of choice of EC on the estimate of gene quantity. Results The expression and validity of candidate ECs (GAPDH, TFRC, ABL, PPIA, HPRT1, RPLP0, B2M, GUSB, MRPL19, PUM1 and PSMC4 was determined in 6 benign and 21 malignant primary breast cancer tissues. Gene expression data was analysed using two different statistical models. MRPL19 and PPIA were identified as the most stable and reliable EC genes, while GUSB, RPLP0 and ABL were least stable. There was a highly significant difference in variance between ECs. ESR1 expression was appreciably higher in malignant compared to benign tissues and there was a significant effect of EC on the magnitude of the error associated with the relative quantity of ESR1. Conclusion We have validated two endogenous control genes, MRPL19 and PPIA, for RQ-PCR analysis of gene expression in primary breast tissue. Of the genes in current use in this field, the above combination offers increased accuracy and resolution in the

  17. Excised porcine skin experimental systems to validate quantitative microdialysis methods for determination of drugs in skin after topical application.

    Science.gov (United States)

    Seki, Toshinobu; Wang, Aiping; Yuan, Dan; Saso, Yuko; Hosoya, Osamu; Chono, Sumio; Morimoto, Kazuhiro

    2004-11-24

    Microdialysis is useful as a method to evaluate the disposition of drugs in the skin to design improved transdermal delivery systems (TDDSs). In this study, quantitative microdialysis methods were validated in excised porcine skin experimental systems in vitro. Flurbiprofen (FP), used as a model drug, showed high affinity for the skin tissues in equilibrium states between the medium and skin. The membrane clearances of FP for permeation through the membrane of a dialysis fiber placed in the skin (CL(m in S)) were lower than that in the medium. The adsorption of components in the skin to the membrane surface of the dialysis fiber and accumulation of FP near the dialysis fiber are the most likely reasons for this. When CL(m in S) was used to predict the extracellular FP concentration in skin (C(T)), the value obtained was lower than that expected from the FP concentration in the medium on the dermis side, which should be equal to C(T) at equilibrium. In the zero net flux (ZNF) method, in which the concentration difference of perfusate (DeltaC) between the inflow and outflow were used to obtain C(T), the predicted C(T) was similar to the expected value. In an in vitro skin permeation experiment, the ZNF method was used for the prediction of C(T) near the dialysis fiber. The predicted C(T) was over 10 times higher than the FP concentration in the medium on the dermis side, suggesting a concentration gradient in the dermis. Although the ZNF method is good for predicting the C(T) in skin, the mass balance has to be considered for the quantitative evaluation of the skin permeation of drugs. In this study, the effect of the mass transfer of FP from the perfusate to the skin on the cumulative amount of FP passing through the skin was relatively low because of the use of suitable solutions as perfusate. The perfusion conditions and schedules should be designed carefully for quantitative evaluations using the ZNF method. These results provide useful information for the in

  18. Validation of the histologic grading for ovarian clear cell adenocarcinoma: a retrospective multi-institutional study by the Japan Clear Cell Carcinoma Study Group.

    Science.gov (United States)

    Yamamoto, Sohei; Kasajima, Atsuko; Takano, Masashi; Yaegashi, Nobuo; Fujiwara, Hiroyuki; Kuzuya, Kazuo; Kigawa, Junzo; Tsuda, Hiroshi; Kurachi, Hirohisa; Kikuchi, Yoshihiro; Sugiyama, Toru; Tsuda, Hitoshi; Moriya, Takuya

    2011-03-01

    Pathologic slides from 150 patients with clear cell adenocarcinoma from the collaborating institutions were reviewed independently by 2 pathologists, and each tumor was graded histologically using the Shimizu-Silverberg and International Federation of Gynecology and Obstetrics (FIGO) grading systems. For the Shimizu-Silverberg grading system, 3 parameters-architectural pattern, nuclear pleomorphism, and mitotic activity-were assessed and scored as 1 to 3. When the summed scores of these parameters were 3 to 5, 6 to 7, and 8 to 9, grades 1, 2, and 3 were assigned, respectively. The FIGO grade was based on the ratio of glandular/papillary growth versus solid growth: grade 1, less than 5% solid tumor; grade 2, 5% to 50% solid tumor; grade 3, greater than 50% solid tumor. Interobserver agreement levels for assignment of both gradings were fair (κ=0.32 and 0.24, respectively). After consensus had been acquired, 82 (55%), 56 (37%), and 12 (8%) tumors were classified as grades 1, 2, and 3 by the Shimizu-Silverberg grading system, and 88 (59%), 38 (25%), and 24 (16%) were classified as grades 1, 2, and 3 by the FIGO grading system, respectively. Survival analyses indicated that patients with grade 3 tumors, as defined by both the grading systems, tended to have a poor outcome, but any differences between them were not statistically significant. Multivariate analysis showed that only the presence of residual tumor after initial surgery was an independent prognostic factor for overall survival. These results suggest that the 2 tested grading systems have limited value for the prognostication of patients with clear cell adenocarcinoma, and that a more effective grading system for this tumor may be required.

  19. Comparison of validity of DIAGNOdent with conventional methods for detection of occlusal caries in primary molars using the histological gold standard: An in vivo study

    Directory of Open Access Journals (Sweden)

    Goel A

    2009-01-01

    Full Text Available Aim: This study was conducted to compare the in vivo effectiveness of DIAGNOdent with other conventional methods (visual, tactile and bitewing radiographs for the detection of occlusal caries in primary molars. Another objective of the study was to calculate new cut-off limits for the detection of caries by DIAGNOdent in primary teeth. Materials and Methods: Eighty-four primary molars in 52 children (aged 8-12 years, which were indicated for extraction, were selected and evaluated for dental caries using DIAGNOdent, visual and tactile examination and bitewing radiographs. Histological examination of the sections, prepared subsequent to extraction of the teeth, served as the gold standard for comparison of the above-mentioned methods. Results: When considering enamel caries, values obtained for sensitivity, specificity and accuracy were 48.15, 100 and 49.40% for visual examination, 48.15, 100.00 and 49.40% for tactile examination, 49.38, 50.00 and 49.40% for bitewing radiographs, 85.19, 50.00 and 84.34% for DIAGNOdent scores interpreted according to manufacturer′s cut-off limits and 81.48, 100.00 and 81.93% for DIAGNOdent scores interpreted according to newly formulated cut-off limits, respectively. At dentin caries cut-off levels, the values of sensitivity, specificity and accuracy for visual examination were 52.78, 89.36 and 73.49%; 50.00, 91.49 and 73.49% for tactile examination; 30.56, 82.98 and 60.24% for bitewing radiographs; 72.22, 76.60 and 74.70% for DIAGNOdent scores when interpreted according to manufacturer′s cut-off limits and 77.48, 74.47 and 75.90%, respectively, for the DIAGNOdent scores when interpreted according to the newly formulated cut-off limits. Conclusions: DIAGNOdent showed higher sensitivity and accuracy as compared with other conventional methods for detection of enamel caries, whereas for detection of dentinal caries, even though the sensitivity was high, accuracy of the DIAGNOdent device was similar to other

  20. Histologic grading of noninvasive papillary urothelial tumors: validation of the 1998 WHO/ISUP system by immunophenotyping and follow-up.

    Science.gov (United States)

    Yin, Hui; Leong, Anthony S Y

    2004-05-01

    Cytokeratin (CK) 20, Ki-67, and p53 were applied to 84 noninvasive papillary urothelial tumors graded by the 1973 World Health Organization (WHO) and 1998 WHO/International Society of Urological Pathology (ISUP) systems. In the WHO/ISUP classification, all benign lesions showed normal CK20 staining and all carcinomas showed abnormal staining. The Ki-67 index was significantly different between benign and malignant lesions (P .05), and there was no difference in p53 staining in grades 1 and 2 carcinomas (P > .05). Recurrences were not different between grades 1, 2, and 3 carcinomas. All biologic markers studied and tumor recurrences were significantly different among papillary lesions classified by the WHO/ISUP system but not by the 1973 WHO system, validating the predictive value of the WHO/ISUP system and providing objective markers for the grading of papillary urothelial tumors.

  1. Clinico-histologic conferences: histology and disease.

    Science.gov (United States)

    Shaw, Phyllis A; Friedman, Erica S

    2012-01-01

    Providing a context for learning information and requiring learners to teach specific content has been demonstrated to enhance knowledge retention. To enhance students' appreciation of the role of science and specifically histology in clinical reasoning, disease diagnosis, and treatment, a new teaching format was created to provide clinical context, promote integration and application of science knowledge, and to foster peer teaching and learning: the Clinico-Histologic Conference (CHC) for the Mount Sinai School of Medicine Histology course. Teams of six students were each assigned specific disease processes and were charged with creating oral presentations and handouts that taught their classmates about the clinical manifestations, etiopathogeneses, diagnoses, and treatments of the assigned processes, along with comparisons of normal histology to the pathology of the disease. Each team also created four questions, some of which were used on Histology written examinations. The physician facilitator evaluated the presentation and handouts. About two-thirds of students agreed the CHC enhanced appreciation of the importance of histology, provided a context for integration and application of basic science to patient care and enhanced their ability to teach their peers. Student feedback demonstrated that the CHCs were successful in promoting teamwork, peer teaching, and the application of histology to diagnose diseases. The authors believe that teaching basic science content in this new format enhanced student learning and application of medical knowledge, and that this new teaching format can be adopted by other medical school courses.

  2. Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.

    Directory of Open Access Journals (Sweden)

    Thrush Anthony

    2010-01-01

    Full Text Available Abstract Background Perennial ryegrass (Lolium perenne L. is an important pasture and turf crop. Biotechniques such as gene expression studies are being employed to improve traits in this temperate grass. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR is among the best methods available for determining changes in gene expression. Before analysis of target gene expression, it is essential to select an appropriate normalisation strategy to control for non-specific variation between samples. Reference genes that have stable expression at different biological and physiological states can be effectively used for normalisation; however, their expression stability must be validated before use. Results Existing Serial Analysis of Gene Expression data were queried to identify six moderately expressed genes that had relatively stable gene expression throughout the year. These six candidate reference genes (eukaryotic elongation factor 1 alpha, eEF1A; TAT-binding protein homolog 1, TBP-1; eukaryotic translation initiation factor 4 alpha, eIF4A; YT521-B-like protein family protein, YT521-B; histone 3, H3; ubiquitin-conjugating enzyme, E2 were validated for qRT-PCR normalisation in 442 diverse perennial ryegrass (Lolium perenne L. samples sourced from field- and laboratory-grown plants under a wide range of experimental conditions. Eukaryotic EF1A is encoded by members of a multigene family exhibiting differential expression and necessitated the expression analysis of different eEF1A encoding genes; a highly expressed eEF1A (h, a moderately, but stably expressed eEF1A (s, and combined expression of multigene eEF1A (m. NormFinder identified eEF1A (s and YT521-B as the best combination of two genes for normalisation of gene expression data in perennial ryegrass following different defoliation management in the field. Conclusions This study is unique in the magnitude of samples tested with the inclusion of numerous field-grown samples

  3. Verification& Validation (V&V) Guidelines and Quantitative Reliability at Confidence (QRC): Basis for an Investment Strategy

    Energy Technology Data Exchange (ETDEWEB)

    Logan, R W; Nitta, C K

    2002-07-17

    This paper represents an attempt to summarize our thoughts regarding various methods and potential guidelines for Verification and Validation (V&V) and Uncertainty Quantification (UQ) that we have observed within the broader V&V community or generated ourselves. Our goals are to evaluate these various methods, to apply them to computational simulation analyses, and integrate them into methods for Quantitative Certification techniques for the nuclear stockpile. We describe the critical nature of high quality analyses with quantified V&V, and the essential role of V&V and UQ at specified Confidence levels in evaluating system certification status. Only after V&V has contributed to UQ at confidence can rational tradeoffs of various scenarios be made. UQ of performance and safety margins for various scenarios and issues are applied in assessments of Quantified Reliability at Confidence (QRC) and we summarize with a brief description of how these V&V generated QRC quantities fold into a Value-Engineering methodology for evaluating investment strategies. V&V contributes directly to the decision process for investment, through quantification of uncertainties at confidence for margin and reliability assessments. These contributions play an even greater role in a Comprehensive Test Ban Treaty (CTBT) environment than ever before, when reliance on simulation in the absence of the ability to perform nuclear testing is critical.

  4. Validation of a quantitative NMR method for suspected counterfeit products exemplified on determination of benzethonium chloride in grapefruit seed extracts.

    Science.gov (United States)

    Bekiroglu, Somer; Myrberg, Olle; Ostman, Kristina; Ek, Marianne; Arvidsson, Torbjörn; Rundlöf, Torgny; Hakkarainen, Birgit

    2008-08-05

    A 1H-nuclear magnetic resonance (NMR) spectroscopy method for quantitative determination of benzethonium chloride (BTC) as a constituent of grapefruit seed extract was developed. The method was validated, assessing its specificity, linearity, range, and precision, as well as accuracy, limit of quantification and robustness. The method includes quantification using an internal reference standard, 1,3,5-trimethoxybenzene, and regarded as simple, rapid, and easy to implement. A commercial grapefruit seed extract was studied and the experiments were performed on spectrometers operating at two different fields, 300 and 600 MHz for proton frequencies, the former with a broad band (BB) probe and the latter equipped with both a BB probe and a CryoProbe. The concentration average for the product sample was 78.0, 77.8 and 78.4 mg/ml using the 300 BB probe, the 600MHz BB probe and CryoProbe, respectively. The standard deviation and relative standard deviation (R.S.D., in parenthesis) for the average concentrations was 0.2 (0.3%), 0.3 (0.4%) and 0.3mg/ml (0.4%), respectively.

  5. Development and validation of an event-specific quantitative PCR method for genetically modified maize MIR162.

    Science.gov (United States)

    Takabatake, Reona; Masubuchi, Tomoko; Futo, Satoshi; Minegishi, Yasutaka; Noguchi, Akio; Kondo, Kazunari; Teshima, Reiko; Kurashima, Takeyo; Mano, Junichi; Kitta, Kazumi

    2014-01-01

    A novel real-time PCR-based analytical method was developed for the event-specific quantification of a genetically modified (GM) maize event, MIR162. We first prepared a standard plasmid for MIR162 quantification. The conversion factor (Cf) required to calculate the genetically modified organism (GMO) amount was empirically determined for two real-time PCR instruments, the Applied Biosystems 7900HT (ABI7900) and the Applied Biosystems 7500 (ABI7500) for which the determined Cf values were 0.697 and 0.635, respectively. To validate the developed method, a blind test was carried out in an interlaboratory study. The trueness and precision were evaluated as the bias and reproducibility of relative standard deviation (RSDr). The determined biases were less than 25% and the RSDr values were less than 20% at all evaluated concentrations. These results suggested that the limit of quantitation of the method was 0.5%, and that the developed method would thus be suitable for practical analyses for the detection and quantification of MIR162.

  6. Bench-top validation testing of selected immunological and molecular Renibacterium salmoninarum diagnostic assays by comparison with quantitative bacteriological culture

    Science.gov (United States)

    Elliott, D.G.; Applegate, L.J.; Murray, A.L.; Purcell, M.K.; McKibben, C.L.

    2013-01-01

    No gold standard assay exhibiting error-free classification of results has been identified for detection of Renibacterium salmoninarum, the causative agent of salmonid bacterial kidney disease. Validation of diagnostic assays for R. salmoninarum has been hindered by its unique characteristics and biology, and difficulties in locating suitable populations of reference test animals. Infection status of fish in test populations is often unknown, and it is commonly assumed that the assay yielding the most positive results has the highest diagnostic accuracy, without consideration of misclassification of results. In this research, quantification of R. salmoninarum in samples by bacteriological culture provided a standardized measure of viable bacteria to evaluate analytical performance characteristics (sensitivity, specificity and repeatability) of non-culture assays in three matrices (phosphate-buffered saline, ovarian fluid and kidney tissue). Non-culture assays included polyclonal enzyme-linked immunosorbent assay (ELISA), direct smear fluorescent antibody technique (FAT), membrane-filtration FAT, nested polymerase chain reaction (nested PCR) and three real-time quantitative PCR assays. Injection challenge of specific pathogen-free Chinook salmon, Oncorhynchus tshawytscha (Walbaum), with R. salmoninarum was used to estimate diagnostic sensitivity and specificity. Results did not identify a single assay demonstrating the highest analytical and diagnostic performance characteristics, but revealed strengths and weaknesses of each test.

  7. Corrected coronary opacification decrease from coronary computed tomography angiography: Validation with quantitative 13N-ammonia positron emission tomography.

    Science.gov (United States)

    Benz, Dominik C; Gräni, Christoph; Ferro, Paola; Neumeier, Luis; Messerli, Michael; Possner, Mathias; Clerc, Olivier F; Gebhard, Catherine; Gaemperli, Oliver; Pazhenkottil, Aju P; Kaufmann, Philipp A; Buechel, Ronny R

    2017-07-06

    To assess the functional relevance of a coronary artery stenosis, corrected coronary opacification (CCO) decrease derived from coronary computed tomography angiography (CCTA) has been proposed. The present study aims at validating CCO decrease with quantitative 13N-ammonia positron emission tomography (PET) myocardial perfusion imaging (MPI). This retrospective study consists of 39 patients who underwent hybrid CCTA/PET-MPI. From CCTA, attenuation in the coronary lumen was measured before and after a stenosis and corrected to the aorta to calculate CCO and its decrease. Relative flow reserve (RFR) was calculated by dividing the stress myocardial blood flow (MBF) of a vessel territory subtended by a stenotic coronary by the stress MBF of the reference territories without stenoses. RFR was abnormal in 11 vessel territories (27%). CCO decrease yielded a sensitivity, specificity, negative predictive value, positive predictive value, and accuracy for prediction of an abnormal RFR of 73%, 70%, 88%, 47%, and 70%, respectively. CCTA-derived CCO decrease has moderate diagnostic accuracy to predict an abnormal RFR in PET-MPI. However, its high negative predictive value to rule out functional relevance of a given lesion may confer clinical implications in the diagnostic work-up of patients with a coronary stenosis.

  8. Identification and Validation of a Major Quantitative Trait Locus for Slow-rusting Resistance to Stripe Rust in Wheat

    Institute of Scientific and Technical Information of China (English)

    Xiaohua Cao; Jianghong Zhou; Xiaoping Gong; Guangyao Zhao; Jizeng Jia; Xiaoquan Qi

    2012-01-01

    Stripe (yellow) rust,caused by Puccinia striiformis Westend.f.sp.tritici Eriks (Pst),is one of the most important wheat (Triticum aestivum L.) diseases and causes significant yield losses.A recombinant inbred (RI) population derived from a cross between Yanzhan 1 and Xichang 76-9 cultivars was evaluated for resistance to wheat stripe rust strain CYR32 at both the seedling and adult plant stages.Four resistance quantitative trait loci (QTLs) were detected in this population,in which the major one,designated as Yrq1,was mapped on chromosome 2DS.The strategy of using the Brachypodium distachyon genome,wheat expressed sequence tags and a draft DNA sequences (scaffolds) of the D-genome (Aegilops tauschii Coss.) for the development of simple sequence repeat (SSR) markers was successfully used to identify 147 SSRs in hexaploid wheat.Of the 19 polymorphic SSRs in the RI population,17 SSRs were mapped in the homeologous group 2 chromosomes near Yrq1 region and eight SSRs were genetically mapped in the 2.7 cM region of Yrq1,providing abundant DNA markers for fine-mapping of Yrq1 and marker-assisted selection in wheat breeding program.The effectiveness of Yrq1 was validated in an independent population,indicating that this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.

  9. Bench-top validation testing of selected immunological and molecular Renibacterium salmoninarum diagnostic assays by comparison with quantitative bacteriological culture.

    Science.gov (United States)

    Elliott, D G; Applegate, L J; Murray, A L; Purcell, M K; McKibben, C L

    2013-09-01

    No gold standard assay exhibiting error-free classification of results has been identified for detection of Renibacterium salmoninarum, the causative agent of salmonid bacterial kidney disease. Validation of diagnostic assays for R. salmoninarum has been hindered by its unique characteristics and biology, and difficulties in locating suitable populations of reference test animals. Infection status of fish in test populations is often unknown, and it is commonly assumed that the assay yielding the most positive results has the highest diagnostic accuracy, without consideration of misclassification of results. In this research, quantification of R. salmoninarum in samples by bacteriological culture provided a standardized measure of viable bacteria to evaluate analytical performance characteristics (sensitivity, specificity and repeatability) of non-culture assays in three matrices (phosphate-buffered saline, ovarian fluid and kidney tissue). Non-culture assays included polyclonal enzyme-linked immunosorbent assay (ELISA), direct smear fluorescent antibody technique (FAT), membrane-filtration FAT, nested polymerase chain reaction (nested PCR) and three real-time quantitative PCR assays. Injection challenge of specific pathogen-free Chinook salmon, Oncorhynchus tshawytscha (Walbaum), with R. salmoninarum was used to estimate diagnostic sensitivity and specificity. Results did not identify a single assay demonstrating the highest analytical and diagnostic performance characteristics, but revealed strengths and weaknesses of each test.

  10. A validated micellar electrokinetic chromatography method for the quantitation of dexamethasone, ondansetron and aprepitant, antiemetic drugs, in organogel.

    Science.gov (United States)

    Bourdon, Florence; Lecoeur, Marie; Duhaut, Marion; Odou, Pascal; Vaccher, Claude; Foulon, Catherine

    2013-12-01

    A micellar electrokinetic chromatography (MEKC) method was developed for the determination of three anti-vomiting drugs (aprepitant, dexamethasone and ondansetron) in pharmaceutical formulations. The method was optimized using a central composite design (CCD). Four main factors (borate buffer concentration, pH, methanol content and sodium dodecyl sulfate concentration) were optimized in order to obtain best resolutions and peak efficiencies in a minimum runtime. The separation was performed in a fused-silica capillary. After optimization, the background electrolyte consisted of a borate buffer (62.5mM, pH 8.75) containing sodium dodecyl sulfate (77.5mM) and methanol (3.75%). Under these conditions, a complete separation of each antiemetic drug and its respective internal standards was achieved in 38min. The method was validated with trueness values from 94.9 to 107.2% and precision results (repeatability and intermediate precision) lower than 5.9%. MEKC-UV was the first method allowing the separation of aprepitant, dexamethasone and ondansetron and was suitable for the quantitation of these three antiemetic drugs in organogel formulations. The rapid sample preparation coupled with an automated separation technique make this method convenient for quality control of extemporaneous magistral ready-to-use formulation.

  11. Validation of Reference Genes for Transcriptional Analyses in Pleurotus ostreatus by Using Reverse Transcription-Quantitative PCR.

    Science.gov (United States)

    Castanera, Raúl; López-Varas, Leticia; Pisabarro, Antonio G; Ramírez, Lucía

    2015-06-15

    Recently, the lignin-degrading basidiomycete Pleurotus ostreatus has become a widely used model organism for fungal genomic and transcriptomic analyses. The increasing interest in this species has led to an increasing number of studies analyzing the transcriptional regulation of multigene families that encode extracellular enzymes. Reverse transcription (RT) followed by real-time PCR is the most suitable technique for analyzing the expression of gene sets under multiple culture conditions. In this work, we tested the suitability of 13 candidate genes for their use as reference genes in P. ostreatus time course cultures for enzyme production. We applied three different statistical algorithms and obtained a combination of stable reference genes for optimal normalization of RT-quantitative PCR assays. This reference index can be used for future transcriptomic analyses and validation of transcriptome sequencing or microarray data. Moreover, we analyzed the expression patterns of a laccase and a manganese peroxidase (lacc10 and mnp3, respectively) in lignocellulose and glucose-based media using submerged, semisolid, and solid-state fermentation. By testing different normalization strategies, we demonstrate that the use of nonvalidated reference genes as internal controls leads to biased results and misinterpretations of the biological responses underlying expression changes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Identification and validation of reference genes for quantitative real-time PCR in Drosophila suzukii (Diptera: Drosophilidae.

    Directory of Open Access Journals (Sweden)

    Yifan Zhai

    Full Text Available To accurately evaluate gene expression levels and obtain more accurate quantitative real-time RT-PCR (qRT-PCR data, normalization relative to reliable reference gene(s is required. Drosophila suzukii, is an invasive fruit pest native to East Asia, and recently invaded Europe and North America, the stability of its reference genes have not been previously investigated. In this study, ten candidate reference genes (RPL18, RPS3, AK, EF-1β, TBP, NADH, HSP22, GAPDH, Actin, α-Tubulin, were evaluated for their suitability as normalization genes under different biotic (developmental stage, tissue and population, and abiotic (photoperiod, temperature conditions. The three statistical approaches (geNorm, NormFinder and BestKeeper and one web-based comprehensive tool (RefFinder were used to normalize analysis of the ten candidate reference genes identified α-Tubulin, TBP and AK as the most stable candidates, while HSP22 and Actin showed the lowest expression stability. We used three most stable genes (α-Tubulin, TBP and AK and one unstably expressed gene to analyze the expression of P-glycoprotein in abamectin-resistant and sensitive strains, and the results were similar to reference genes α-Tubulin, TBP and AK, which show good stability, while the result of HSP22 has a certain bias. The three validated reference genes can be widely used for quantification of target gene expression with qRT-PCR technology in D.suzukii.

  13. Validation of Direct Analysis Real Time source/Time-of-Flight Mass Spectrometry for organophosphate quantitation on wafer surface.

    Science.gov (United States)

    Hayeck, Nathalie; Ravier, Sylvain; Gemayel, Rachel; Gligorovski, Sasho; Poulet, Irène; Maalouly, Jacqueline; Wortham, Henri

    2015-11-01

    Microelectronic wafers are exposed to airborne molecular contamination (AMC) during the fabrication process of microelectronic components. The organophosphate compounds belonging to the dopant group are one of the most harmful groups. Once adsorbed on the wafer surface these compounds hardly desorb and could diffuse in the bulk of the wafer and invert the wafer from p-type to n-type. The presence of these compounds on wafer surface could have electrical effect on the microelectronic components. For these reasons, it is of importance to control the amount of these compounds on the surface of the wafer. As a result, a fast quantitative and qualitative analytical method, nondestructive for the wafers, is needed to be able to adjust the process and avoid the loss of an important quantity of processed wafers due to the contamination by organophosphate compounds. Here we developed and validated an analytical method for the determination of organic compounds adsorbed on the surface of microelectronic wafers using the Direct Analysis in Real Time-Time of Flight-Mass Spectrometry (DART-ToF-MS) system. Specifically, the developed methodology concerns the organophosphate group.

  14. Validation of Body Condition Indices and Quantitative Magnetic Resonance in Estimating Body Composition in a Small Lizard

    Science.gov (United States)

    WARNER, DANIEL A.; JOHNSON, MARIA S.; NAGY, TIM R.

    2017-01-01

    Measurements of body condition are typically used to assess an individual’s quality, health, or energetic state. Most indices of body condition are based on linear relationships between body length and mass. Although these indices are simple to obtain, nonlethal, and useful indications of energetic state, their accuracy at predicting constituents of body condition (e.g., fat and lean mass) are often unknown. The objectives of this research were to (1) validate the accuracy of another simple and noninvasive method, quantitative magnetic resonance (QMR), at estimating body composition in a small-bodied lizard, Anolis sagrei, and (2) evaluate the accuracy of two indices of body condition (based on length–mass relationships) at predicting body fat, lean, and water mass. Comparisons of results from QMR scans to those from chemical carcass analysis reveal that QMR measures body fat, lean, and water mass with excellent accuracy in male and female lizards. With minor calibration from regression equations, QMR will be a reliable method of estimating body composition of A. sagrei. Body condition indices were positively related to absolute estimates of each constituent of body composition, but these relationships showed considerable variation around regression lines. In addition, condition indices did not predict fat, lean, or water mass when adjusted for body mass. Thus, our results emphasize the need for caution when interpreting body condition based upon linear measurements of animals. Overall, QMR provides an alternative noninvasive method for accurately measuring fat, lean, and water mass in these small-bodied animals. PMID:28035770

  15. 3D soft tissue predictions with a tetrahedral mass tensor model for a maxillofacial planning system: a quantitative validation study

    Science.gov (United States)

    Mollemans, W.; Schutyser, F.; Nadjmi, N.; Maes, F.; Suetens, P.

    2006-03-01

    In this paper we present an extensive quantitative validation on 3D facial soft tissue simulation for maxillofacial surgery planning. The study group contained 10 patients. In previous work we presented a new Mass Tensor Model to simulate the new facial appearance after maxillofacial surgery in a fast way. 10 patients were preoperatively CT-scanned and the surgical intervention was planned. 4 months after surgery, a post-operative control CT was acquired. In this study, the simulated facial outlook is compared with post-operative image data. After defining corresponding points between the predicted and actual post-operative facial skin surface, using a variant of the non-rigid TPS-RPM algorithm, distances between these correspondences are quantified and visualized in 3D. As shown, the average median distance measures only 0.60 mm and the average 90% percentile stays below 1.5 mm. We can conclude that our model clearly provides an accurate prediction of the real post-operative outcome and is therefore suitable for use in clinical practice.

  16. Validation of an Ultraviolet-visible (UV-Vis) technique for the quantitative determination of curcumin in poly(L-lactic acid) nanoparticles.

    Science.gov (United States)

    Silva-Buzanello, Rosana Aparecida da; Ferro, Ana Caroline; Bona, Evandro; Cardozo-Filho, Lúcio; Araújo, Pedro Henrique Hermes de; Leimann, Fernanda Vitória; Gonçalves, Odinei Hess

    2015-04-01

    Curcumin is a natural yellow-orange pigment extracted from turmeric and is a potential substitute of health-dangerous artificial dyes. Nanoencapsulation in biodegradable polymers is a promising alternative to improve curcumin stability and water solubility but curcumin concentration inside the nanoparticles must be precisely known. A reliable method to determine the actual curcumin concentration must be validated since the validation procedures warrant that the method is adequate and sufficient for the specific application involved. This work describes the validation parameters given by the International Conference on Harmonisation (ICH) guidelines to adopt an analytical method based on Ultraviolet-visible spectroscopy for the quantitative determination of curcumin encapsulated in poly(l-lactic acid) nanoparticles. This method was validated in respect to linearity, detection limit, quantification limit, accuracy and precision. Studies on the analytical procedure validation warranted safety in final results obtained for the curcumin concentration in the nanoparticles. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Validation of reference genes in Penicillium echinulatum to enable gene expression study using real-time quantitative RT-PCR.

    Science.gov (United States)

    Zampieri, Denise; Nora, Luísa C; Basso, Vanessa; Camassola, Marli; Dillon, Aldo J P

    2014-08-01

    Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is a methodology that facilitates the quantification of mRNA expression in a given sample. Analysis of relative gene expression by qRT-PCR requires normalization of the data using a reference gene that is expressed at a similar level in all evaluated conditions. Determining an internal control gene is essential for gene expression studies. Gene expression studies in filamentous fungi frequently use the β-actin gene (actb), β-tubulin, and glyceraldehyde-3-phosphate dehydrogenase as reference genes because they are known to have consistent expression levels. Until now, no study has been performed to select an internal control gene for the filamentous fungal species Penicillium echinulatum. The aim of this study was to evaluate and validate internal control genes to enable the study of gene expression in P. echinulatum using qRT-PCR. P. echinulatum strain S1M29 was grown in conditions to either induce (cellulose and sugar cane bagasse) or repress (glucose) gene expression to analyze 23 candidate normalization genes for stable expression. Two software programs, BestKeeper and geNorm, were used to assess the expression of the candidate normalization genes. The results indicate that the actb reference gene is more stably expressed in P. echinulatum. This is the first report in the literature that determines a normalization gene for this fungus. From the results obtained, we recommend the use of the P. echinulatum actb gene as an endogenous control for gene expression studies of cellulases and hemicellulases by qRT-PCR.

  18. A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila.

    Science.gov (United States)

    Hoermann, Astrid; Cicin-Sain, Damjan; Jaeger, Johannes

    2016-03-15

    Understanding eukaryotic transcriptional regulation and its role in development and pattern formation is one of the big challenges in biology today. Most attempts at tackling this problem either focus on the molecular details of transcription factor binding, or aim at genome-wide prediction of expression patterns from sequence through bioinformatics and mathematical modelling. Here we bridge the gap between these two complementary approaches by providing an integrative model of cis-regulatory elements governing the expression of the gap gene giant (gt) in the blastoderm embryo of Drosophila melanogaster. We use a reverse-engineering method, where mathematical models are fit to quantitative spatio-temporal reporter gene expression data to infer the regulatory mechanisms underlying gt expression in its anterior and posterior domains. These models are validated through prediction of gene expression in mutant backgrounds. A detailed analysis of our data and models reveals that gt is regulated by domain-specific CREs at early stages, while a late element drives expression in both the anterior and the posterior domains. Initial gt expression depends exclusively on inputs from maternal factors. Later, gap gene cross-repression and gt auto-activation become increasingly important. We show that auto-regulation creates a positive feedback, which mediates the transition from early to late stages of regulation. We confirm the existence and role of gt auto-activation through targeted mutagenesis of Gt transcription factor binding sites. In summary, our analysis provides a comprehensive picture of spatio-temporal gene regulation by different interacting enhancer elements for an important developmental regulator.

  19. Genome-Wide Identification and Validation of Reference Genes in Infected Tomato Leaves for Quantitative RT-PCR Analyses.

    Directory of Open Access Journals (Sweden)

    Oliver A Müller

    Full Text Available The Gram-negative bacterium Xanthomonas campestris pv. vesicatoria (Xcv causes bacterial spot disease of pepper and tomato by direct translocation of type III effector proteins into the plant cell cytosol. Once in the plant cell the effectors interfere with host cell processes and manipulate the plant transcriptome. Quantitative RT-PCR (qRT-PCR is usually the method of choice to analyze transcriptional changes of selected plant genes. Reliable results depend, however, on measuring stably expressed reference genes that serve as internal normalization controls. We identified the most stably expressed tomato genes based on microarray analyses of Xcv-infected tomato leaves and evaluated the reliability of 11 genes for qRT-PCR studies in comparison to four traditionally employed reference genes. Three different statistical algorithms, geNorm, NormFinder and BestKeeper, concordantly determined the superiority of the newly identified reference genes. The most suitable reference genes encode proteins with homology to PHD finger family proteins and the U6 snRNA-associated protein LSm7. In addition, we identified pepper orthologs and validated several genes as reliable normalization controls for qRT-PCR analysis of Xcv-infected pepper plants. The newly identified reference genes will be beneficial for future qRT-PCR studies of the Xcv-tomato and Xcv-pepper pathosystems, as well as for the identification of suitable normalization controls for qRT-PCR studies of other plant-pathogen interactions, especially, if related plant species are used in combination with bacterial pathogens.

  20. Development and validation of a quantitative, high-throughput, fluorescent-based bioassay to detect schistosoma viability.

    Directory of Open Access Journals (Sweden)

    Emily Peak

    Full Text Available BACKGROUND: Schistosomiasis, caused by infection with the blood fluke Schistosoma, is responsible for greater than 200,000 human deaths per annum. Objective high-throughput screens for detecting novel anti-schistosomal targets will drive 'genome to drug' lead translational science at an unprecedented rate. Current methods for detecting schistosome viability rely on qualitative microscopic criteria, which require an understanding of parasite morphology, and most importantly, must be subjectively interpreted. These limitations, in the current state of the art, have significantly impeded progress into whole schistosome screening for next generation chemotherapies. METHODOLOGY/PRINCIPAL FINDINGS: We present here a microtiter plate-based method for reproducibly detecting schistosomula viability that takes advantage of the differential uptake of fluorophores (propidium iodide and fluorescein diacetate by living organisms. We validate this high-throughput system in detecting schistosomula viability using auranofin (a known inhibitor of thioredoxin glutathione reductase, praziquantel and a range of small compounds with previously-described (gambogic acid, sodium salinomycin, ethinyl estradiol, fluoxetidine hydrochloride, miconazole nitrate, chlorpromazine hydrochloride, amphotericin b, niclosamide or suggested (bepridil, ciclopirox, rescinnamine, flucytosine, vinblastine and carbidopa anti-schistosomal activities. This developed method is sensitive (200 schistosomula/well can be assayed, relevant to industrial (384-well microtiter plate compatibility and academic (96-well microtiter plate compatibility settings, translatable to functional genomics screens and drug assays, does not require a priori knowledge of schistosome biology and is quantitative. CONCLUSIONS/SIGNIFICANCE: The wide-scale application of this fluorescence-based bioassay will greatly accelerate the objective identification of novel therapeutic lead targets/compounds to combat

  1. HistologiQuiz

    DEFF Research Database (Denmark)

    Brent, Mikkel Bo

    2015-01-01

    HistologiQuiz er en quiz-app udviklet til almen og speciel histologi. Den består af mere end 1400 spørgsmål og over 320 histologiske billeder. Alle spørgsmål tager udgangspunkt i lærebogen Genesers Histologi af Annemarie Brüel m.fl.......HistologiQuiz er en quiz-app udviklet til almen og speciel histologi. Den består af mere end 1400 spørgsmål og over 320 histologiske billeder. Alle spørgsmål tager udgangspunkt i lærebogen Genesers Histologi af Annemarie Brüel m.fl....

  2. Validity of semi-quantitative scale for brain MRI in unilateral cerebral palsy due to periventricular white matter lesions: Relationship with hand sensorimotor function and structural connectivity

    Directory of Open Access Journals (Sweden)

    Simona Fiori

    2015-01-01

    Conclusion: The sqMRI scale demonstrates first evidence of construct validity against impaired motor and sensory function measures and brain structural connectivity in a cohort of children with UCP due to PWM lesions. More severe lesions correlated with poorer paretic hand sensorimotor function and impaired structural connectivity in the hemisphere contralateral to the clinical side of hemiplegia. The quantitative structural MRI scoring may be a useful clinical tool for studying brain structure–function relationships but requires further validation in other populations of CP.

  3. Appearance normalization of histology slides.

    Science.gov (United States)

    Vicory, Jared; Couture, Heather D; Thomas, Nancy E; Borland, David; Marron, J S; Woosley, John; Niethammer, Marc

    2015-07-01

    This paper presents a method for automatic color and intensity normalization of digitized histology slides stained with two different agents. In comparison to previous approaches, prior information on the stain vectors is used in the plane estimation process, resulting in improved stability of the estimates. Due to the prevalence of hematoxylin and eosin staining for histology slides, the proposed method has significant practical utility. In particular, it can be used as a first step to standardize appearance across slides and is effective at countering effects due to differing stain amounts and protocols and counteracting slide fading. The approach is validated against non-prior plane-fitting using synthetic experiments and 13 real datasets. Results of application of the method to adjustment of faded slides are given, and the effectiveness of the method in aiding statistical classification is shown.

  4. Clinico-Histologic Conferences: Histology and Disease

    Science.gov (United States)

    Shaw, Phyllis A.; Friedman, Erica S.

    2012-01-01

    Providing a context for learning information and requiring learners to teach specific content has been demonstrated to enhance knowledge retention. To enhance students' appreciation of the role of science and specifically histology in clinical reasoning, disease diagnosis, and treatment, a new teaching format was created to provide clinical…

  5. Clinico-Histologic Conferences: Histology and Disease

    Science.gov (United States)

    Shaw, Phyllis A.; Friedman, Erica S.

    2012-01-01

    Providing a context for learning information and requiring learners to teach specific content has been demonstrated to enhance knowledge retention. To enhance students' appreciation of the role of science and specifically histology in clinical reasoning, disease diagnosis, and treatment, a new teaching format was created to provide clinical…

  6. Effect of carbon monoxide on gene expression in cerebrocortical astrocytes: Validation of reference genes for quantitative real-time PCR.

    Science.gov (United States)

    Oliveira, Sara R; Vieira, Helena L A; Duarte, Carlos B

    2015-09-15

    Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a widely used technique to characterize changes in gene expression in complex cellular and tissue processes, such as cytoprotection or inflammation. The accurate assessment of changes in gene expression depends on the selection of adequate internal reference gene(s). Carbon monoxide (CO) affects several metabolic pathways and de novo protein synthesis is crucial in the cellular responses to this gasotransmitter. Herein a selection of commonly used reference genes was analyzed to identify the most suitable internal control genes to evaluate the effect of CO on gene expression in cultured cerebrocortical astrocytes. The cells were exposed to CO by treatment with CORM-A1 (CO releasing molecule A1) and four different algorithms (geNorm, NormFinder, Delta Ct and BestKeeper) were applied to evaluate the stability of eight putative reference genes. Our results indicate that Gapdh (glyceraldehyde-3-phosphate dehydrogenase) together with Ppia (peptidylpropyl isomerase A) is the most suitable gene pair for normalization of qRT-PCR results under the experimental conditions used. Pgk1 (phosphoglycerate kinase 1), Hprt1 (hypoxanthine guanine phosphoribosyl transferase I), Sdha (Succinate Dehydrogenase Complex, Subunit A), Tbp (TATA box binding protein), Actg1 (actin gamma 1) and Rn18s (18S rRNA) genes presented less stable expression profiles in cultured cortical astrocytes exposed to CORM-A1 for up to 60 min. For validation, we analyzed the effect of CO on the expression of Bdnf and bcl-2. Different results were obtained, depending on the reference genes used. A significant increase in the expression of both genes was found when the results were normalized with Gapdh and Ppia, in contrast with the results obtained when the other genes were used as reference. These findings highlight the need for a proper and accurate selection of the reference genes used in the quantification of qRT-PCR results

  7. Interactive Atlas of Histology

    Science.gov (United States)

    Goubran, Emile Z.; Vinjamury, Sivarama P.

    2007-01-01

    Purpose: An interactive atlas of histology was developed for online use by chiropractic students to enable them to practice and self-assess their ability to identify various histological structures. This article discusses the steps in the development, implementation, and usefulness of an interactive atlas of histology for students who take histology examinations. Methods: The atlas was developed by digitizing images imported through a video-microscope using actual microscope slides. Leica EWS 2100 and PowerPoint software were used to construct the atlas. The usefulness of the atlas was assessed through a comparison of histology exam scores between four classes before and four classes after the use of the atlas. Analysis of admissions data, including overall grade point average (GPA), science and nonscience GPA, and a number of course units, was done initially to avoid any identifiable differences in the academic competency between the two being compared. A survey of the students was also done to assess atlas usefulness and students' satisfaction with the atlas. Results: Analysis of histology exam scores showed that the average scores in the lab exam were significantly higher for the classes that used the atlas. Survey results showed a high level of student satisfaction with the atlas. Conclusion: The development and use of an online interactive atlas of histology for chiropractic students helped to improve lab exams scores. In addition, students were satisfied with the features and usefulness of this atlas. PMID:18483638

  8. Validation of Reference Genes for Relative Quantitative Gene Expression Studies in Cassava (Manihot esculenta Crantz) by Using Quantitative Real-Time PCR.

    Science.gov (United States)

    Hu, Meizhen; Hu, Wenbin; Xia, Zhiqiang; Zhou, Xincheng; Wang, Wenquan

    2016-01-01

    Reverse transcription quantitative real-time polymerase chain reaction (real-time PCR, also referred to as quantitative RT-PCR or RT-qPCR) is a highly sensitive and high-throughput method used to study gene expression. Despite the numerous advantages of RT-qPCR, its accuracy is strongly influenced by the stability of internal reference genes used for normalizations. To date, few studies on the identification of reference genes have been performed on cassava (Manihot esculenta Crantz). Therefore, we selected 26 candidate reference genes mainly via the three following channels: reference genes used in previous studies on cassava, the orthologs of the most stable Arabidopsis genes, and the sequences obtained from 32 cassava transcriptome sequence data. Then, we employed ABI 7900 HT and SYBR Green PCR mix to assess the expression of these genes in 21 materials obtained from various cassava samples under different developmental and environmental conditions. The stability of gene expression was analyzed using two statistical algorithms, namely geNorm and NormFinder. geNorm software suggests the combination of cassava4.1_017977 and cassava4.1_006391 as sufficient reference genes for major cassava samples, the union of cassava4.1_014335 and cassava4.1_006884 as best choice for drought stressed samples, and the association of cassava4.1_012496 and cassava4.1_006391 as optimal choice for normally grown samples. NormFinder software recommends cassava4.1_006884 or cassava4.1_006776 as superior reference for qPCR analysis of different materials and organs of drought stressed or normally grown cassava, respectively. Results provide an important resource for cassava reference genes under specific conditions. The limitations of these findings were also discussed. Furthermore, we suggested some strategies that may be used to select candidate reference genes.

  9. Histological assessment in peripheral nerve tissue engineering

    Institute of Scientific and Technical Information of China (English)

    Vctor Carriel; Ingrid Garzn; Miguel Alaminos; Maria Cornelissen

    2014-01-01

    The histological analysis of peripheral nerve regeneration is one of the most used methods to demonstrate the success of the regeneration through nerve conduits. Nowadays, it is possible to evaluate different parameters of nerve regeneration by using histological, histochemical, immunohistochemical and ultrastructural techniques. The histochemical methods are very sensible and are useful tools to evaluate the extracellular matrix remodeling and the myelin sheath, but they are poorly speciifc. In contrast, the immunohistochemical methods are highly speciifc and are frequently used for the identiifcation of the regenerated axons, Schwann cells and proteins associated to nerve regeneration or neural linage. The ultrastructural techniques offer the possibility to perform a high resolution morphological and quantitative analysis of the nerve regeneration. However, the use of a single histological method may not be enough to assess the degree of regeneration, and the combination of different histological techniques could be necessary.

  10. Validation of a quantitative flow cytometer assay for monitoring HER-2/neu expression level in cell-based cancer immunotherapy products.

    Science.gov (United States)

    Randlev, Britta; Huang, Li-chun; Watatsu, Mitsuko; Marcus, Matthew; Lin, Andy; Shih, Shian-Jiun

    2010-03-01

    GVAX immunotherapy for prostate cancer is comprised of two genetically modified prostate cancer cell lines, CG1940 and CG8711, engineered to secrete granulocyte macrophage-colony-stimulating factor. As part of the matrix of potency assays, CG1940 and CG8711 are tested for the expression level of cell surface HER-2/neu using a quantitative flow cytometer assay. This assay reports the antibody binding capacity value of the cells as a measure of HER-2/neu expression using cells immediately after thawing from cryogenic storage. With optimized cell handling and staining procedure and appropriate system suitability controls, the assay was validated as a quantitative assay. The validation results showed that assay accuracy, specificity, precision, linearity, and range were suitable for the intended use of ensuring lot-to-lot consistency of HER-2/neu expression. Assay robustness was demonstrated using design of experiments that evaluated critical assay parameters. Finally, the assay was successfully transferred to a current good manufacturing practice Quality Control laboratory in a separate facility. Since the overall precision of this assay is better than that of ELISA methods and it can be performed with ease and high throughput, quantitative flow cytometer-based assays may be an appropriate immunological assay platform for Quality Control laboratories for characterization and release of cell-based therapies.

  11. Development and validation of an UPLC-Q/TOF-MS assay for the quantitation of neopanaxadiol in beagle dog plasma: Application to a pharmacokinetic study.

    Science.gov (United States)

    Geng, Cong; Wang, Chun-Hong; Hu, Hong; Gao, Xiao-Ping; Gong, Ai-Hua; Lin, Ying-Wei; Fan, Xiu-Shuang; Li, Heng; Yin, Jian-Yuan

    2016-10-27

    Neopanaxadiol (NPD), the main panaxadiol constituent of Panax ginseng C. A. Meyer (Araliaceae), has been regarded as the active component for the treatment of Alzheimer's disease. However, few references are available about pharmacokinetic evaluation for NPD. Accordingly, a rapid and sensitive method for quantitative analysis of NPD in beagle dog plasma based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry was developed and validated. Analytes were extracted from plasma by liquid-liquid extraction and chromatographic separation was achieved on an Agilent Zorbax Stable Bond C18 column. Detection was performed in the positive ion mode using multiple reaction monitoring of the transitions both at m/z 461.4 → 425.4 for NPD and internal standard of panaxadiol. All validation parameters, such as lower limit of quantitation, linearity, specificity, precision, accuracy, extraction recovery, matrix effect and stability, were within acceptable ranges and the method was appropriate for multitude sample determination. After oral intake, NPD was slowly absorbed and eliminated from circulatory blood system and corresponding plasma exposure was low. Application of this quantitative method will yield the first pharmacokinetic profile after oral administration of NPD to beagle dog. The information obtained here will be useful to understand the pharmacological effects of NPD.

  12. Kinematic Validation of a Multi-Kinect v2 Instrumented 10-Meter Walkway for Quantitative Gait Assessments

    OpenAIRE

    Daphne J Geerse; Bert H Coolen; Melvyn Roerdink

    2015-01-01

    Walking ability is frequently assessed with the 10-meter walking test (10MWT), which may be instrumented with multiple Kinect v2 sensors to complement the typical stopwatch-based time to walk 10 meters with quantitative gait information derived from Kinect's 3D body point's time series. The current study aimed to evaluate a multi-Kinect v2 set-up for quantitative gait assessments during the 10MWT against a gold-standard motion-registration system by determining between-systems agreement for b...

  13. Validation and standardization of gene expression data for microarray and real time quantitative PCR using universal external RNA controls

    Science.gov (United States)

    This presentation will introduce newly developed universal external ribonucleic acid (RNA) controls and their applications on different platforms of microarray and quantitative real time polymerase chain reaction (qRT-PCR) including SYBR Green® and TaqMan® probe-based chemistries. Data obtained fro...

  14. The validity of commercial LIBS for quantitative analysis of brass alloy — comparison of WDXRF and AAS

    Science.gov (United States)

    Shaltout, Abdallah A.; Abdel-Aal, M. S.; Mostafa, N. Y.

    2011-09-01

    Commercial low-cost laser induced breakdown spectroscopy (LIBS) has been successfully employed for the quantitative analysis of a Cu-based alloy using a Nd:YAG laser at 1064 nm. The main aim of the present investigation is to explore the benefits of a commercial low-cost LIBS setup. It was recognized that some trace elements such as Al and S could not be detected by LIBS even with a high-resolution spectrometer. The main difficulties in quantifying Cu as a basic component of a brass alloy are related to the self-absorption of Cu spectral lines, with the effect complicated at Cu concentrations higher than 65%. However, few Cu lines such as that at 330.795 nm would be helpful to use due to their lower susceptibility to self-absorption. LIBS, flame atomic absorption spectrometry (FAAS), and wavelength dispersive X-ray fluorescence (WDXRF) were compared for the detection of major and trace metals in the Cu-based alloy. In the case of WDXRF, the brass samples were identified by using a standardless quantitative analysis program depending on a fundamental parameter approach. The quantitative analysis results were acceptable for most of the major and minor elements of the brass sample. Therefore, commercial low cost LIBS would be useful for quantitative analysis of most elements in different types of alloys.

  15. Histological image segmentation using fast mean shift clustering method

    OpenAIRE

    Wu, Geming; Zhao, Xinyan; Luo, Shuqian; Shi, Hongli

    2015-01-01

    Background Colour image segmentation is fundamental and critical for quantitative histological image analysis. The complexity of the microstructure and the approach to make histological images results in variable staining and illumination variations. And ultra-high resolution of histological images makes it is hard for image segmentation methods to achieve high-quality segmentation results and low computation cost at the same time. Methods Mean Shift clustering approach is employed for histol...

  16. Quantitative Validation of the Presto Blue Metabolic Assay for Online Monitoring of Cell Proliferation in a 3D Perfusion Bioreactor System.

    Science.gov (United States)

    Sonnaert, Maarten; Papantoniou, Ioannis; Luyten, Frank P; Schrooten, Jan Ir

    2015-06-01

    As the fields of tissue engineering and regenerative medicine mature toward clinical applications, the need for online monitoring both for quantitative and qualitative use becomes essential. Resazurin-based metabolic assays are frequently applied for determining cytotoxicity and have shown great potential for monitoring 3D bioreactor-facilitated cell culture. However, no quantitative correlation between the metabolic conversion rate of resazurin and cell number has been defined yet. In this work, we determined conversion rates of Presto Blue, a resazurin-based metabolic assay, for human periosteal cells during 2D and 3D static and 3D perfusion cultures. Our results showed that for the evaluated culture systems there is a quantitative correlation between the Presto Blue conversion rate and the cell number during the expansion phase with no influence of the perfusion-related parameters, that is, flow rate and shear stress. The correlation between the cell number and Presto Blue conversion subsequently enabled the definition of operating windows for optimal signal readouts. In conclusion, our data showed that the conversion of the resazurin-based Presto Blue metabolic assay can be used as a quantitative readout for online monitoring of cell proliferation in a 3D perfusion bioreactor system, although a system-specific validation is required.

  17. Development and validation of a TLC-densitometric method for the simultaneous quantitation of strychnine and brucine from Strychnos spp. and its formulations.

    Science.gov (United States)

    Dhalwal, Kamlesh; Shinde, Vaibhav M; Namdeo, Ajay G; Mahadik, Kakasaheb R; Kadam, Shivajirao S

    2007-01-01

    A simple, sensitive, and specific thin-layer chromatography densitometric method has been developed for the simultaneous quantitation of strychnine and brucine. These two marker compounds are quantitated in the seeds of Strychnos nux-vomica, Strychnos ignatii, and its formulations. The method involves densitometric evaluation of strychnine and brucine after resolving it by high-performance TLC on silica gel plate with toluene-ethyl acetate-diethyl amine-methanol (7:2:1:0.3 v/v) as the mobile phase. The method is validated for precision (interday and intraday), repeatability, and accuracy. The relationship between the concentration of standard solutions and the peak response is linear within the concentration range of 160 to 480 ng/spot for strychnine and 80 to 480 ng/spot for brucine. Instrumental precision is found to be 0.54 and 0.78 (% CV), and repeatability of the method is 1.01 and 1.06 (% CV) for strychnine and brucine, respectively. Accuracy of the method is checked by recovery study conducted at three different levels and the average percentage recovery is found to be 99.13% for strychnine and 100.16% for brucine. The proposed HPTLC method for the simultaneous quantitation of strychnine and brucine is found to be simple, precise, specific, sensitive, and accurate, and it can be used for routine quality control of raw material of Strychnos spp. It also can be applied in quantitating any of these marker compounds in other formulations.

  18. A Novel HPLC Method for the Concurrent Analysis and Quantitation of Seven Water-Soluble Vitamins in Biological Fluids (Plasma and Urine: A Validation Study and Application

    Directory of Open Access Journals (Sweden)

    Margherita Grotzkyj Giorgi

    2012-01-01

    Full Text Available An HPLC method was developed and validated for the concurrent detection and quantitation of seven water-soluble vitamins (C, B1, B2, B5, B6, B9, B12 in biological matrices (plasma and urine. Separation was achieved at 30°C on a reversed-phase C18-A column using combined isocratic and linear gradient elution with a mobile phase consisting of 0.01% TFA aqueous and 100% methanol. Total run time was 35 minutes. Detection was performed with diode array set at 280 nm. Each vitamin was quantitatively determined at its maximum wavelength. Spectral comparison was used for peak identification in real samples (24 plasma and urine samples from abstinent alcohol-dependent males. Interday and intraday precision were <4% and <7%, respectively, for all vitamins. Recovery percentages ranged from 93% to 100%.

  19. Optimization and validation of DNA extraction and real-time PCR assay for the quantitative measurement of residual host cell DNA in biopharmaceutical products.

    Science.gov (United States)

    Hu, B; Sellers, J; Kupec, J; Ngo, W; Fenton, S; Yang, T-Y; Grebanier, A

    2014-01-01

    Host cell DNA contamination occurs during the production of biopharmaceuticals and must be controlled and monitored for the purity and safety of the drug products. A sodium iodide-based DNA extraction and a subsequent real time PCR assay were developed and validated for the quantitative measurement of residual host cell DNA impurity in monoclonal antibody therapeutic products. A sodium iodide-based commercial kit was optimized for the removal of interfering matrices. Several incubation steps from the kit protocol were combined and a neutralization buffer was introduced to protein digestion step to eliminate any precipitation from the detergent. The elimination of the two washing steps significantly reduced assay variability from loss of DNA pellets. The optimized DNA extraction procedure can recover DNA close to 100% for DNA concentrations from 10 to 100,000pg/mL. Of the published sequences of repetitive interspersed nuclear elements, we identified a nucleotide mismatch from the published CHO probe. Correction of this nucleotide increased DNA amplification by a thousand fold. The optimized assay was further validated for the quantitation of residual CHO DNA according to ICH guidelines with preset assay acceptance criteria. The method met all assay acceptance criteria and was found linear, accurate and precise for the quantitation of residual CHO in the linear range of 10-100,000pg DNA/mL. LOQ was measured at 10pg DNA/mL and LOD at 1pg DNA/mL. No matrix interference to our validated assay was detected from bioreactor harvest, Protein A eluate or eluate from ion exchange columns.

  20. Absolute quantitation of myocardial blood flow with {sup 201}Tl and dynamic SPECT in canine: optimisation and validation of kinetic modelling

    Energy Technology Data Exchange (ETDEWEB)

    Iida, Hidehiro; Kim, Kyeong-Min; Nakazawa, Mayumi; Sohlberg, Antti; Zeniya, Tsutomu; Hayashi, Takuya; Watabe, Hiroshi [National Cardiovascular Center Research Institute, Department of Investigative Radiology, Suita City, Osaka (Japan); Eberl, Stefan [National Cardiovascular Center Research Institute, Department of Investigative Radiology, Suita City, Osaka (Japan); Royal Prince Alfred Hospital, PET and Nuclear Medicine Department, Camperdown, NSW (Australia); Tamura, Yoshikazu [Akita Kumiai General Hospital, Department of Cardiology, Akita City (Japan); Ono, Yukihiko [Akita Research Institute of Brain, Akita City (Japan)

    2008-05-15

    {sup 201}Tl has been extensively used for myocardial perfusion and viability assessment. Unlike {sup 99m}Tc-labelled agents, such as {sup 99m}Tc-sestamibi and {sup 99m}Tc-tetrofosmine, the regional concentration of {sup 201}Tl varies with time. This study is intended to validate a kinetic modelling approach for in vivo quantitative estimation of regional myocardial blood flow (MBF) and volume of distribution of {sup 201}Tl using dynamic SPECT. Dynamic SPECT was carried out on 20 normal canines after the intravenous administration of {sup 201}Tl using a commercial SPECT system. Seven animals were studied at rest, nine during adenosine infusion, and four after beta-blocker administration. Quantitative images were reconstructed with a previously validated technique, employing OS-EM with attenuation-correction, and transmission-dependent convolution subtraction scatter correction. Measured regional time-activity curves in myocardial segments were fitted to two- and three-compartment models. Regional MBF was defined as the influx rate constant (K{sub 1}) with corrections for the partial volume effect, haematocrit and limited first-pass extraction fraction, and was compared with that determined from radio-labelled microspheres experiments. Regional time-activity curves responded well to pharmacological stress. Quantitative MBF values were higher with adenosine and decreased after beta-blocker compared to a resting condition. MBFs obtained with SPECT (MBF{sub SPECT}) correlated well with the MBF values obtained by the radio-labelled microspheres (MBF{sub MS}) (MBF{sub SPECT} = -0.067 + 1.042 x MBF{sub MS}, p < 0.001). The three-compartment model provided better fit than the two-compartment model, but the difference in MBF values between the two methods was small and could be accounted for with a simple linear regression. Absolute quantitation of regional MBF, for a wide physiological flow range, appears to be feasible using {sup 201}Tl and dynamic SPECT. (orig.)

  1. International ring trial for the validation of an event-specific Golden Rice 2 quantitative real-time polymerase chain reaction method.

    Science.gov (United States)

    Jacchia, Sara; Nardini, Elena; Bassani, Niccolò; Savini, Christian; Shim, Jung-Hyun; Trijatmiko, Kurniawan; Kreysa, Joachim; Mazzara, Marco

    2015-05-27

    This article describes the international validation of the quantitative real-time polymerase chain reaction (PCR) detection method for Golden Rice 2. The method consists of a taxon-specific assay amplifying a fragment of rice Phospholipase D α2 gene, and an event-specific assay designed on the 3' junction between transgenic insert and plant DNA. We validated the two assays independently, with absolute quantification, and in combination, with relative quantification, on DNA samples prepared in haploid genome equivalents. We assessed trueness, precision, efficiency, and linearity of the two assays, and the results demonstrate that both the assays independently assessed and the entire method fulfill European and international requirements for methods for genetically modified organism (GMO) testing, within the dynamic range tested. The homogeneity of the results of the collaborative trial between Europe and Asia is a good indicator of the robustness of the method.

  2. Definitions and validation criteria for biomarkers and surrogate endpoints: development and testing of a quantitative hierarchical levels of evidence schema

    DEFF Research Database (Denmark)

    Lassere, Marissa N; Johnson, Kent R; Boers, Maarten

    2007-01-01

    OBJECTIVE: There are clear advantages to using biomarkers and surrogate endpoints, but concerns about clinical and statistical validity and systematic methods to evaluate these aspects hinder their efficient application. Our objective was to review the literature on biomarkers and surrogates to d...

  3. Quantitative myocardial perfusion PET combined with coronary anatomy derived from CT angiography. Validation of a new fusion and visualisation software

    Energy Technology Data Exchange (ETDEWEB)

    Fricke, Harald; Weise, Reiner; Burchert, Wolfgang; Fricke, Eva [Inst. of Radiology, Nuclear Medicine and Molecular Imaging, Heart and Diabetes Centre North Rhine-Westphalia, Ruhr-Univ. Bochum, Bad Oeynhausen (Germany); Elsner, Andreas; Bolte, Matthias; Domik, Gitta [Research Group Computergraphics, Visualization and Image Processing, Univ. of Paderborn (Germany); Hoff, Joerg van den [PET Center, Inst. of Radiopharmacy, Research Center Rossendorf, Dresden (Germany)

    2009-07-01

    Aim: Dynamic perfusion PET offers a clinical relevant advantage over myocardial perfusion scintigraphy due to its ability to measure myocardial blood flow quantitatively. This leads to an improved detection of multivessel disease and the possibility to assess not only the culprit lesion but lower grade stenoses as well. For appropriate revascularization, perfusion defects must be matched to coronary lesions. It has been shown that image fusion of morphological and functional images is superior to side-by-side analysis. Still, software for quantitative perfusion PET combined with CT angiography is rare. In this paper we present a new software tool for image fusion and visualization of quantitative perfusion PET and coronary morphology derived from CT angiography. Methods: In our software, a PET uptake image is used for manual co-registration. Co-registration results are then applied to the functional data derived from compartment modelling. To evaluate the reproducibility of the manual co-registration, we calculated the deviation between a series of manual co-registrations performed on nine pairs of unregistered PET and CT datasets by five trained participants. Two dimensional transfer functions were used to highlight the coronary arteries from the CT study in the combined data sets. Results: The average Euclidian distances for three references points were between 3.7 and 4.1 mm. The maximum distance was 10.6 mm. By the use of the two dimensional transfer functions, coronary anatomy could be easily visualised either by user-interaction or automatically by use of neuronal networks. Conclusions: With this approach it is possible to combine quantitative perfusion PET with coronary anatomy derived from CT angiography. Our first experiences indicate that manual image fusion with our tool is reproducible and that visualisation of the combined datasets is achieved within short time. (orig.)

  4. Salaries in histology.

    Science.gov (United States)

    Buesa, René J

    2008-04-01

    An analysis of histology salaries from the last 4 national surveys conducted by the American Society of Clinical Pathologists is presented. The regional variations within and between years for histology salaries presented in the last 4 national surveys of medical laboratory specialties are not statistically significant. Local variations greater than the national variations reflect the preponderant effect of local supply and demand over regional characteristics. Salaries by hospitals are significantly different only between 2 size categories and the supervisors' salary. There is no correlation between the salary increase for any histology position in any one year and the vacancy level in the previous year. On the other hand, the correlation between histotechnicians' salaries and both the cost of living and the median income are significant, as well as between the latter and the supervisors' salary. The histotechnologists' salaries are significantly correlated with the consumer price index but not with the inflation rate. A survey of histology salaries in foreign countries was also undertaken and compared with salaries in the United States. National salaries rank close to the general average for 10 foreign countries when expressed as ratios with the personal gross domestic product or with the countries' minimum wage. For the midpoint salary ranges, the United States ranks fourth after Canada, the United Kingdom, and Australia, the latter 3 countries with structured pay rates adjusted to local costs of living in contrast with United States' salary characteristics. Histology salaries rest on negotiations within each employer's salary structure and fluctuate according to license level, documented studies, special training(s), years of experience, references, and the ability to negotiate, where each side tries to take advantage of the other. The result is a heterogeneous and chaotic salary situation driven by personal and local needs, where the histology worker usually

  5. Cerebrovascular reactivity by quantitative magnetic resonance angiography with a co{sub 2} challenge. Validation as a new imaging biomarker

    Energy Technology Data Exchange (ETDEWEB)

    Caputi, Luigi, E-mail: lcaputi@istituto-besta.it [Department of Cerebrovascular Diseases, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Ghielmetti, Francesco, E-mail: Francesco.Ghielmetti@istituto-besta.it [Department of Neuroradiology, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Faragò, Giuseppe, E-mail: Giuseppe.Farago@istituto-besta.it [Department of Neuroradiology, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Longaretti, Fabio, E-mail: fabio.longaretti@libero.it [Department of Neuroradiology, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Lamperti, Massimo, E-mail: docmassimomd@gmail.com [Department of Neuroanesthesia and Intensive Care, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Anzola, Gian Paolo, E-mail: gpanzola@speedyposta.it [Service of Neurology, S. Orsola Hospital, Fondazione Poliambulanza, Via Vittorio Emanuele II 27, 25122 Brescia (Italy); Carriero, Maria Rita, E-mail: MariaRita.Carriero@istituto-besta.it [Department of Cerebrovascular Diseases, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Charbel, Fady T., E-mail: fcharbel@uic.edu [Department of Neurosurgery, University of Illinois at Chicago College of Medicine, Chicago, IL 60612 (United States); Bruzzone, Maria Grazia, E-mail: Maria.Bruzzone@istituto-besta.it [Department of Neuroradiology, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Parati, Eugenio, E-mail: Eugenio.Parati@istituto-besta.it [Department of Cerebrovascular Diseases, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy); Ciceri, Elisa, E-mail: Elisa.Ciceri@istituto-besta.it [Department of Neuroradiology, Fondazione IRCCS Neurological Institute C. Besta, Via Celoria 11, 20133 Milan (Italy)

    2014-06-15

    Assessment of cerebrovascular reactivity (CVR) is essential in cerebrovascular diseases, as exhausted CVR may enhance the risk of cerebral ischemic events. Transcranial Doppler (TCD) with a vasodilatory stimulus is currently used for CVR evaluation. Scanty data are available for Quantitative Magnetic Resonance Angiography (QMRA), which supplies higher spatial resolution and quantitative cerebral blood flow values. Aims of our pilot study were: (a) to assess safety and feasibility of CO{sub 2} administration during QMRA, (b) evaluation of CVR under QMRA compared to TCD, and (c) quantitative evaluation of blood flow from the major intracranial arterial vessels both at rest and after CO{sub 2}. CVR during 5% CO{sub 2} air breathing was measured with TCD as a reference method and compared with QMRA. Fifteen healthy subjects (age 60.47 ± 2.24; male 11/15) were evaluated at rest and during CO{sub 2} challenge. Feasibility and safety of QMRA under CO{sub 2} were ensured in all subjects. CVR from middle cerebral artery territory was not statistically different between TCD and MRI (p > 0.05). Mean arterial pressure (MAP) and heart rate (HR) increased during QMRA and TCD (MAP p = 0.007 and p = 0.001; HR p = 0.043 and p = 0.068, respectively). Blood flow values from all intracranial vessels increased after CO{sub 2} inhalation (p < 0.001). CO{sub 2} administration during QMRA sessions is safe and feasible. Good correlation in terms of CVR was obtained comparing TCD and QMRA. Blood flow values significantly increased from all intracranial arterial vessels after CO{sub 2}. Studies regarding CVR in physiopathological conditions might consider the utilization of QMRA both in routine clinical settings and in research projects.

  6. Development and validation of stability indicating method for the quantitative determination of venlafaxine hydrochloride in extended release formulation using high performance liquid chromatography

    Directory of Open Access Journals (Sweden)

    Jaspreet Kaur

    2010-01-01

    Full Text Available Objective : Venlafaxine,hydrochloride is a structurally novel phenethyl bicyclic antidepressant, and is usually categorized as a serotonin-norepinephrine reuptake inhibitor (SNRI but it has been referred to as a serotonin-norepinephrine-dopamine reuptake inhibitor. It inhibits the reuptake of dopamine. Venlafaxine HCL is widely prescribed in the form of sustained release formulations. In the current article we are reporting the development and validation of a fast and simple stability indicating, isocratic high performance liquid chromatographic (HPLC method for the determination of venlafaxine hydrochloride in sustained release formulations. Materials and Methods : The quantitative determination of venlafaxine hydrochloride was performed on a Kromasil C18 analytical column (250 x 4.6 mm i.d., 5 μm particle size with 0.01 M phosphate buffer (pH 4.5: methanol (40: 60 as a mobile phase, at a flow rate of 1.0 ml/min. For HPLC methods, UV detection was made at 225 nm. Results : During method validation, parameters such as precision, linearity, accuracy, stability, limit of quantification and detection and specificity were evaluated, which remained within acceptable limits. Conclusions : The method has been successfully applied for the quantification and dissolution profiling of Venlafaxine HCL in sustained release formulation. The method presents a simple and reliable solution for the routine quantitative analysis of Venlafaxine HCL.

  7. Development and Validation of Stability-Indicating GC-FID Method for the Quantitation of Memantine Hydrochloride and Its Nonchromophoric Impurities in Bulk and Pharmaceutical Dosages

    Directory of Open Access Journals (Sweden)

    Sanjay A. Jadhav

    2012-01-01

    Full Text Available A stability-indicating method has been developed and validated for the quantitative determination of memantine hydrochloride and its nonchromophoric impurities in drug substance and drug product using gas chromatography coupled with flame ionization detector (GC-FID. The stability-indicating nature of the method has been proved by establishing peak purity and confirming the mass balance of all samples by subjecting them to stress conditions like hydrolysis, oxidation, photolysis, and thermal degradation studies. The chromatographic separation was performed on a fused silica capillary (HP-5, 30 meter, 0.32 mm and 0.25 μm film thickness column. The method validation results indicate that the method has acceptable specificity, accuracy, linearity, precision, robustness, and high sensitivity with detection limits and quantitation limits ranging from 0.001% to 0.01% and 0.004% to 0.03%, respectively. The effectiveness of the technique was demonstrated by analysis of different bulk sample of Memantine hydrochloride. The proposed GC-FID method was also found to be specific and selective for the analysis of commercial formulation samples.

  8. Development and validation of a quantitative PCR assay using multiplexed hydrolysis probes for detection and quantification of Theileria orientalis isolates and differentiation of clinically relevant subtypes.

    Science.gov (United States)

    Bogema, D R; Deutscher, A T; Fell, S; Collins, D; Eamens, G J; Jenkins, C

    2015-03-01

    Theileria orientalis is an emerging pathogen of cattle in Asia, Australia, and New Zealand. This organism is a vector-borne hemoprotozoan that causes clinical disease characterized by anemia, abortion, and death, as well as persistent subclinical infections. Molecular methods of diagnosis are preferred due to their sensitivity and utility in differentiating between pathogenic and apathogenic genotypes. Conventional PCR (cPCR) assays for T. orientalis detection and typing are laborious and do not provide an estimate of parasite load. Current real-time PCR assays cannot differentiate between clinically relevant and benign genotypes or are only semiquantitative without a defined clinical threshold. Here, we developed and validated a hydrolysis probe quantitative PCR (qPCR) assay which universally detects and quantifies T. orientalis and identifies the clinically associated Ikeda and Chitose genotypes (UIC assay). Comparison of the UIC assay results with previously validated universal and genotype-specific cPCR results demonstrated that qPCR detects and differentiates T. orientalis with high sensitivity and specificiy. Comparison of quantitative results based on percent parasitemia, determined via blood film analysis and packed cell volume (PCV) revealed significant positive and negative correlations, respectively. One-way analysis of variance (ANOVA) indicated that blood samples from animals with clinical signs of disease contained statistically higher concentrations of T. orientalis DNA than animals with subclinical infections. We propose clinical thresholds to assist in classifying high-, moderate-, and low-level infections and describe how parasite load and the presence of the Ikeda and Chitose genotypes relate to disease.

  9. Validation of a stability-indicating hydrophilic interaction liquid chromatographic method for the quantitative determination of vitamin k3 (menadione sodium bisulfite) in injectable solution formulation.

    Science.gov (United States)

    Ghanem, Mashhour M; Abu-Lafi, Saleh A; Hallak, Hussein O

    2013-01-01

    A simple, specific, accurate, and stability-indicating method was developed and validated for the quantitative determination of menadione sodium bisulfite in the injectable solution formulation. The method is based on zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) coupled with a photodiode array detector. The desired separation was achieved on the ZIC-HILIC column (250 mm × 4.6 mm, 5 μm) at 25°C temperature. The optimized mobile phase consisted of an isocratic solvent mixture of 200mM ammonium acetate (NH4AC) solution and acetonitrile (ACN) (20:80; v/v) pH-adjusted to 5.7 by glacial acetic acid. The mobile phase was fixed at 0.5 ml/min and the analytes were monitored at 261 nm using a photodiode array detector. The effects of the chromatographic conditions on the peak retention, peak USP tailing factor, and column efficiency were systematically optimized. Forced degradation experiments were carried out by exposing menadione sodium bisulfite standard and the injectable solution formulation to thermal, photolytic, oxidative, and acid-base hydrolytic stress conditions. The degradation products were well-resolved from the main peak and the excipients, thus proving that the method is a reliable, stability-indicating tool. The method was validated as per ICH and USP guidelines (USP34/NF29) and found to be adequate for the routine quantitative estimation of menadione sodium bisulfite in commercially available menadione sodium bisulfite injectable solution dosage forms.

  10. Development and Validation of a Multiplexed Protein Quantitation Assay for the Determination of Three Recombinant Proteins in Soybean Tissues by Liquid Chromatography with Tandem Mass Spectrometry.

    Science.gov (United States)

    Hill, Ryan C; Oman, Trent J; Shan, Guomin; Schafer, Barry; Eble, Julie; Chen, Cynthia

    2015-08-26

    Currently, traditional immunochemistry technologies such as enzyme-linked immunosorbent assays (ELISA) are the predominant analytical tool used to measure levels of recombinant proteins expressed in genetically engineered (GE) plants. Recent advances in agricultural biotechnology have created a need to develop methods capable of selectively detecting and quantifying multiple proteins in complex matrices because of increasing numbers of transgenic proteins being coexpressed or "stacked" to achieve tolerance to multiple herbicides or to provide multiple modes of action for insect control. A multiplexing analytical method utilizing liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been developed and validated to quantify three herbicide-tolerant proteins in soybean tissues: aryloxyalkanoate dioxygenase (AAD-12), 5-enol-pyruvylshikimate-3-phosphate synthase (2mEPSPS), and phosphinothricin acetyltransferase (PAT). Results from the validation showed high recovery and precision over multiple analysts and laboratories. Results from this method were comparable to those obtained with ELISA with respect to protein quantitation, and the described method was demonstrated to be suitable for multiplex quantitation of transgenic proteins in GE crops.

  11. Quantitative validation experiment on Newton third law%定量验证牛顿第三定律

    Institute of Scientific and Technical Information of China (English)

    陈芳; 周晓棣; 拾景忠

    2016-01-01

    通过2台电子天平的示数变化,定量地探究作用力与反作用力的关系,验证压力、浮力、磁力等多种形式的力均满足牛顿第三定律。%The relationship between action and reaction was quantitatively explored by the changes of the display of the two electronic balances ,and all kinds of forces ,such as pressure ,buoyancy and magnetic force ,were verified to obey Newton third law .

  12. Validation of the method of quantitative phase analysis by X-ray diffraction in API: case of Tibolone

    Science.gov (United States)

    Silva, R. P.; Ambrósio, M. F. S.; Epprecht, E. K.; Avillez, R. R.; Achete, C. A.; Kuznetsov, A.; Visentin, L. C.

    2016-07-01

    In this study, different structural and microstructural models applied to X-ray analysis of powder diffraction data of polymorphic mixtures of known concentrations of Tibolone were investigated. The X-ray data obtained in different diffraction instruments were analysed via Rietveld method using the same analytical models. The results of quantitative phase analysis show that regardless of the instrument used, the values of the calculated concentrations follow the same systematics with respect to the final errors. The strategy to select a specific analytical model that leads to lower measurement errors is here presented.

  13. Development and Validation of a Liquid Chromatography-Tandem Mass Spectrometry Method for the Quantitation of Microcystins in Blue-Green Algal Dietary Supplements.

    Science.gov (United States)

    Parker, Christine H; Stutts, Whitney L; DeGrasse, Stacey L

    2015-12-02

    A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the simultaneous detection and quantitation of seven microcystin congeners (1-7) and nodularin-R (8) in blue-green algal dietary supplements. Single-laboratory method validation data were collected in four supplement matrices (capsule, liquid, powder, and tablet) fortified at toxin concentrations from 0.25-2.00 μg/g (ppm). Average recoveries and relative standard deviations (RSD) using matrix-corrected solvent calibration curves were 101% (6% RSD) for all congeners and supplements investigated. Limits of detection (0.006-0.028 μg/g) and quantitation (0.018-0.084 μg/g) were sufficient to confirm the presence of microcystin contamination at the Oregon-mandated guidance concentration of 1.0 μg of microcystin-LReq/g. Quantitated concentrations of microcystin contamination in market-available Aphanizomenon flos-aquae blue-green algal supplements ranged from 0.18-1.87 μg of microcystin-LReq/g for detected congeners microcystin-LR, microcystin-LA, and microcystin-LY (3-5). Microcystin-RR, -YR, -LW, and -LF and nodularin-R (1, 2, and 6-8) were not detected in the supplements examined.

  14. Quantitative Analysis of Tetramethylenedisulfotetramine ("Tetramine") Spiked into Beverages by Liquid Chromatography Tandem Mass Spectrometry with Validation by Gas Chromatography Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Owens, J; Hok, S; Alcaraz, A; Koester, C

    2008-11-13

    Tetramethylenedisulfotetramine, commonly known as tetramine, is a highly neurotoxic rodenticide (human oral LD{sub 50} = 0.1 mg/kg) used in hundreds of deliberate food poisoning events in China. Here we describe a method for quantitation of tetramine spiked into beverages, including milk, juice, tea, cola, and water and cleaned up by C8 solid phase extraction and liquid-liquid extraction. Quantitation by high performance liquid chromatography tandem mass spectrometry (LC/MS/MS) was based upon fragmentation of m/z 347 to m/z 268. The method was validated by gas chromatography mass spectrometry (GC/MS) operated in SIM mode for ions m/z 212, 240, and 360. The limit of quantitation was 0.10 {micro}g/mL by LC/MS/MS versus 0.15 {micro}g/mL for GC/MS. Fortifications of the beverages at 2.5 {micro}g/mL and 0.25 {micro}g/mL were recovered ranging from 73-128% by liquid-liquid extraction for GC/MS analysis, 13-96% by SPE and 10-101% by liquid-liquid extraction for LC/MS/MS analysis.

  15. Salbutamol extraction from urine and its stability in different solutions: identification of methylation products and validation of a quantitative analytical method.

    Science.gov (United States)

    Garrido, Bruno Carius; Silva, Mayra Leal Chrisóstomo; Borges, Ricardo Moreira; Padilha, Monica Costa; de Aquino Neto, Francisco Radler

    2013-12-01

    Salbutamol is commonly used in asthma treatment, being considered a short-effect bronchodilator. This drug poses special interest in certain fields of chemical analysis, such as food, clinical and doping analyses, in which it needs to be analyzed with quantitative precision and accuracy. Salbutamol, however, is known to degrade under certain conditions and this is critical if quantitative results must be generated. The present work aimed to investigate salbutamol extraction from urine samples, to determine whether salbutamol is unstable in other solvents as well as in urine samples, to elucidate the structures of the possible degradation products and to validate an analytical method using the extraction procedure evaluated. Stability investigations were performed in urine at different pH values, in methanol and acetone at different temperatures. Semi-preparative liquid chromatography was performed for the isolation of degradation products, and gas chromatography coupled to mass spectrometry as well as nuclear magnetic resonance were used for identification. Three unreported methylation products were detected in methanolic solutions and had their structures elucidated. Urine samples showed a reduction in salbutamol concentration of up to 25.8% after 5 weeks. These results show that special care must be taken regarding salbutamol quantitative analyses, since degradation either in standard solutions or in urine could lead to incorrect values.

  16. Preliminary validity of the barriers to treatment adherence questionnaire in fibromyalgia: combining quantitative and focus group data.

    Science.gov (United States)

    Dobkin, Patricia L; De Civita, Mirella; Bernatsky, Sasha; Filipski, Marta; Sita, Aurelio; Baron, Murray

    2009-10-01

    The goals of this study were to (1) provide preliminary reliability and validity of the Barriers to Treatment Adherence Questionnaire, developed for patients with fibromyalgia, and (2) examine barriers to adherence and general adherence to multimodal treatment during a 3-mo. period. A secondary goal was to explore in a focus discussion group format patients' perceptions of the adherence process and ways of managing the treatment program. 39 fibromyalgia patients were followed while participating in a combined outpatient program of physiotherapy, occupational therapy, nursing, and cognitive behavioral therapy. The Barriers to Treatment Adherence Questionnaire demonstrated good reliability. Construct validity of the Barriers to Treatment Adherence Questionnaire was supported through significant positive correlations with the General Adherence Scale at Months 1 and 3. In addition, a significant change was observed in scores on the Barriers to Treatment Adherence Questionnaire for the physiotherapy component of treatment, with scores decreasing between Months 2 and 3. Addressing barriers to improve adherence may maximize the benefit of treatment programs.

  17. Multianalytical Method Validation for Qualitative and Quantitative Analysis of Solvents of Abuse in Oral Fluid by HS-GC/MS

    Directory of Open Access Journals (Sweden)

    Bruna Claudia Coppe

    2016-01-01

    Full Text Available The use of oral fluid as a biological matrix to monitor the use of drugs of abuse is a global trend because it presents several advantages and good correlation to the blood level. Thus, the present work aimed to develop and validate an analytical method for quantification and detection of solvents used as inhalants of abuse in oral fluid (OF, using Quantisal™ as collector device by headspace and gas chromatography coupled with a mass detector (HS-GC/MS. Chromatographic separation was performed with a ZB-BAC1 column and the total time of analysis was 11.8 min. The method showed good linearity (correlation coefficient higher than 0.99 for all solvents. The limits of detection ranged from 0.05 to 5 mg/L, while the lower limits of quantification ranged from 2.5 to 12.5 mg/L. Accuracy, precision, matrix effect, and residual effect presented satisfactory results, meeting the criteria accepted for the validation of bioanalytical methods. The method showed good selectivity considering that, for solvents coeluting at the same retention time, resolution was performed by the mass detector. The method developed proved to be adequate when applied in OF samples from users of drugs and may be used to monitor the abuse of inhalants in routine forensic analyses.

  18. Standardization and validation of a new atomic absorption spectroscopy technique for determination and quantitation of aluminium adjuvant in immunobiologicals.

    Science.gov (United States)

    Mishra, Arti; Bhalla, Sumir Rai; Rawat, Sameera; Bansal, Vivek; Sehgal, Rakesh; Kumar, Sunil

    2007-10-01

    In the present study, Aluminium quantification in immunobiologicals has been described using atomic absorption spectroscopy (AAS) technique. The assay was found to be linear in 25-125 microg/ml Aluminium range. The procedure was found to be accurate for different vaccines with recoveries of external additions ranging between 93.26 and 103.41%. The mean Limit of Variation (L.V.) for both intra- and inter-assay precision was calculated to be 1.62 and 2.22%, respectively. Further the procedure was found to be robust in relation to digestion temperature, alteration in acid (HNO(3) and H(2)SO(4)) ratio used for sample digestion and storage of digested vaccine samples up to a period of 15 days. After validation, AAS method was compared for its equivalency with routinely used complexometric titration method. On simultaneously applying on seven different groups of both bacterial and viral vaccines, viz., DPT, DT, TT, Hepatitis-A and B, Antirabies vaccine (cell culture) and tetravalent DPT-Hib, a high degree of positive correlation (+0.85-0.998) among AAS and titration methods was observed. Further AAS method was found to have an edge over complexometric titration method that a group of vaccines, viz., ARV (cell culture, adsorbed) and Hepatitis-A, in which Aluminium estimation is not feasible by pharmacopoeial approved complexometric titration method (possibly due to some interference in the sample matrix), this newly described and validated AAS assay procedure delivered accurate and reproducible results.

  19. Validation of a carnation-specific gene, ANS, used as an endogenous reference gene in qualitative and real-time quantitative PCR for carnations.

    Science.gov (United States)

    Zhu, Hong; Jiang, Lingxi; Tao, Shiru; Lin, Heyan; Wang, Jinbin; Tan, Furong; Zhao, Kai; Wu, Xiao; Li, Peng; Pan, Aihu; Jia, Junwei; Tang, Xueming

    2011-01-01

    The validation of the anthocyanin synthase (ANS) gene as a carnation endogenous reference gene applicable both in classical and real-time PCR methods is a prerequisite for the development of PCR assays for genetically modified (GM) carnation detection. This is important due to the fact that GM carnation lines, developed by Florigene Pty Ltd, have been approved for commercialization. In this study, both methods were tested on 14 different carnation cultivars, and identical amplification products were obtained with all of them. No amplification products were observed with samples from 14 other plant species, which demonstrated that the system was specific to carnation. The results of Southern blot analysis confirmed that the ANS gene had a low copy number in the 10 tested carnation varieties. In qualitative and real-time PCR assays, the LOD values of 0.05 and 0.005 ng carnation DNA, respectively, were validated. Moreover, the real-time PCR system was validated with high PCR efficiency and linearity. Thus, the ANS gene had species specificity, low heterogeneity, and low copy number among the tested cultivars. These results provide evidence that the gene can be used as an endogenous reference gene of carnation, as well as in qualitative and quantitative PCR systems.

  20. A validated assay to quantitate serotonin in lamb plasma using ultrahigh-performance liquid chromatography-tandem mass spectrometry: applications with LC/MS3.

    Science.gov (United States)

    Szeitz, András; Nguyen, Tuan-Anh T; Riggs, K Wayne; Rurak, Dan

    2014-08-01

    An ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC/MS/MS) method was developed and validated for the quantification of serotonin (5-HT) in lamb plasma using [(2)d(4)]-serotonin ([(2)d(4)]-5-HT) as an internal standard. Charcoal-stripped human plasma was used as the blank matrix during validation, and 5-HT was quantitated using selected reaction monitoring. The UHPLC/MS/MS system consisted of an Agilent 1290 Infinity ultrahigh-performance liquid chromatograph coupled with an AB SCIEX QTRAP(®) 5500 hybrid linear ion trap triple quadrupole mass spectrometer. The method was validated for accuracy, precision, linearity, lower limit of quantification (LLOQ), selectivity, and other parameters. The LLOQ was 1.0 ng/mL, requiring 100 μL of sample. The method was applied to monitor the 5-HT levels in lamb plasma after the administration of fluoxetine. Tandem mass spectrometry cubed (MS(3)) experiments were also performed to investigate the fragmentation pattern of 5-HT and [(2)d(4)]-5-HT. A liquid chromatography-MS(3) (LC/MS(3)) method was developed, and the UHPLC/MS/MS and the LC/MS(3) methods were compared for performance.

  1. Development and validation of sensitive LC/MS/MS method for quantitative bioanalysis of levonorgestrel in rat plasma and application to pharmacokinetics study.

    Science.gov (United States)

    Ananthula, Suryatheja; Janagam, Dileep R; Jamalapuram, Seshulatha; Johnson, James R; Mandrell, Timothy D; Lowe, Tao L

    2015-10-15

    Rapid, sensitive, selective and accurate LC/MS/MS method was developed for quantitative determination of levonorgestrel (LNG) in rat plasma and further validated for specificity, linearity, accuracy, precision, sensitivity, matrix effect, recovery efficiency and stability. Liquid-liquid extraction procedure using hexane:ethyl acetate mixture at 80:20 v:v ratio was employed to efficiently extract LNG from rat plasma. Reversed phase Luna column C18(2) (50×2.0mm i.d., 3μM) installed on a AB SCIEX Triple Quad™ 4500 LC/MS/MS system was used to perform chromatographic separation. LNG was identified within 2min with high specificity. Linear calibration curve was drawn within 0.5-50ng·mL(-1) concentration range. The developed method was validated for intra-day and inter-day accuracy and precision whose values fell in the acceptable limits. Matrix effect was found to be minimal. Recovery efficiency at three quality control (QC) concentrations 0.5 (low), 5 (medium) and 50 (high) ng·mL(-1) was found to be >90%. Stability of LNG at various stages of experiment including storage, extraction and analysis was evaluated using QC samples, and the results showed that LNG was stable at all the conditions. This validated method was successfully used to study the pharmacokinetics of LNG in rats after SubQ injection, providing its applicability in relevant preclinical studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans

    Directory of Open Access Journals (Sweden)

    Vandesompele Jo

    2008-01-01

    Full Text Available Abstract Background In the nematode Caenorhabditis elegans the conserved Ins/IGF-1 signaling pathway regulates many biological processes including life span, stress response, dauer diapause and metabolism. Detection of differentially expressed genes may contribute to a better understanding of the mechanism by which the Ins/IGF-1 signaling pathway regulates these processes. Appropriate normalization is an essential prerequisite for obtaining accurate and reproducible quantification of gene expression levels. The aim of this study was to establish a reliable set of reference genes for gene expression analysis in C. elegans. Results Real-time quantitative PCR was used to evaluate the expression stability of 12 candidate reference genes (act-1, ama-1, cdc-42, csq-1, eif-3.C, mdh-1, gpd-2, pmp-3, tba-1, Y45F10D.4, rgs-6 and unc-16 in wild-type, three Ins/IGF-1 pathway mutants, dauers and L3 stage larvae. After geNorm analysis, cdc-42, pmp-3 and Y45F10D.4 showed the most stable expression pattern and were used to normalize 5 sod expression levels. Significant differences in mRNA levels were observed for sod-1 and sod-3 in daf-2 relative to wild-type animals, whereas in dauers sod-1, sod-3, sod-4 and sod-5 are differentially expressed relative to third stage larvae. Conclusion Our findings emphasize the importance of accurate normalization using stably expressed reference genes. The methodology used in this study is generally applicable to reliably quantify gene expression levels in the nematode C. elegans using quantitative PCR.

  3. Development and validation of InnoQuant(®) HY, a system for quantitation and quality assessment of total human and male DNA using high copy targets.

    Science.gov (United States)

    Loftus, Andrew; Murphy, Gina; Brown, Hiromi; Montgomery, Anne; Tabak, Jonathan; Baus, James; Carroll, Marion; Green, André; Sikka, Suresh; Sinha, Sudhir

    2017-07-01

    The development and validation of InnoQuant(®) HY, a real-time PCR system containing four DNA targets-two RE autosomal targets of different sizes, male specific targets, and an internal positive control target-are described herein. The ratio of the two autosomal targets provides a Degradation Index, or a quantitative value of a sample's degradation state. The male specific targets are multi-copy targets located on the Y chromosome, which provides information about a sample's male DNA composition. The experimental results demonstrate InnoQuant HY as a robust qPCR method producing accurate DNA quantitation results even at low dynamic ranges, with reproducibility among population groups. The system is human specific with low level higher primate cross reactivity and is able to consistently and reproducibly detect sub-picogram concentrations of human and human male DNA. The use of high copy number Alu and SVA (>1000 copies per genome) retrotransposable elements as the two autosomal targets significantly enhances both sensitivity and reproducibility of determination of DNA quantitation as well as DNA degradation in forensic samples. The inclusion of a sensitive multi-copy Y-chromosome specific target provides accurate quantitation of DNA from a male in challenging male-female mixtures (i.e. sexual assault samples). Even in the presence of a large excess of DNA from a female, accurate quantitation was achieved with a male to female ratio of 1:128,000. Population database studies reveal an average Short/Y target ratio of the quantification values across all four populations tested was 1.124±0.282, exhibiting the system's reproducibility across multiple populations. The results from InnoQuant HY provide a tool equipping a forensic analyst with crucial data about a sample's DNA quantitation, male:female ratio, degradation state, and the presence or absence of PCR inhibitors. With the information gained from the InnoQuant HY kit, a more streamlined and efficient workflow

  4. Quantitative and qualitative validations of a sonication-based DNA extraction approach for PCR-based molecular biological analyses.

    Science.gov (United States)

    Dai, Xiaohu; Chen, Sisi; Li, Ning; Yan, Han

    2016-05-15

    The aim of this study was to comprehensively validate the sonication-based DNA extraction method, in hope of the replacement of the so-called 'standard DNA extraction method' - the commercial kit method. Microbial cells in the digested sludge sample, containing relatively high amount of PCR-inhibitory substances, such as humic acid and protein, were applied as the experimental alternatives. The procedure involving solid/liquid separation of sludge sample and dilution of both DNA templates and inhibitors, the minimum templates for PCR-based analyses, and the in-depth understanding from the bias analysis by pyrosequencing technology were obtained and confirmed the availability of the sonication-based DNA extraction method. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Analytical and Clinical Validation of the Immulite 1000 hCG Assay for Quantitative Analysis in Urine

    Science.gov (United States)

    Cate, Frances L.; Moffett, Courtney; Gronowski, Ann M.; Grenache, David G.; Hartmann, Katherine E.; Woodworth, Alison

    2013-01-01

    Background The Siemens Immulite hCG assay detects all major hCG variants in serum. Currently, this assay is only FDA approved for qualitative measurement of hCG in urine. Methods Complete validation of the hCG assay in urine was performed on the Siemens Immulite 1000 immunoassay platform. Reference intervals were established for females hCG assay was precise for measuring hCG in urine from pregnant patients with intra- and inter-assay imprecision of hCG and hCGβ respectively. The assay was non-linear for hCGβcf. No hook effect was observed at concentrations up to 1,200,000 pmol/l, for hCGβ or hCGβcf. The reference intervals were hCG assay can accurately quantify hCG in urine. PMID:23470427

  6. Validation of a quantitative real-time PCR assay for HTLV-1 proviral load in peripheral blood mononuclear cells.

    Science.gov (United States)

    Rosadas, Carolina; Cabral-Castro, Mauro Jorge; Vicente, Ana Carolina Paulo; Peralta, José Mauro; Puccioni-Sohler, Marzia

    2013-11-01

    The objective of this study was to validate a TaqMan real-time PCR assay for HTLV-1 proviral load detection in peripheral blood mononuclear cells. TARL-2 cells were used to generate a standard curve. Peripheral blood mononuclear cell gDNA from 27 seropositive and 23 seronegative samples was analyzed. The sensitivity, specificity, accuracy, precision, dynamic range of the standard curve and qPCR efficiency were evaluated. All of the positive samples amplified the target gene. All of the negative samples amplified only the control gene (β-actin). The assay presented 100% specificity and sensibility. The intra- and inter-assay variability was 2.4% and 2.2%, respectively. The qPCR efficiency, slope and correlation coefficients (r2) were all acceptable. The limit of detection was 1 copy/rxn. This assay can reliably quantify HTLV-1 proviral load.

  7. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    Science.gov (United States)

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, Ma Victoria

    2016-05-01

    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit.

  8. Development and Validation of a Stability-Indicating RP-HPLC Method for the Quantitative Analysis of Anagrelide Hydrochloride.

    Science.gov (United States)

    Pujeri, Sudhakar S; Khader, Addagadde M A; Seetharamappa, Jaldappagari

    2012-01-01

    A simple, rapid, and stability-indicating reverse-phase liquid chromatographic assay method was developed for Anagrelide Hydrochloride (ANG) in the presence of its degradation products generated from forced decomposition studies. The HPLC separation was achieved on a C18 Inertsil column (250 mm × 4.6 mm i.d. particle size is 5 μm), using solution A, a mixture of 0.03 M potassium di-hydrogen phosphate pH-adjusted to 3.0 using ortho-phosphoric acid (buffer): methanol: acetonitrile (90:5:5, v/v/v), and solution B, which contains a mixture of buffer: acetonitrile (10:90, v/v). The UV detector was operated at 251 nm while column temperature was maintained at 40°C, and the gradient program had the flow rate of 1.0 mL min(-1). The developed method was validated as per ICH guidelines with respect to specificity, linearity, precision, accuracy, robustness, and limit of quantification. The method was found to be simple, specific, precise, accurate, and reproducible. Selectivity was validated by subjecting the stock solution of ANG to acidic, basic, photolysis, oxidative, and thermal degradation. The calibration curve was found to be linear in the concentration range of 0.05-152 μg mL(-1) (R(2) = 0.9991). The peaks of degradation products did not interfere with that of pure ANG. The utility of the developed method was examined by analyzing the tablets containing ANG.

  9. Validation of reference genes for quantitative real-time PCR in Périgord black truffle (Tuber melanosporum) developmental stages.

    Science.gov (United States)

    Zarivi, Osvaldo; Cesare, Patrizia; Ragnelli, Anna Maria; Aimola, Pierpaolo; Leonardi, Marco; Bonfigli, Antonella; Colafarina, Sabrina; Poma, Anna Maria; Miranda, Michele; Pacioni, Giovanni

    2015-08-01

    The symbiotic fungus Tuber melanosporum Vittad. (Périgord black truffle) belongs to the Ascomycota and forms mutualistic symbiosis with tree and shrub roots. This truffle has a high value in a global market and is cultivated in many countries of both hemispheres. The publication of the T. melanosporum genome has given researchers unique opportunities to learn more about the biology of the fungus. Real-time quantitative PCR (qRT-PCR) is a definitive technique for quantitating differences in transcriptional gene expression levels between samples. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. These housekeeping genes must show stable expression under given experimental conditions for the qRT-PCR results to be accurate. Unfortunately, there are no studies on the stability of housekeeping genes used in T. melanosporum development. In this study, we present a morphological and microscopical classification of the developmental stages of T. melanosporum fruit body, and investigate the expression levels of 12 candidate reference genes (18S rRNA; 5.8S rRNA; Elongation factor 1-alpha; Elongation factor 1-beta; α-tubulin; 60S ribosomal protein L29; β-tubulin; 40S ribosomal protein S1; 40S ribosomal protein S3; Glucose-6-phosphate dehydrogenase; β-actin; Ubiquitin-conjugating enzyme). To evaluate the suitability of these genes as endogenous controls, five software-based approaches and one web-based comprehensive tool (RefFinder) were used to analyze and rank the tested genes. We demonstrate here that the 18S rRNA gene shows the most stable expression during T. melanosporum development and that a set of three genes, 18S rRNA, Elongation factor 1-alpha and 40S ribosomal protein S3, is the most suitable to normalize qRT-PCR data from all the analyzed developmental stages; conversely, 18S rRNA, Glucose-6-phosphate dehydrogenase and Elongation factor 1-alpha are the most suitable

  10. Kinematic Validation of a Multi-Kinect v2 Instrumented 10-Meter Walkway for Quantitative Gait Assessments.

    Science.gov (United States)

    Geerse, Daphne J; Coolen, Bert H; Roerdink, Melvyn

    2015-01-01

    Walking ability is frequently assessed with the 10-meter walking test (10MWT), which may be instrumented with multiple Kinect v2 sensors to complement the typical stopwatch-based time to walk 10 meters with quantitative gait information derived from Kinect's 3D body point's time series. The current study aimed to evaluate a multi-Kinect v2 set-up for quantitative gait assessments during the 10MWT against a gold-standard motion-registration system by determining between-systems agreement for body point's time series, spatiotemporal gait parameters and the time to walk 10 meters. To this end, the 10MWT was conducted at comfortable and maximum walking speed, while 3D full-body kinematics was concurrently recorded with the multi-Kinect v2 set-up and the Optotrak motion-registration system (i.e., the gold standard). Between-systems agreement for body point's time series was assessed with the intraclass correlation coefficient (ICC). Between-systems agreement was similarly determined for the gait parameters' walking speed, cadence, step length, stride length, step width, step time, stride time (all obtained for the intermediate 6 meters) and the time to walk 10 meters, complemented by Bland-Altman's bias and limits of agreement. Body point's time series agreed well between the motion-registration systems, particularly so for body points in motion. For both comfortable and maximum walking speeds, the between-systems agreement for the time to walk 10 meters and all gait parameters except step width was high (ICC ≥ 0.888), with negligible biases and narrow limits of agreement. Hence, body point's time series and gait parameters obtained with a multi-Kinect v2 set-up match well with those derived with a gold standard in 3D measurement accuracy. Future studies are recommended to test the clinical utility of the multi-Kinect v2 set-up to automate 10MWT assessments, thereby complementing the time to walk 10 meters with reliable spatiotemporal gait parameters obtained

  11. Kinematic Validation of a Multi-Kinect v2 Instrumented 10-Meter Walkway for Quantitative Gait Assessments.

    Directory of Open Access Journals (Sweden)

    Daphne J Geerse

    Full Text Available Walking ability is frequently assessed with the 10-meter walking test (10MWT, which may be instrumented with multiple Kinect v2 sensors to complement the typical stopwatch-based time to walk 10 meters with quantitative gait information derived from Kinect's 3D body point's time series. The current study aimed to evaluate a multi-Kinect v2 set-up for quantitative gait assessments during the 10MWT against a gold-standard motion-registration system by determining between-systems agreement for body point's time series, spatiotemporal gait parameters and the time to walk 10 meters. To this end, the 10MWT was conducted at comfortable and maximum walking speed, while 3D full-body kinematics was concurrently recorded with the multi-Kinect v2 set-up and the Optotrak motion-registration system (i.e., the gold standard. Between-systems agreement for body point's time series was assessed with the intraclass correlation coefficient (ICC. Between-systems agreement was similarly determined for the gait parameters' walking speed, cadence, step length, stride length, step width, step time, stride time (all obtained for the intermediate 6 meters and the time to walk 10 meters, complemented by Bland-Altman's bias and limits of agreement. Body point's time series agreed well between the motion-registration systems, particularly so for body points in motion. For both comfortable and maximum walking speeds, the between-systems agreement for the time to walk 10 meters and all gait parameters except step width was high (ICC ≥ 0.888, with negligible biases and narrow limits of agreement. Hence, body point's time series and gait parameters obtained with a multi-Kinect v2 set-up match well with those derived with a gold standard in 3D measurement accuracy. Future studies are recommended to test the clinical utility of the multi-Kinect v2 set-up to automate 10MWT assessments, thereby complementing the time to walk 10 meters with reliable spatiotemporal gait parameters

  12. Hernia sacs: is histological examination necessary?

    Science.gov (United States)

    Wang, Tao; Vajpeyi, Rajkumar

    2013-12-01

    The hernia sac is a common surgical pathology specimen which can occasionally yield unexpected diagnoses. The College of American Pathologists recommends microscopic examination of abdominal hernias, but leaves submission of inguinal hernias for histology to the discretion of the pathologist. To validate this approach at a tertiary care centre, we retrospectively reviewed 1426 hernia sacs derived from inguinal, femoral and abdominal wall hernias. The majority of pathologies noted were known to the clinician, including herniated bowel, lipomas and omentum. A malignancy was noted in three of 800 inguinal hernias and seven of 576 abdominal wall hernias; five of these lesions were not seen on gross examination. Other interesting findings in hernia sacs included appendices, endometriosis, a perivascular epithelioid cell tumour, and pseudomyxoma peritoneii. All hernia sacs should be examined grossly as most pathologies are grossly visible. The decision to submit inguinal hernias for histology may be left to the discretion of the pathologist, but abdominal and femoral hernias should be submitted for histology.

  13. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

    Science.gov (United States)

    Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

    2014-10-01

    Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

  14. Validation of reference genes for quantitative gene expression studies in Volvox carteri using real-time RT-PCR.

    Science.gov (United States)

    Kianianmomeni, Arash; Hallmann, Armin

    2013-12-01

    Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is a sensitive technique for analysis of gene expression under a wide diversity of biological conditions. However, the identification of suitable reference genes is a critical factor for analysis of gene expression data. To determine potential reference genes for normalization of qRT-PCR data in the green alga Volvox carteri, the transcript levels of ten candidate reference genes were measured by qRT-PCR in three experimental sample pools containing different developmental stages, cell types and stress treatments. The expression stability of the candidate reference genes was then calculated using the algorithms geNorm, NormFinder and BestKeeper. The genes for 18S ribosomal RNA (18S) and eukaryotic translation elongation factor 1α2 (eef1) turned out to have the most stable expression levels among the samples both from different developmental stages and different stress treatments. The genes for the ribosomal protein L23 (rpl23) and the TATA-box binding protein (tbpA) showed equivalent transcript levels in the comparison of different cell types, and therefore, can be used as reference genes for cell-type specific gene expression analysis. Our results indicate that more than one reference gene is required for accurate normalization of qRT-PCRs in V. carteri. The reference genes in our study show a much better performance than the housekeeping genes used as a reference in previous studies.

  15. Validation of electrical impedance tomography qualitative and quantitative values and comparison of the numeric pain distress score against mammography.

    Science.gov (United States)

    Juliana, Norsham; Shahar, Suzana; Chelliah, Kanaga Kumari; Ghazali, Ahmad Rohi; Osman, Fazilah; Sahar, Mohd Azmani

    2014-01-01

    Electrical impedance tomography (EIT) is a potential supplement for mammogram screening. This study aimed to evaluate and feasibility of EIT as opposed to mammography and to determine pain perception with both imaging methods. Women undergoing screening mammography at the Radiology Department of National University of Malaysia Medical Centre were randomly selected for EIT imaging. All women were requested to give a pain score after each imaging session. Two independent raters were chosen to define the image findings of EIT. A total of 164 women in the age range from 40 to 65-year-old participated and were divided into two groups; normal and abnormal. EIT sensitivity and specificity for rater 1 were 69.4% and 63.3, whereas for rater 2 they were 55.3% and 57.0% respectively. The reliability for each rater ranged between good to very good (pQuantitative values of EIT showed there were significant differences in all values between groups (ANCOVA, pquantitative values, EIT has the potential as a health discriminating index. Its ability to replace image findings from mammography needs further investigation.

  16. Reference Gene Validation for Quantitative PCR Under Various Biotic and Abiotic Stress Conditions in Toxoptera citricida (Hemiptera, Aphidiae).

    Science.gov (United States)

    Shang, Feng; Wei, Dan-Dan; Jiang, Xuan-Zhao; Wei, Dong; Shen, Guang-Mao; Feng, Ying-Cai; Li, Ting; Wang, Jin-Jun

    2015-08-01

    The regulation of mRNA expression level is critical for gene expression studies. Currently, quantitative reverse transcription polymerase chain reaction (qRT-PCR) is commonly used to investigate mRNA expression level of genes under various experimental conditions. An important factor that determines the optimal quantification of qRT-PCR data is the choice of the reference gene for normalization. To advance gene expression studies in Toxoptera citricida (Kirkaldy), an important citrus pest and a main vector of the Citrus tristeza virus, we used five tools (GeNorm, NormFinder, BestKeeper, ΔCt methods, and RefFinder) to evaluate seven candidate reference genes (elongation factor-1 alpha [EF1α], beta tubulin [β-TUB], 18S ribosomal RNA [18S], RNA polymerase II large subunit (RNAP II), beta actin (β-ACT), alpha tubulin, and glyceraldhyde-3-phosphate dehydrogenase) under different biotic (developmental stages and wing dimorphism) and abiotic stress (thermal, starvation, and UV irradiation) conditions. The results showed that EF1α and 18S were the most stable genes under various biotic states, β-ACT and β-TUB during thermal stress, EF1α and RNAP II under starvation stress, and RNAP II, β-ACT, and EF1α under UV irradiation stress conditions. This study provides useful resources for the transcriptional profiling of genes in T. citricida and closely related aphid species.

  17. SU-F-R-36: Validating Quantitative Radiomic Texture Features for Oncologic PET: A Digital Phantom Study

    Energy Technology Data Exchange (ETDEWEB)

    Yang, F; Yang, Y [University of Miami Miller School of Medicine, Miami, FL (United States); Young, L [University of Washington Medical Center, Seattle, WA (United States)

    2016-06-15

    Purpose: Radiomic texture features derived from the oncologic PET have recently been brought under intense investigation within the context of patient stratification and treatment outcome prediction in a variety of cancer types; however, their validity has not yet been examined. This work is aimed to validate radiomic PET texture metrics through the use of realistic simulations in the ground truth setting. Methods: Simulation of FDG-PET was conducted by applying the Zubal phantom as an attenuation map to the SimSET software package that employs Monte Carlo techniques to model the physical process of emission imaging. A total of 15 irregularly-shaped lesions featuring heterogeneous activity distribution were simulated. For each simulated lesion, 28 texture features in relation to the intensity histograms (GLIH), grey-level co-occurrence matrices (GLCOM), neighborhood difference matrices (GLNDM), and zone size matrices (GLZSM) were evaluated and compared with their respective values extracted from the ground truth activity map. Results: In reference to the values from the ground truth images, texture parameters appearing on the simulated data varied with a range of 0.73–3026.2% for GLIH-based, 0.02–100.1% for GLCOM-based, 1.11–173.8% for GLNDM-based, and 0.35–66.3% for GLZSM-based. For majority of the examined texture metrics (16/28), their values on the simulated data differed significantly from those from the ground truth images (P-value ranges from <0.0001 to 0.04). Features not exhibiting significant difference comprised of GLIH-based standard deviation, GLCO-based energy and entropy, GLND-based coarseness and contrast, and GLZS-based low gray-level zone emphasis, high gray-level zone emphasis, short zone low gray-level emphasis, long zone low gray-level emphasis, long zone high gray-level emphasis, and zone size nonuniformity. Conclusion: The extent to which PET imaging disturbs texture appearance is feature-dependent and could be substantial. It is thus

  18. Development and validation of a real-time quantitative PCR assay for rapid identification of Bacillus anthracis in environmental samples.

    Science.gov (United States)

    Irenge, Léonid M; Durant, Jean-François; Tomaso, Herbert; Pilo, Paola; Olsen, Jaran S; Ramisse, Vincent; Mahillon, Jacques; Gala, Jean-Luc

    2010-11-01

    A real-time polymerase chain reaction (PCR) assay was developed for rapid identification of Bacillus anthracis in environmental samples. These samples often harbor Bacillus cereus bacteria closely related to B. anthracis, which may hinder its specific identification by resulting in false positive signals. The assay consists of two duplex real-time PCR: the first PCR allows amplification of a sequence specific of the B. cereus group (B. anthracis, B. cereus, Bacillus thuringiensis, Bacillus weihenstephanensis, Bacillus pseudomycoides, and Bacillus mycoides) within the phosphoenolpyruvate/sugar phosphotransferase system I gene and a B. anthracis specific single nucleotide polymorphism within the adenylosuccinate synthetase gene. The second real-time PCR assay targets the lethal factor gene from virulence plasmid pXO1 and the capsule synthesis gene from virulence plasmid pXO2. Specificity of the assay is enhanced by the use of minor groove binding probes and/or locked nucleic acids probes. The assay was validated on 304 bacterial strains including 37 B. anthracis, 67 B. cereus group, 54 strains of non-cereus group Bacillus, and 146 Gram-positive and Gram-negative bacteria strains. The assay was performed on various environmental samples spiked with B. anthracis or B. cereus spores. The assay allowed an accurate identification of B. anthracis in environmental samples. This study provides a rapid and reliable method for improving rapid identification of B. anthracis in field operational conditions.

  19. Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida

    Directory of Open Access Journals (Sweden)

    Hause Bettina

    2010-01-01

    Full Text Available Abstract Background Identification of genes with invariant levels of gene expression is a prerequisite for validating transcriptomic changes accompanying development. Ideally expression of these genes should be independent of the morphogenetic process or environmental condition tested as well as the methods used for RNA purification and analysis. Results In an effort to identify endogenous genes meeting these criteria nine reference genes (RG were tested in two Petunia lines (Mitchell and V30. Growth conditions differed in Mitchell and V30, and different methods were used for RNA isolation and analysis. Four different software tools were employed to analyze the data. We merged the four outputs by means of a non-weighted unsupervised rank aggregation method. The genes identified as optimal for transcriptomic analysis of Mitchell and V30 were EF1α in Mitchell and CYP in V30, whereas the least suitable gene was GAPDH in both lines. Conclusions The least adequate gene turned out to be GAPDH indicating that it should be rejected as reference gene in Petunia. The absence of correspondence of the best-suited genes suggests that assessing reference gene stability is needed when performing normalization of data from transcriptomic analysis of flower and leaf development.

  20. Method development and validation study for quantitative determination of nifedipine and related substances by ultra-high-performance liquid chromatography.

    Science.gov (United States)

    Galan-Rodriguez, Cristobal; González-Álvarez, Jaime; Valls-Remolí, Màrius

    2015-02-01

    A novel stability-indicating reversed phase ultra-high performance liquid chromatography (UPLC) coupled photodiode array gradient method was developed for determination of the nifedipine and related compounds. Furthermore, based on the chromatographic conditions and forced degradation studies performed through the development of the related substances method a UPLC isocratic method was validated for the determination of the assay of this active substance. An Acquity Shield RP18 (50 × 3.0 mm 1.7 µm) column was used for separation of nifedipine and its five potential impurities within 11 min, which is 5-fold less than the official method. A mobile phase consisting of 10 mm ammonium formate (pH 4.5) and methanol, delivered at a flow rate 0.5 mL/min, was employed to achieve a minimum resolution of 2.0 for all consecutive pairs of compounds. The precision value expressed as percentage relative standard deviation for method repeatability and reproducibility was <5.0%. The recoveries for all the related compounds were in the range of 99-105.0%. Linearity was found to be acceptable over the concentration range of 0.25-1.5 µg/mL for nifedipine and its impurities. The limit of quantification for nifedipine was 0.05 µg/mL, which is much less than the European Pharmacopoeia method.

  1. [Method validation according to ISO 15189 and SH GTA 04: application for the extraction of DNA and its quantitative evaluation by a spectrophotometric assay].

    Science.gov (United States)

    Harlé, Alexandre; Lion, Maëva; Husson, Marie; Dubois, Cindy; Merlin, Jean-Louis

    2013-01-01

    According to the French legislation on medical biology (January 16th, 2010), all biological laboratories must be accredited according to ISO 15189 for at least 50% of their activities before the end of 2016. The extraction of DNA from a sample of interest, whether solid or liquid is one of the critical steps in molecular biology and specifically in somatic or constitutional genetic. The extracted DNA must meet a number of criteria such quality and also be in sufficient concentration to allow molecular biology assays such as the detection of somatic mutations. This paper describes the validation of the extraction and purification of DNA using chromatographic column extraction and quantitative determination by spectrophotometric assay, according to ISO 15189 and the accreditation technical guide in Human Health SH-GTA-04.

  2. Relative validity and reproducibility of a parent-administered semi-quantitative FFQ for assessing food intake in Danish children aged 3-9 years

    DEFF Research Database (Denmark)

    Buch-Andersen, Tine; Perez-Cueto Eulert, Federico Jose Armando; Toft, Ulla

    2016-01-01

    OBJECTIVE: To assess the relative validity and reproducibility of the semi-quantitative FFQ (SFFQ) applied in the evaluation of a community intervention study, SoL-Bornholm, for estimating food intakes. DESIGN: The reference measure was a 4 d estimated food record. The SFFQ was completed two times...... with the food records, especially for vegetables. For most intakes, the mean difference increased with increasing intake. Gross misclassification was on average higher for energy and nutrients (17 %) than for foods (8 %). Spearman correlation coefficients were significant for twelve out of fourteen intakes......, ranging from 0·29 to 0·63 for foods and from 0·12 to 0·48 for energy and nutrients. Comparing the repeated SFFQ administrations, the intakes of the first SFFQ were slightly higher than those of the second SFFQ. Gross misclassification was low for most intakes; on average 6 % for foods and 8 % for energy...

  3. One Size Fits All: Evaluation of the Transferability of a New "Learning" Histologic Image Analysis Application.

    Science.gov (United States)

    Arlt, Janine; Homeyer, André; Sänger, Constanze; Dahmen, Uta; Dirsch, Olaf

    2016-01-01

    Quantitative analysis of histologic slides is of importance for pathology and also to address surgical questions. Recently, a novel application was developed for the automated quantification of whole-slide images. The aim of this study was to test and validate the underlying image analysis algorithm with respect to user friendliness, accuracy, and transferability to different histologic scenarios. The algorithm splits the images into tiles of a predetermined size and identifies the tissue class of each tile. In the training procedure, the user specifies example tiles of the different tissue classes. In the subsequent analysis procedure, the algorithm classifies each tile into the previously specified classes. User friendliness was evaluated by recording training time and testing reproducibility of the training procedure of users with different background. Accuracy was determined with respect to single and batch analysis. Transferability was demonstrated by analyzing tissue of different organs (rat liver, kidney, small bowel, and spleen) and with different stainings (glutamine synthetase and hematoxylin-eosin). Users of different educational background could apply the program efficiently after a short introduction. When analyzing images with similar properties, accuracy of >90% was reached in single images as well as in batch mode. We demonstrated that the novel application is user friendly and very accurate. With the "training" procedure the application can be adapted to novel image characteristics simply by giving examples of relevant tissue structures. Therefore, it is suitable for the fast and efficient analysis of high numbers of fully digitalized histologic sections, potentially allowing "high-throughput" quantitative "histomic" analysis.

  4. Comparative Validation of Five Quantitative Rapid Test Kits for the Analysis of Salt Iodine Content: Laboratory Performance, User- and Field-Friendliness.

    Directory of Open Access Journals (Sweden)

    Fabian Rohner

    Full Text Available Iodine deficiency has important health and development consequences and the introduction of iodized salt as national programs has been a great public health success in the past decades. To render national salt iodization programs sustainable and ensure adequate iodization levels, simple methods to quantitatively assess whether salt is adequately iodized are required. Several methods claim to be simple and reliable, and are available on the market or are in development.This work has validated the currently available quantitative rapid test kits (quantRTK in a comparative manner for both their laboratory performance and ease of use in field settings.Laboratory performance parameters (linearity, detection and quantification limit, intra- and inter-assay imprecision were conducted on 5 quantRTK. We assessed inter-operator imprecision using salt of different quality along with the comparison of 59 salt samples from across the globe; measurements were made both in a laboratory and a field setting by technicians and non-technicians. Results from the quantRTK were compared against iodometric titration for validity. An 'ease-of-use' rating system was developed to identify the most suitable quantRTK for a given task.Most of the devices showed acceptable laboratory performance, but for some of the devices, use by non-technicians revealed poorer performance when working in a routine manner. Of the quantRTK tested, the iCheck® and I-Reader® showed most consistent performance and ease of use, and a newly developed paper-based method (saltPAD holds promise if further developed.User- and field-friendly devices are now available and the most appropriate quantRTK can be selected depending on the number of samples and the budget available.

  5. Development and validation of a quantitative competitive ELISA for potency testing of equine anti rabies sera with other potential use.

    Science.gov (United States)

    Korimbocus, Jehanara; Dehay, Nicolas; Tordo, Noël; Cano, François; Morgeaux, Sylvie

    2016-06-14

    In case of a bite by a rabies infected animal, the World Health Organisation recommends a prophylactic treatment including the administration of Human Rabies Immunoglobulins (HRIGs) or highly purified F(ab')2 fragments produced from Equine Rabies Immunoglobulin (F(ab')2 - ERIGs). According to international regulation, quality control of F(ab')2 - ERIGs lots requires potency testing by the in vivo Mouse Neutralisation Test (MNT) prior marketing. However, the strategy of the 3Rs (Reduce, Refine, Replace) for animal testing required by the European Directive encourages the replacement of the in vivo potency test by an in vitro assay. In this context, a competitive ELISA method (c-ELISA) has been developed by the Agence Nationale de Sécurité du Médicament et des Produits de Santé where F(ab')2 - ERIGs are in competition with a monoclonal antibody recognizing the trimeric native form of the rabies glycoprotein. After a full validation study, the c-ELISA has been applied to commercial batches of F(ab')2 - ERIGs. A correlation study with the MNT demonstrated a similarity between the two methods (r=0.751). Moreover, the c-ELISA method which does not need any species specific reagent has been applied to HRIGs potency testing as an alternative method to Rapid Fluorescent Focus Inhibition Test (RFFIT), thus avoiding the handling of live rabies virus in BSL3 containment. In conclusion, the c-ELISA has shown its potential to replace MNT and possibly RFFIT for the quantification of rabies immunoglobulin. After optimisation it may be used for the quantification of rabies immunoglobulin in any animal species, notably for rabies immunogenicity assay in mice. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Development and validation of a stability-indicating analytical method for the quantitation of oxytocin in pharmaceutical dosage forms.

    Science.gov (United States)

    Chaibva, F A; Walker, R B

    2007-01-04

    A single stability-indicating assay for oxytocin (OT) in pharmaceutical dosage forms using gradient elution over 21 min has been reported in the literature. Furthermore, published and compendial methods for the analysis of OT containing dosage forms also involve using HPLC with gradient elution and complicated mobile phases that include hydrophobic ion pairing agents. A simple isocratic and stability-indicating assay was developed and validated. The conditions are as follows, column: Phenomenex C18 Hypersil, 5 microm packing, 4.6 mm x 150 mm with acetonitrile-phosphate buffer (pH 5; 0.08 M) (20:80) as the mobile phase with UV detection at 220 nm The method was found to be specific for OT in the presence of degradation products and chlorbutol (preservative) with an overall analytical run time of 16 min. Accuracy was determined to be 0.77-1.18% bias for all samples tested. Intra-assay precision (repeatability) was found to be 0.22-1.04%R.S.D. while the inter-day precision (intermediate precision) was found to be 1.27-1.68%R.S.D. for the samples studied. The calibration curve was found to be linear with the equation y = 1.81x + 0.02 and a linear regression coefficient of 0.9991 over the range 0.4-12.0 IU/ml. The LOD and the LOQ were determined to be 0.1 and 0.4 IU/ml, respectively. Syntocinon, a commercially available dosage form of OT was assayed resulting in 100.5-106.6% recovery of the label claim and an average of 10.04 IU/ml.

  7. Validation of quantitative brain dopamine D2 receptor imaging with a conventional single-head SPET camera

    Energy Technology Data Exchange (ETDEWEB)

    Nikkinen, P. (Helsinki Univ. (Finland). Dept. of Clinical Chemistry); Liewendahl, K. (Helsinki Univ. (Finland). Dept. of Clinical Chemistry); Savolainen, S. (Helsinki Univ. (Finland). Dept. of Physics); Launes, J. (Helsinki Univ. (Finland). Dept. of Neurology)

    1993-08-01

    Phantom measurements were performed with a conventional single-head single-photon emission tomography (SPET) camera in order to validate the relevance of the basal ganglia/frontal cortex iodine-123 iodobenzamide (IBZM) uptake ratios measured in patients. Inside a cylindrical phantom (diameter 22 cm), two cylinders with a diameter of 3.3 cm were inserted. The activity concentrations of the cylinders ranged from 6.0 to 22.6 kBq/ml and the cylinder/background activity ratios varied from 1.4 to 3.8. From reconstructed SPET images the cylinder/background activity ratios were calculated using three different regions of interest (ROIs). A linear relationship between the measured activity ratio and the true activity ratio was obtained. In patient studies, basal ganglia/frontal cortex IBZM uptake ratios determined from the reconstructed slices using attentuation correction prior to reconstruction were 1.30 [+-]0.03 in idiopathic Parkinson's disease (n = 9), 1,33 [+-]0.09 in infantile and juvenile neuronal ceroid lipofuscinosis (n = 7) and 1.34 [+-]0.05 in narcolepsy (n = 8). Patients with Huntington's disease had significantly lower ratios (1.09 [+-]0.04, n = 5). The corrected basal ganglia/frontal cortex ratios, determined using linear regression, were about 80 % higher. The use of dual-window scatter correction increased the measured ratios by about 10 %. Although comprehensive correction methods can further improve the resolution in SPET images, the resolution of the SPET system used by us (1.5 - 2 cm) will determine what is achievable in basal ganglia D2 receptor imaging. (orig.)

  8. Intracranial aneurysm segmentation in 3D CT angiography: Method and quantitative validation with and without prior noise filtering

    Energy Technology Data Exchange (ETDEWEB)

    Firouzian, Azadeh, E-mail: a.firouzian@erasmusmc.nl [Department of Medical Informatics, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Department of Radiology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Manniesing, Rashindra, E-mail: r.manniesing@erasmusmc.nl [Department of Medical Informatics, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Department of Radiology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Flach, Zwenneke H., E-mail: zwenneke.flach@gmail.com [Department of Radiology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Risselada, Roelof, E-mail: r.risselada@erasmusmc.nl [Department of Medical Informatics, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Kooten, Fop van, E-mail: f.vankooten@erasmusmc.nl [Department of Neurology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Sturkenboom, Miriam C.J.M., E-mail: m.sturkenboom@erasmusmc.nl [Department of Medical Informatics, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Department of Epidemiology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Lugt, Aad van der, E-mail: a.vanderlugt@erasmusmc.nl [Department of Radiology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Niessen, Wiro J., E-mail: w.niessen@erasmusmc.nl [Department of Medical Informatics, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Department of Radiology, Erasmus MC, University Medical Centre Rotterdam (Netherlands); Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology (Netherlands)

    2011-08-15

    Intracranial aneurysm volume and shape are important factors for predicting rupture risk, for pre-surgical planning and for follow-up studies. To obtain these parameters, manual segmentation can be employed; however, this is a tedious procedure, which is prone to inter- and intra-observer variability. Therefore there is a need for an automated method, which is accurate, reproducible and reliable. This study aims to develop and validate an automated method for segmenting intracranial aneurysms in Computed Tomography Angiography (CTA) data. Also, it is investigated whether prior smoothing improves segmentation robustness and accuracy. The proposed segmentation method is implemented in the level set framework, more specifically Geodesic Active Surfaces, in which a surface is evolved to capture the aneurysmal wall via an energy minimization approach. The energy term is composed of three different image features, namely; intensity, gradient magnitude and intensity variance. The method requires minimal user interaction, i.e. a single seed point inside the aneurysm needs to be placed, based on which image intensity statistics of the aneurysm are derived and used in defining the energy term. The method has been evaluated on 15 aneurysms in 11 CTA data sets by comparing the results to manual segmentations performed by two expert radiologists. Evaluation measures were Similarity Index, Average Surface Distance and Volume Difference. The results show that the automated aneurysm segmentation method is reproducible, and performs in the range of inter-observer variability in terms of accuracy. Smoothing by nonlinear diffusion with appropriate parameter settings prior to segmentation, slightly improves segmentation accuracy.

  9. New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

    Directory of Open Access Journals (Sweden)

    Jakob Nikolas Kather

    Full Text Available Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions.In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images.To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images.Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

  10. [The validation of kit of reagents for quantitative detection of DNA of human cytomegalovirus in biological material using polymerase chain reaction technique in real time operation mode].

    Science.gov (United States)

    Sil'veĭstrova, O Iu; Domonova, É A; Shipulina, O Iu

    2014-04-01

    The validation of kit of reagents destined to detection and quantitative evaluation of DNA of human cytomegalovirus in biological material using polymerase chain reaction technique in real time operation mode was implemented. The comparison was made against international WHO standard--The first WHO international standard for human cytomegalovirus to implement measures the kit of reagents "AmpliSens CMV-screen/monitor-FL" and standard sample of enterprise DNA HCMV (The central research institute of epidemiology of Rospotrebnadzor) was applied. The fivefold dilution of international WHO standard and standard sample of enterprise were carried out in concentrations of DNA HCMV from 106 to 102. The arrangement of polymerase chain reaction and analysis of results were implemented using programed amplifier with system of detection of fluorescent signal in real-time mode "Rotor-Gene Q" ("Qiagen", Germany). In the total of three series of experiments, all stages of polymerase chain reaction study included, the coefficient of translation of quantitative evaluation of DNA HCMV from copy/ml to ME/ml equal to 0.6 was introduced for this kit of reagents.

  11. Development and validation of an improved method for the quantitation of sertraline in human plasma using LC-MS-MS and its application to bioequivalence studies.

    Science.gov (United States)

    Zhang, Mengliang; Gao, Feng; Cui, Xiangyong; Zhang, Yunhui; Sun, Yantong; Gu, Jingkai

    2011-02-01

    A rapid and sensitive LC-MS-MS method for the quantitation of sertraline in human plasma was developed and validated. Sertraline and the internal standard, telmisartan, were cleaned up by protein precipitation from 100 μL of plasma sample, and analyzed on a TC-C18 column (5 μm, 150 × 4.6 mm i.d.) using 70% acetonitrile and 30% 10 mM ammonium acetate (0.1% formic acid) as mobile phase. The method was demonstrated to be linear from 0.1 ng/mL to 50 ng/mL with the lower limit of quantitation of 0.1 ng/mL. Intra- and inter-day precision were below 4.40% and 3.55%. Recoveries of sertraline at low, medium, and high levels were 88.0 ± 2.3%, 88.2 ± 1.9%, and 90.0 ± 2.0%, respectively. The method was successfully applied to a bioequivalence study of sertraline after a single oral administration of 50 mg sertraline hydrochloride tablets.

  12. Validated UPLC-MS/MS Methods To Quantitate Free and Conjugated Alternaria Toxins in Commercially Available Tomato Products and Fruit and Vegetable Juices in Belgium.

    Science.gov (United States)

    Walravens, Jeroen; Mikula, Hannes; Rychlik, Michael; Asam, Stefan; Devos, Tom; Njumbe Ediage, Emmanuel; Diana Di Mavungu, José; Jacxsens, Liesbeth; Van Landschoot, Anita; Vanhaecke, Lynn; De Saeger, Sarah

    2016-06-22

    Ultraperformance liquid chromatography tandem mass spectrometry and Quick, Easy, Cheap, Effective, Rugged, and Safe based analytical methodologies to quantitate both free (alternariol (1), alternariol monomethyl ether (2), tenuazonic acid (3), tentoxin (4), altenuene (5), altertoxin-I (6)) and conjugated (sulfates and glucosides of 1 and 2) Alternaria toxins in fruit and vegetable juices and tomato products were developed and validated. Acceptable limits of quantitation (0.7-5.7 μg/kg), repeatability (RSDr < 15.7%), reproducibility (RSDR < 17.9%), and apparent recovery (87.0-110.6%) were obtained for all analytes in all matrices investigated. 129 commercial foodstuffs were analyzed, and 3 was detected in 100% of tomato product samples (

  13. Quantitative multi-parameter mapping of R1, PD*, MT and R2* at 3T: a multi-center validation

    Directory of Open Access Journals (Sweden)

    Nikolaus eWeiskopf

    2013-06-01

    Full Text Available Multi-center studies using magnetic resonance imaging facilitate studying small effect sizes, global population variance and rare diseases. The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points. The level of inter-site comparability is still controversial for conventional anatomical T1-weighted MRI data. Quantitative multi-parameter mapping (MPM was designed to provide MR parameter measures that are comparable across sites and time points, i.e., 1mm high-resolution maps of the longitudinal relaxation rate (R1=1/T1, effective proton density (PD*, magnetization transfer saturation (MT and effective transverse relaxation rate (R2*=1/T2*. MPM was validated at 3T for use in multi-center studies by scanning five volunteers at three different sites. We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV for typical morphometric measures (i.e., gray matter probability maps used in voxel-based morphometry and the four quantitative parameters. The inter-site bias and CoV were smaller than 3.1% and 8%, respectively, except for the inter-site CoV of R2* (< 20%. The gray matter probability maps based on the MT parameter maps had a 14% higher inter-site reproducibility than maps based on conventional T1-weighted images. The low inter-site bias and variance in the parameters and derived gray matter probability maps confirm the high comparability of the quantitative maps across sites and time points. The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.

  14. Selection and validation of appropriate reference genes for quantitative real-time PCR analysis of gene expression in Lycoris aurea

    Directory of Open Access Journals (Sweden)

    Rui eMa

    2016-04-01

    Full Text Available Lycoris aurea (L' Hér. Herb, a perennial grass species, produces a unique variety of pharmacologically active Amaryllidaceae alkaloids. However, the key enzymes and their expression pattern involved in the biosynthesis of Amaryllidaceae alkaloids (especially for galanthamine are far from being fully understood. Quantitative real-time polymerase chain reaction (qRT-PCR, a commonly used method for quantifying gene expression, requires stable reference genes to normalize its data. In this study, to choose the appropriate reference genes under different experimental conditions, 14 genes including YLS8 (mitosis protein YLS8, CYP2 (Cyclophilin 2, CYP 1 (Cyclophilin 1, TIP41 (TIP41-like protein, EXP2 (Expressed protein 2, PTBP1 (Polypyrimidine tract-binding protein 1, EXP1 (Expressed protein 1, PP2A (Serine/threonine-protein phosphatase 2A, β-TUB (β-tubulin, α-TUB (α-tubulin, EF1-α (Elongation factor 1-α, UBC (Ubiquitin-conjugating enzyme, ACT (Actin and GAPDH (Glyceraldehyde 3-phosphate dehydrogenase were selected from the transcriptome datasets of L. aurea. And then, expressions of these genes were assessed by qRT-PCR in various tissues and the roots under different treatments. The expression stability of the 14 candidates was analyzed by three commonly used software programs (geNorm, NormFinder, and BestKeeper, and their results were further integrated into a comprehensive ranking based on the geometric mean. The results show the relatively stable genes for each subset as follows: (1 EXP1 and TIP41 for all samples; (2 UBC and EXP1 for NaCl stress; (3 PTBP1 and EXP1 for heat stress, polyethylene glycol (PEG stress and ABA treatment; (4 UBC and CYP2 for cold stress; (5 PTBP1 and PP2A for sodium nitroprusside (SNP treatment; (6 CYP1 and TIP41 for methyl jasmonate (MeJA treatment; and (7 EXP1 and TIP41 for various tissues. The reliability of these results was further enhanced through comparison between part qRT-PCR result and RNA sequencing (RNA

  15. Quantitative Analysis of Cereulide Toxin from Bacillus cereus in Rice and Pasta Using Synthetic Cereulide Standard and 13C6-Cereulide Standard—A Short Validation Study

    Directory of Open Access Journals (Sweden)

    Aida Zuberovic Muratovic

    2014-12-01

    Full Text Available A single laboratory validation study of a rapid and sensitive quantitative method for the analysis of cereulide toxin produced by Bacillus cereus using ultra high performance liquid chromatography-electrospray-tandem mass spectrometry is presented. The analysis of this cyclic peptide toxin was validated for pasta and rice samples using a newly presented synthetic cereulide peptide standard, together with 13C6-cereulide that previously have not been commercially available. The use of cereulide standard was also compared to the most frequently used surrogate standard, the antibiotic valinomycin. The performance of the method was evaluated by analyzing spiked sample pools from different types of rice and pasta, as well as 21 individual rice and pasta samples from differently prepared meals. Inoculation of samples with three cereulide toxin-producing strains of Bacillus cereus was finally used to mimic naturally contaminated foods. The quantification range of the method was 1–500 ng/g (R2 = 0.999 and the limits of detection and quantification were 0.1 and 1 ng/g, respectively. The precision varied from 3% to 7% relative standard deviation and the trueness from −2% to +6% relative bias at different concentration levels in cooked rice and pasta.

  16. Quantitative analysis of cereulide toxin from Bacillus cereus in rice and pasta using synthetic cereulide standard and 13C6-cereulide standard - a short validation study.

    Science.gov (United States)

    Zuberovic Muratovic, Aida; Tröger, Rikard; Granelli, Kristina; Hellenäs, Karl-Erik

    2014-12-11

    A single laboratory validation study of a rapid and sensitive quantitative method for the analysis of cereulide toxin produced by Bacillus cereus using ultra high performance liquid chromatography-electrospray-tandem mass spectrometry is presented. The analysis of this cyclic peptide toxin was validated for pasta and rice samples using a newly presented synthetic cereulide peptide standard, together with 13C6-cereulide that previously have not been commercially available. The use of cereulide standard was also compared to the most frequently used surrogate standard, the antibiotic valinomycin. The performance of the method was evaluated by analyzing spiked sample pools from different types of rice and pasta, as well as 21 individual rice and pasta samples from differently prepared meals. Inoculation of samples with three cereulide toxin-producing strains of Bacillus cereus was finally used to mimic naturally contaminated foods. The quantification range of the method was 1-500 ng/g (R2 = 0.999) and the limits of detection and quantification were 0.1 and 1 ng/g, respectively. The precision varied from 3% to 7% relative standard deviation and the trueness from -2% to +6% relative bias at different concentration levels in cooked rice and pasta.

  17. Development and Validation of an Inductively Coupled Plasma Mass Spectrometry (ICP-MS) Method for Quantitative Analysis of Platinum in Plasma, Urine, and Tissues.

    Science.gov (United States)

    Zhang, Ti; Cai, Shuang; Forrest, Wai Chee; Mohr, Eva; Yang, Qiuhong; Forrest, M Laird

    2016-09-01

    Cisplatin, a platinum chemotherapeutic, is one of the most commonly used chemotherapeutic agents for many solid tumors. In this work, we developed and validated an inductively coupled plasma mass spectrometry (ICP-MS) method for quantitative determination of platinum levels in rat urine, plasma, and tissue matrices including liver, brain, lungs, kidney, muscle, heart, spleen, bladder, and lymph nodes. The tissues were processed using a microwave accelerated reaction system (MARS) system prior to analysis on an Agilent 7500 ICP-MS. According to the Food and Drug Administration guidance for industry, bioanalytical validation parameters of the method, such as selectivity, accuracy, precision, recovery, and stability were evaluated in rat biological samples. Our data suggested that the method was selective for platinum without interferences caused by other presenting elements, and the lower limit of quantification was 0.5 ppb. The accuracy and precision of the method were within 15% variation and the recoveries of platinum for all tissue matrices examined were determined to be 85-115% of the theoretical values. The stability of the platinum-containing solutions, including calibration standards, stock solutions, and processed samples in rat biological matrices was investigated. Results indicated that the samples were stable after three cycles of freeze-thaw and for up to three months. © The Author(s) 2016.

  18. Quantitative Determination of ABT-925 in Human Plasma by On-Line SPE and LC-MS/MS: Validation and Sample Analysis in Phase II Studies

    Directory of Open Access Journals (Sweden)

    Katty Wan

    2010-05-01

    Full Text Available A fully automated 96-well On-Line Solid Phase Extraction (SPE followed by High Performance Liquid Chromatography (HPLC-Tandem Mass Spectrometric (MS/MS method for the determination of ABT-925 (2-{3-[4-(2-tert-Butyl-6-trifluoromethyl-pyrimidin-4-yl-piperazin-1-yl-propyl-sulfanyl}-3H-pyrimidin-4-one fumarate in human plasma was developed, validated and utilized in Phase II clinical studies. 50 µL of plasma sample was fortified with internal standard (IS, d8-ABT-925 and extracted on-line with Cohesive Turbo Flow Cyclone P HTLC column. The chromatographic separation was performed on Aquasil C18 (3 μm 50 × 3 mm HPLC column with a mobile phase consisting of 50/50/0.1 (v/v/v ACN/H2O/formic acid. The mass spectrometric measurement was conducted under positive ion mode using multiple reaction monitoring (MRM of m/z 457.4 → 329.4 for analyte and m/z 465.5 → 337.5 for IS.The peak area ratio (analyte/IS was used to quantitate ABT-925. A dynamic range of 0.0102 μg/mL to 5.24 μg/mL was established after the validation. The validated method was then used for two Phase II studies. To demonstrate the method reproducibility, approximately 10% of the incurred samples from one study were repeated in singlet. The repeated values were compared to the initial values. All repeated values agreed within ±15% of the mean values.

  19. Quantitative Determination of ABT-925 in Human Plasma by On-Line SPE and LC-MS/MS: Validation and Sample Analysis in Phase II Studies.

    Science.gov (United States)

    Wan, Katty; Rieser, Matthew; El-Shourbagy, Tawakol

    2010-05-04

    A fully automated 96-well On-Line Solid Phase Extraction (SPE) followed by High Performance Liquid Chromatography (HPLC)-Tandem Mass Spectrometric (MS/MS) method for the determination of ABT-925 (2-{3-[4-(2-tert-Butyl-6-trifluoromethyl-pyrimidin-4-yl)-piperazin-1-yl)-propyl-sulfanyl}-3H-pyrimidin-4-one fumarate) in human plasma was developed, validated and utilized in Phase II clinical studies. 50 µL of plasma sample was fortified with internal standard (IS, d8-ABT-925) and extracted on-line with Cohesive Turbo Flow Cyclone P HTLC column. The chromatographic separation was performed on Aquasil C18 (3 μm 50 × 3 mm) HPLC column with a mobile phase consisting of 50/50/0.1 (v/v/v) ACN/H₂O/formic acid. The mass spectrometric measurement was conducted under positive ion mode using multiple reaction monitoring (MRM) of m/z 457.4 → 329.4 for analyte and m/z 465.5 → 337.5 for IS.The peak area ratio (analyte/IS) was used to quantitate ABT-925. A dynamic range of 0.0102 μg/mL to 5.24 μg/mL was established after the validation. The validated method was then used for two Phase II studies. To demonstrate the method reproducibility, approximately 10% of the incurred samples from one study were repeated in singlet. The repeated values were compared to the initial values. All repeated values agreed within ±15% of the mean values.

  20. Ecosystem services - from assessements of estimations to quantitative, validated, high-resolution, continental-scale mapping via airborne LIDAR

    Science.gov (United States)

    Zlinszky, András; Pfeifer, Norbert

    2016-04-01

    service potential" which is the ability of the local ecosystem to deliver various functions (water retention, carbon storage etc.), but can't quantify how much of these are actually used by humans or what the estimated monetary value is. Due to its ability to measure both terrain relief and vegetation structure in high resolution, airborne LIDAR supports direct quantification of the properties of an ecosystem that lead to it delivering a given service (such as biomass, water retention, micro-climate regulation or habitat diversity). In addition, its high resolution allows direct calibration with field measurements: routine harvesting-based ecological measurements, local biodiversity indicator surveys or microclimate recordings all take place at the human scale and can be directly linked to the local value of LIDAR-based indicators at meter resolution. Therefore, if some field measurements with standard ecological methods are performed on site, the accuracy of LIDAR-based ecosystem service indicators can be rigorously validated. With this conceptual and technical approach high resolution ecosystem service assessments can be made with well established credibility. These would consolidate the concept of ecosystem services and support both scientific research and evidence-based environmental policy at local and - as data coverage is continually increasing - continental scale.

  1. Optimization and validation of a quantitative liquid chromatography-tandem mass spectrometric method covering 295 bacterial and fungal metabolites including all regulated mycotoxins in four model food matrices.

    Science.gov (United States)

    Malachová, Alexandra; Sulyok, Michael; Beltrán, Eduardo; Berthiller, Franz; Krska, Rudolf

    2014-10-01

    An LC-MS/MS "dilute and shoot" method for the determination of 295 fungal and bacterial metabolites was optimized and validated according to the guidelines established in the Directorate General for Health and Consumer Affairs of the European Commission (SANCO) document No. 12495/2011. Four different types of food matrices were chosen for validation: apple puree for infants (high water content), hazelnuts (high fat content), maize (high starch and low fat content) and green pepper (difficult or unique matrix). Method accuracy and precision was evaluated using spiked samples in five replicates at two concentration levels. Method trueness was demonstrated through participation in various proficiency tests. Although the method covers a total number of 331 analytes, validation data were acquired only for 295 analytes, either due to the non-availability of analytical standards or due other reasons described in this paper. Concerning the apparent recovery, the percentage of 295 analytes matching the acceptable recovery range of 70-120% lied down by SANCO varied from 21% in green pepper to 74% in apple puree at the highest spiking level. At the levels close to limit of quantification only 20-58% of the analytes fulfilled this criterion. The extent of matrix effects was strongly dependent on the analyte/matrix combination. In general, the lowest matrix effects were observed in apple puree (59% of analytes were not influenced by enhancement/suppression at all at the highest validation level). The highest matrix effects were observed in green pepper, where only 10% of analytes did not suffer from signal suppression/enhancement. The repeatability of the method was acceptable (RSD≤20) for 97% of all analytes in apple puree and hazelnuts, for 95% in maize and for 89% in green pepper. Concerning the trueness of the method, Z-scores were generally between -2 and 2, despite a broad variety of different matrices. Based on these results it can be concluded that quantitative

  2. Relative validity of a semi-quantitative, web-based FFQ used in the ‘Snart Forældre’ cohort – a Danish study of diet and fertility

    DEFF Research Database (Denmark)

    Knudsen, Vibeke Kildegaard; Hatch, Elizabeth E.; Cueto, Heidi

    2015-01-01

    Objective: To assess the relative validity of a semi-quantitative, web-based FFQ completed by female pregnancy planners in the Danish ‘Snart Forældre’ study. Design: We validated a web-based FFQ based on the FFQ used in the Danish National Birth Cohort against a 4 d food diary (FD) and assessed...... and nutrients and, thus, provides a solid basis for investigating associations between diet and fertility....

  3. Histology without xylene.

    Science.gov (United States)

    Buesa, René J; Peshkov, Maxim V

    2009-08-01

    After the hazardous effects of xylene became indisputable in the 1970s, many potential substitutes became available, some with as many if not more hazards. This article discusses the inadequacy of 5 vegetable oils as substitutes, as well as the characteristics of 22 D-limonene-based substitutes, all less effective in their chemical role, some capable of inducing health problems, and costing more than twice as much as xylene. Some of the 35 alkane-based substitutes discussed are effective for tissue processing, less toxic, with a cost about the same as xylene, but are not very effective for dewaxing and other staining tasks. Isopropanol (2-propanol) alone or mixed with molten paraffin is a technically acceptable and cost-effective substitute for xylene for tissue processing, but in this study, we demonstrate that the best clearing agents from the sectioning quality and diagnostic value point of view, with automated or manual protocols, are mixtures of 5:1 and 2:1 isopropanol and mineral oil, followed by undiluted mineral oil, all at 50 degrees C, making them a safer and cheaper substitute than xylene. Using a 1.7% dishwasher soap aqueous solution at 90 degrees C to dewax before staining and oven drying the stained sections before coverslipping will eliminate xylene from the staining tasks. Tissue processors retorts and conduits can be dewaxed with a 2% solution of a strong glassware laboratory detergent. These 4 methodologies will make the histology laboratory xylene-free but, due to the natural resistance to change, many histotechs will be reluctant to adopt them if they think that their technical expertise could be jeopardized, and the only way these changes will succeed is if the pathologists, as stewards of the histology laboratory, commit to their implementation.

  4. Analytical validation of a quantitative reverse transcriptase polymerase chain reaction assay for evaluation of T-cell targeted immunosuppressive therapy in the dog.

    Science.gov (United States)

    Riggs, C; Archer, T; Fellman, C; Figueiredo, A S; Follows, J; Stokes, J; Wills, R; Mackin, A; Bulla, C

    2013-12-15

    Cyclosporine is an immunosuppressive agent that inhibits T-cell function by decreasing production of cytokines such as interleukin-2 (IL-2) and interferon-γ(IFN-γ). In dogs, there is currently no reliable analytical method for determining effective cyclosporine dosages in individual patients. Our laboratory has developed a quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assay that measures IL-2 and IFN-γ gene expression, with the goal of quantifying immunosuppression in dogs treated with cyclosporine. This study focuses on analytical validation of our assay, and on the effects of sample storage conditions on cyclosporine-exposed samples. Heparinized whole blood collected from healthy adult dogs was exposed to a typical post-treatment blood concentration for cyclosporine(500 ng/mL) for 1 h, and then stored for 0, 24, and 48 h at both room temperature and 4 ◦C.The study was then repeated using a cyclosporine concentration of 75 ng/mL, with sample storage for 0, 24, and 48 h at 4 ◦C. Cytokine gene expression was measured using RT-qPCR,and assay efficiency and inter- and intra-assay variability were determined. Storage for upto 24 h at room temperature, and up to 48 h at 4 ◦C, did not significantly alter results compared to samples that were processed immediately. Validation studies showed our assay to be highly efficient and reproducible and robust enough to be feasible under standard practice submission conditions. © 2013 Elsevier B.V. All rights reserved.

  5. Development, validation and field evaluation of a quantitative real-time PCR able to differentiate between field Mycoplasma synoviae and the MS-H-live vaccine strain.

    Science.gov (United States)

    Dijkman, R; Feberwee, A; Landman, W J M

    2017-08-01

    A quantitative PCR (qPCR) able to differentiate between field Mycoplasma synoviae and MS-H vaccine strain was developed, validated and evaluated. It was developed using nucleotide differences in the obg gene. Analytical specificity and sensitivity assessed using DNA from 194 M. synoviae field samples, three different batches of MS-H vaccine and from 43 samples representing four other avian Mycoplasma species proved to be 100%. The detection limit for field M. synoviae and MS-H vaccine strain was 10(2-3) and 10(2) colony-forming units PCR equivalents/g trachea mucus, respectively. The qPCR was able to detect both, field M. synoviae and MS-H vaccine strain in ratios of 1:100 determined both using spiked and field samples. One hundred and twenty samples from M. synoviae-infected non-vaccinated birds, 110 samples from M. synoviae-vaccinated birds from a bird experiment and 224 samples from M. synoviae negative (serology and PCR) birds were used to determine the relative sensitivity and specificity using a previously described M. synoviae PCR as reference. The relative sensitivity and specificity for field M. synoviae were 95.0% and 99.6%, respectively, and 94.6% and 100% for the MS-H-live vaccine, respectively. Field validation and confirmation by multi locus sequence typing revealed that the qPCR correctly distinguished between MS-H and field M. synoviae. Evaluation of the differentiating M. synoviae qPCR in three commercial flocks suggested transmission of MS-H-live vaccine from vaccinated to non-vaccinated flocks at the same farm. Furthermore, it showed evidence for the colonization with field M. synoviae in MS-H-vaccinated flocks.

  6. Validation of a quantitative and confirmatory method for residue analysis of aminoglycoside antibiotics in poultry, bovine, equine and swine kidney through liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Almeida, M P; Rezende, C P; Souza, L F; Brito, R B

    2012-01-01

    The use of aminoglycoside antibiotics in food animals is approved in Brazil. Accordingly, Brazilian food safety legislation sets maximum levels for these drugs in tissues from these animals in an effort to guarantee that food safety is not compromised. Aiming to monitor the levels of these drugs in tissues from food animals, the validation of a quantitative, confirmatory method for the detection of residues of 10 aminoglycosides antibiotics in poultry, swine, equine and bovine kidney, with extraction using a solid phase and detection and quantification by LC-MS/MS was performed. The procedure is an adaptation of the US Department of Agriculture, Food Safety and Inspection Service (USDA-FSIS) qualitative method, with the inclusion of additional clean-up and quantification at lower levels, which proved more efficient. Extraction was performed using a phosphate buffer containing trifluoroacetic acid followed by neutralization, purification on a cationic exchange SPE cartridge, with elution with methanol/acetic acid, evaporation, and dilution in ion-pair solvent. The method was validated according to the criteria and requirements of the European Commission Decision 2002/657/EC, showing selectivity with no matrix interference. Linearity was established for all analytes using the method of weighted minimum squares. CCα and CCβ varied between 1036 and 12,293 µg kg(-1), and between 1073 and 14,588 µg kg(-1), respectively. The limits of quantification varied between 27 and 688 µg kg(-1). The values of recovery for all analytes in poultry kidney, fortified in the range of 500-1500 µg kg(-1), were higher than 90%, and the relative standard deviations were lower than 15%, except spectinomycin (21.8%). Uncertainty was estimated using a simplified methodology of 'bottom-up' and 'top-down' strategies. The results showed that this method is effective for the quantification and confirmation of aminoglycoside residues and could be used by the Brazilian programme of residue

  7. Validation of an HPLC Analytical Method for the Quantitative/Qualitative Determination of Fluticasone Propionate in Inhalation Particles on Several Matrices.

    Science.gov (United States)

    Sá Couto, André R; Cardoso, Daniela Espinha; Cabral-Marques, Helena Maria

    2014-01-01

    Fluticasone propionate is a highly potent corticosteroid used to treat asthma and allergic rhinitis. It is a very effective drug, but has the inconvenient factor of being insoluble in water. Cyclodextrins were used to improve this limitation because of their ability to form inclusion complexes with guest drug molecules as well as increase the stability and bioavailability of the drugs. A rapid and simple HPLC method was developed to detect and quantify fluticasone propionate in inhalation particles on several matrices. Liquid chromatography with a UV detector at a wavelength of 236 nm, using a C18 column, was employed in this study. Isocratic elution was employed using a mixture of acetonitrile and water (60:40, v/v). The analytical method validation was performed in accordance with ICH guidelines, which included selectivity, range, linearity, accuracy, detection limit, quantitation limit, precision, robustness, and stability of solutions. This method showed to be selective and specific. Acceptable assay precision and accuracy (100 ± 5.0%) were obtained at 50- 150% of the analytical concentration of fluticasone propionate at the target concentration of 0.060 mg/mL, and good linearity (0.9958) was achieved over a range of 0.03 to 0.09 mg/mL for fluticasone propionate. The proposed HPLC method proved to be reliable. The validation and application of this method can be adopted for determining the fluticasone propionate in: assays, impingers and impactors, diffusion cells, dissolutions, and other tests. In addition, this method can be adapted and used in the pharmaceutical industry for routine analysis.

  8. Quantitative evaluation of ultrasonic wave propagation in inhomogeneous anisotropic austenitic welds using 3D ray tracing method. Numerical and experimental validation

    Energy Technology Data Exchange (ETDEWEB)

    Kolkoori, Sanjeevareddy

    2014-07-01

    relations as well as transmission coefficients. The ray tracing model is able to determine the ultrasonic wave fields generated by a point source as well as finite dimension array transducers. The influence of inhomogenity on ultrasonic ray propagation and its interaction with defects in inhomogeneous austenitic welds is presented. The applications of 3D ray tracing model for optimizing experimental parameters during the ultrasonic non-destructive testing of transversal cracks in austenitic welds are presented. An ultrasonic C-scan image in homogeneous and multi-layered anisotropic austenitic steel materials is quantitatively evaluated using a novel 3D ray tracing method. The influence of the columnar grain orientation and the layback orientation on an ultrasonic C-scan image is presented. The ray tracing model results are validated first time quantitatively with the results obtained from 2D Elastodynamic Finite Integration Technique (EFIT) on several important configurations such as anisotropic and homogeneous austenitic steel material, layered austenitic steel and inhomogeneous weld materials which are generally occurring in the ultrasonic NDT of anisotropic materials. Quantitatively, a deviation of 8.6% was observed in the point source generated ultrasonic fields whereas in the case of array source ultrasound fields a deviation of 10.2% was observed. The predicted ultrasonic fields for array transducers in an inhomogeneous austenitic weld material with spatially varying columnar grain orientation using ray tracing method are validated against the results of a commercially available NDT simulation tool (CIVA). The result shows that an accuracy of 89.5% was achieved in the presented ray tracing model in this thesis. Experiments have been conducted on 32 mm thick inhomogeneous austenitic weld material, 62 mm thick austenitic clad material and quantitatively measured the ultrasound beam distortion and field profiles using electrodynamical probes. The inhomogenity in the weld

  9. Extraction of Artemisinin, an Active Antimalarial Phytopharmaceutical from Dried Leaves of Artemisia annua L., Using Microwaves and a Validated HPTLC-Visible Method for Its Quantitative Determination

    Directory of Open Access Journals (Sweden)

    Himanshu Misra

    2014-01-01

    Full Text Available A simple, rapid, precise, and accurate high-performance thin-layer chromatographic method coupled with visible densitometric detection of artemisinin is developed and validated. Samples of the dried Artemisia annua leaves were extracted via microwaves using different solvents. This method shows the advantage of shorter extraction time of artemisinin from leaves under the influence of electromagnetic radiations. Results obtained from microwave-assisted extraction (MAE were compared with hot soxhlet extraction. Chromatographic separation of artemisinin from plant extract was performed over silica gel 60 F254 HPTLC plate using n-hexane : ethyl acetate as mobile phase in the ratio of 75 : 25, v/v. The plate was developed at room temperature 25 ± 2.0°C. Artemisinin separation over thin-layer plate was visualized after postchromatographic derivatization with anisaldehyde-sulphuric acid reagent. HPTLC plate was scanned in a CAMAG’s TLC scanner 3 at 540 nm. Artemisinin responses were found to be linear over a range of 400–2800 ng spot−1 with a correlation coefficient 0.99754. Limits of detection and quantification were 40 and 80 ng spot−1, respectively. The HPTLC method was validated in terms of system suitability, precision, accuracy, sensitivity (LOD and LOQ, and robustness. Additionally, calculation of plate efficiency and flow constant were included as components of validation. Extracts prepared from different parts of the plant (leaves, branches, main stem, and roots were analyzed for artemisinin content, in which, artemisinin content was found higher in the leaf extract with respect to branches and main stem extracts; however, no artemisinin was detected in root extract. The developed HPTLC-visible method of artemisinin determination will be very useful for pharmaceutical industries, which are involved in monitoring of artemisinin content during different growth stages (in vitro and in vivo of A. annua for qualitative

  10. Quantitative bioanalysis of antibody-conjugated payload in monkey plasma using a hybrid immuno-capture LC-MS/MS approach: Assay development, validation, and a case study.

    Science.gov (United States)

    Liu, Ang; Kozhich, Alexander; Passmore, David; Gu, Huidong; Wong, Richard; Zambito, Frank; Rangan, Vangipuram S; Myler, Heather; Aubry, Anne-Françoise; Arnold, Mark E; Wang, Jian

    2015-10-01

    Antibody drug conjugates (ADCs) are complex molecules composed of two pharmacologically distinct components, the cytotoxic payload and the antibody. The measurement of the payload molecules that are attached to the antibody in vivo is important for the evaluation of the safety and efficacy of ADCs, and can also provide distinct information compared to the antibody-related analytes. However, analyzing the antibody-conjugated payload is challenging and in some cases may not be feasible. The in vivo change in drug antibody ratio (DAR), due to deconjugation, biotransformation or other clearance phenomena, generates unique and additional challenges for ADC analysis in biological samples. Here, we report a novel hybrid approach with immuno-capture of the ADC, payload cleavage by specific enzyme, and LC-MS/MS of the cleaved payload to quantitatively measure the concentration of payload molecules still attached to the antibody via linker in plasma. The ADC reference material used for the calibration curve is not likely to be identical to the ADC measured in study samples due to the change in DAR distribution over the PK time course. The assay clearly demonstrated that there was no bias in the measurement of antibody-conjugated payload for ADC with varying DAR, which thus allowed accurate quantification even when the DAR distribution dynamically changes in vivo. This hybrid assay was fully validated based on a combination of requirements for both chromatographic and ligand binding methods, and was successfully applied to support a GLP safety study in monkeys.

  11. Quantitative prediction of radio frequency induced local heating derived from measured magnetic field maps in magnetic resonance imaging: A phantom validation at 7 T

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiaotong; Liu, Jiaen [Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Van de Moortele, Pierre-Francois; Schmitter, Sebastian [Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota 55455 (United States); He, Bin, E-mail: binhe@umn.edu [Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States); Institute for Engineering in Medicine, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    2014-12-15

    Electrical Properties Tomography (EPT) technique utilizes measurable radio frequency (RF) coil induced magnetic fields (B1 fields) in a Magnetic Resonance Imaging (MRI) system to quantitatively reconstruct the local electrical properties (EP) of biological tissues. Information derived from the same data set, e.g., complex numbers of B1 distribution towards electric field calculation, can be used to estimate, on a subject-specific basis, local Specific Absorption Rate (SAR). SAR plays a significant role in RF pulse design for high-field MRI applications, where maximum local tissue heating remains one of the most constraining limits. The purpose of the present work is to investigate the feasibility of such B1-based local SAR estimation, expanding on previously proposed EPT approaches. To this end, B1 calibration was obtained in a gelatin phantom at 7 T with a multi-channel transmit coil, under a particular multi-channel B1-shim setting (B1-shim I). Using this unique set of B1 calibration, local SAR distribution was subsequently predicted for B1-shim I, as well as for another B1-shim setting (B1-shim II), considering a specific set of parameter for a heating MRI protocol consisting of RF pulses plaid at 1% duty cycle. Local SAR results, which could not be directly measured with MRI, were subsequently converted into temperature change which in turn were validated against temperature changes measured by MRI Thermometry based on the proton chemical shift.

  12. Development and validation of HPLC-DAD-CAD-MS(3) method for qualitative and quantitative standardization of polyphenols in Agrimoniae eupatoriae herba (Ph. Eur).

    Science.gov (United States)

    Granica, Sebastian; Krupa, Katarzyna; Kłębowska, Agnieszka; Kiss, Anna K

    2013-12-01

    A reversed phase high performance liquid chromatography method (HPLC) coupled with a diode array, charged aerosol detector or mass spectrometer was developed for the quantitative and qualitative standardization of Agrimoniae eupatoriae herba (Ph. Eur). Twenty four constituents comprising phenolic acids, flavan-3-ol derivatives, ellagitannin and flavonoids were fully or partially identified. Eight of detected compounds were reported from common agrimony for the first time. Fourteen major polyphenols were quantified using validated HPLC method with UV-vis and corona charged detection. Both detectors were shown to be equal for the quantification of selected polyphenols. Some limitations of universal response of corona charged detector for phenolic compounds were discussed. Using obtained data for DAD detector the sum of tannins, flavonoids and phenolic acids quantified in examined plant material was determined. Investigated samples contained 8.2-10.9mg/g of flavonoids, 6.3-10.9mg/g of tannins (among which agrimoniin was dominating constituent 2.6-5.4mg/g) and 0.6-0.9mg/g of phenolic acids proving that flavonoids should be considered as second major group of constituents in common agrimony.

  13. Development and validation of an HPTLC method for simultaneous quantitation of isoorientin, isovitexin, orientin, and vitexin in bamboo-leaf flavonoids.

    Science.gov (United States)

    Wang, Jin; Tang, Feng; Yue, Yongde; Guo, Xuefeng; Yao, Xi

    2010-01-01

    A simple HPTLC method has been developed for the simultaneous determination of isoorientin, isovitexin, orientin, and vitexin, both pure and in commercial samples of bamboo-leaf flavonoids. The flavone C-glycosides, including isoorientin, isovitexin, orientin, and vitexin, were extracted from bamboo-leaf flavonoids with methanol and chromatographed on silica gel 60 plates in an automatic developing chamber with tetrahydrofuran-toluene-formic acid-water (16 + 8 + 2 + 1, v/v/v/v) mobile phase. Quantitation was obtained with UV detection at 350 nm. Polynomial calibration plots were constructed in the concentration range 200-1200 ng/zone for isoorientin, 100-600 ng/zone for isovitexin, 160-960 ng/zone for orientin, and 30-360 ng/zone for vitexin with good correlation coefficients (r > or = 0.9995). The method was validated for precision (interday and intraday), repeatability, and accuracy. Accuracy of the method was evaluated by a recovery study conducted at three different levels, and the average recovery was found to be 93.95% for isoorientin, 95.30% for isovitexin, 99.79% for orientin, and 100.46% for vitexin. The proposed HPTLC method for estimation of isoorientin, isovitexin, orientin, and vitexin was found to be simple, precise, specific, and accurate and can be used for manufacturing QC of bamboo-leaf flavonoids or for governmental regulatory purposes.

  14. Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements

    Science.gov (United States)

    Devès, Guillaume; Cohen-Bouhacina, Touria; Ortega, Richard

    2004-10-01

    We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm).

  15. Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements

    Energy Technology Data Exchange (ETDEWEB)

    Deves, Guillaume [Laboratoire de chimie nucleaire analytique et bioenvironnementale, UMR 5084, CNRS-Universite de Bordeaux 1, BP 120 Chemin du solarium, F33175 Gradignan cedex (France)]. E-mail: deves@cenbg.in2p3.fr; Cohen-Bouhacina, Touria [Centre de Physique Moleculaire Optique et Hertzienne, Universite de Bordeaux 1, 351, cours de la Liberation, F33405 Talence cedex (France); Ortega, Richard [Laboratoire de chimie nucleaire analytique et bioenvironnementale, UMR 5084, CNRS-Universite de Bordeaux 1, BP 120 Chemin du solarium, F33175 Gradignan cedex (France)

    2004-10-08

    We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm)

  16. Development and validation of a simple, sensitive, selective and stability-indicating RP-UPLC method for the quantitative determination of ritonavir and its related compounds.

    Science.gov (United States)

    Koppala, Srinivasarao; Panigrahi, Bibhuranjan; Raju, S V N; Padmaja Reddy, K; Ranga Reddy, V; Anireddy, Jaya Shree

    2015-01-01

    A simple, sensitive, selective and reproducible stability-indicating ultra-performance liquid chromatographic method was developed for the quantitative determination of degradation products and process-related impurities of Ritonavir in a pharmaceutical dosage form. Chromatographic separation was achieved on a polar embedded Waters Acquity BEH Shield RP18 (100 × 2.1 mm, 1.7 μm) column thermostated at 50°C under gradient elution by using a binary mixture of potassium dihydrogen phosphate (0.01 M, pH 3.5) and acetonitrile at a flow rate of 0.5 mL/min. Chromatogram was monitored at 240 nm using a photodiode array detector. The drug and its related impurities are eluted within 20 min. To prove the stability-indicating power of the method, the drug was subjected to hydrolytic (acid, alkaline and water), oxidative, photolytic and thermal stress conditions. The unknown degradants were identified by the LC-MS-MS method, which revealed protonated molecular ion peaks [M + H](+) at m/z 551.40 for hydrolytic degradants, and m/z 737.60 and m/z 753.40 for photolytic degradants. A plausible mechanism for the formation of degradation and process impurities was proposed. The performance of the method was validated according to the International Conference on Harmonization guidelines.

  17. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    NARCIS (Netherlands)

    Zhu, Mingyao; Bzdusek, Karl; Brink, Carsten; Eriksen, Jesper Grau; Hansen, Olfred; Jensen, Helle Anita; Gay, Hiram A.; Thorstad, Wade; Widder, Joachim; Brouwer, Charlotte L.; Steenbakkers, Roel J. H. M.; Vanhauten, Hubertus A. M.; Cao, Jeffrey Q.; McBrayne, Gail; Patel, Salil H.; Cannon, Donald M.; Hardcastle, Nicholas; Tome, Wolfgang A.; Guckenberg, Matthias; Parikh, Parag J.

    2013-01-01

    Purpose: Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE). Methods and Materials: CT images of 125 treated patients (32 head and neck [HN], 40 thorax, 23 liver, and 30 prostate) in 7 independe

  18. Quantitative research.

    Science.gov (United States)

    Watson, Roger

    2015-04-01

    This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

  19. Quantitative Autonomic Testing

    OpenAIRE

    Novak, Peter

    2011-01-01

    Disorders associated with dysfunction of autonomic nervous system are quite common yet frequently unrecognized. Quantitative autonomic testing can be invaluable tool for evaluation of these disorders, both in clinic and research. There are number of autonomic tests, however, only few were validated clinically or are quantitative. Here, fully quantitative and clinically validated protocol for testing of autonomic functions is presented. As a bare minimum the clinical autonomic laboratory shoul...

  20. Microgravity validation of a novel system for RNA isolation and multiplex quantitative real time PCR analysis of gene expression on the International Space Station.

    Science.gov (United States)

    Parra, Macarena; Jung, Jimmy; Boone, Travis D; Tran, Luan; Blaber, Elizabeth A; Brown, Mark; Chin, Matthew; Chinn, Tori; Cohen, Jacob; Doebler, Robert; Hoang, Dzung; Hyde, Elizabeth; Lera, Matthew; Luzod, Louie T; Mallinson, Mark; Marcu, Oana; Mohamedaly, Youssef; Ricco, Antonio J; Rubins, Kathleen; Sgarlato, Gregory D; Talavera, Rafael O; Tong, Peter; Uribe, Eddie; Williams, Jeffrey; Wu, Diana; Yousuf, Rukhsana; Richey, Charles S; Schonfeld, Julie; Almeida, Eduardo A C

    2017-01-01

    The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit. This includes a novel fluidic RNA Sample Preparation Module and fluid transfer devices, all-in-one lyophilized PCR assays, centrifuge, and a real-time PCR thermal cycler. Here we describe the results from the WetLab-2 validation experiments conducted in microgravity during ISS increment 47/SPX-8. Specifically, quantitative PCR was performed on a concentration series of DNA calibration standards, and Reverse Transcriptase-quantitative PCR was conducted on RNA extracted and purified on-orbit from frozen Escherichia coli and mouse liver tissue. Cycle threshold (Ct) values and PCR efficiencies obtained on-orbit from DNA standards were similar to Earth (1 g) controls. Also, on-orbit multiplex analysis of gene expression from bacterial cells and mammalian tissue RNA samples was successfully conducted in about 3 h, with data transmitted within 2 h of experiment completion. Thermal cycling in microgravity resulted in the trapping of gas bubbles inside septa cap assay tubes, causing small but measurable increases in Ct curve noise and variability. Bubble formation was successfully suppressed in a rapid follow-up on-orbit experiment using standard caps to pressurize PCR tubes and reduce gas release during heating cycles. The WetLab-2 facility now provides a novel operational on-orbit research capability for molecular biology and

  1. Mapping and validation of quantitative trait loci for resistance to Cercospora zeae-maydis infection in tropical maize (Zea mays L.).

    Science.gov (United States)

    Pozar, Gilberto; Butruille, David; Silva, Heyder Diniz; McCuddin, Zoe Patterson; Penna, Julio Cesar Viglioni

    2009-02-01

    Breeding for resistance to gray leaf spot, caused by Cercospora zeae-maydis (Cz) is paramount for many maize environments, in particular under warm and humid growing conditions. In this study, we mapped and characterized quantitative trait loci (QTL) involved in the resistance of maize against Cz. We confirmed the impact of the QTL on disease severity using near-isogenic lines (NILs), and estimated their effects on three major agronomic traits using their respective near isogenic hybrids (NIHs), which we obtained by crossing the NILs with an inbred from a complementary heterotic pool. We further validated three of the four QTL that were mapped using the Multiple Interval Mapping approach and showed LOD values>2.5. NILs genotype included all combinations between favorable alleles of the two QTL located in chromosome 1 (Q1 in bin 1.05 and Q2 in bin 1.07), and the allele in chromosome 3 (Q3 in bin 3.07). Each of the three QTL separately significantly reduced the severity of Cz. However, we found an unfavorable epistatic interaction between Q1 and Q2: presence of the favorable allele at one of the QTL allele effectively nullified the effect of the favorable allele at the other. In contrast, the interaction between Q2 and Q3 was additive, promoting the reduction of the severity to a greater extent than the sum of their individual effects. When evaluating the NIH we found significant individual effects for Q1 and Q3 on gray leaf spot severity, for Q2 on stalk lodging and grain yield, and for Q3 on grain moisture and stalk lodging. We detected significant epitasis between Q1 and Q2 for grain moisture and between Q1 and Q3 for stalk lodging. These results suggest that the combination of QTL impacts the effectiveness of marker-assisted selection procedures in commercial product development programs.

  2. Analytical validation of a reverse transcriptase droplet digital PCR (RT-ddPCR) for quantitative detection of infectious hematopoietic necrosis virus

    Science.gov (United States)

    Jia, Peng; Purcell, Maureen; Pan, Guang; Wang, Jinjin; Kan, Shifu; Liu, Yin; Zheng, Xiaocong; SHi, Xiujie; He, Junqiang; Yu, Li; Hua, Qunyi; Lu, Tikang; Lan, Wensheng; Winton, James; Jin, Ningyi; Liu, Hong

    2017-01-01

    Infectious hematopoietic necrosis virus (IHNV) is an important pathogen of salmonid fishes. A validated universal reverse transcriptase quantitative PCR (RT-qPCR) assay that can quantify levels of IHNV in fish tissues has been previously reported. In the present study, we adapted the published set of IHNV primers and probe for use in a reverse-transcriptase droplet digital PCR (RT-ddPCR) assay for quantification of the virus in fish tissue samples. The RT-ddPCR and RT-qPCR assays detected 13 phylogenetically diverse IHNV strains, but neither assay produced detectable amplification when RNA from other fish viruses was used. The RT-ddPCR assay had a limit of detection (LOD) equating to 2.2 plaque forming units (PFU)/μl while the LOD for the RT-qPCR was 0.2 PFU/μl. Good agreement (69.4–100%) between assays was observed when used to detect IHNV RNA in cell culture supernatant and tissues from IHNV infected rainbow trout (Oncorhynchus mykiss) and arctic char (Salvelinus alpinus). Estimates of RNA copy number produced by the two assays were significantly correlated but the RT-qPCR consistently produced higher estimates than the RT-ddPCR. The analytical properties of the N gene RT-ddPCR test indicated that this method may be useful to assess IHNV RNA copy number for research and diagnostic purposes. Future work is needed to establish the within and between laboratory diagnostic performance of the RT-ddPCR assay.

  3. Quantitative T2 mapping for detecting myocardial edema after reperfusion of myocardial infarction: validation and comparison with T2-weighted images.

    Science.gov (United States)

    Park, Chul Hwan; Choi, Eui-Young; Kwon, Hyuck Moon; Hong, Bum Kee; Lee, Byoung Kwon; Yoon, Young Won; Min, Pil-Ki; Greiser, Andreas; Paek, Mun Young; Yu, Wei; Sung, Yon Mi; Hwang, Sung Ho; Hong, Yoo Jin; Kim, Tae Hoon

    2013-06-01

    This study evaluates the clinical usefulness of T2 mapping for the detection of myocardial edema in the re-perfused acute myocardial infarction (MI). Cardiac MRIs were reviewed in 20 patients who had acute MI after reperfusion therapy. The regional T2 values and T2-weighted image (T2WI) signal intensities (SI) were measured in the infarcted and remote zones of the myocardium. Patients were divided into three groups according to the signal patterns of the infarcted myocardium on the T2WIs. The T2 values of the infarcted zones were compared on the T2 maps among the three groups. Validation of the T2 values was performed in the normal myocardium of seven healthy volunteers. There were no significant differences in mean T2WI-SI or T2 values in the normal myocardium of healthy volunteers compared to the remote myocardium of acute MI patients (p > 0.05). Mean SI on the T2WIs was significantly higher in the infarcted myocardium (81.3 ± 37.6) than in the remote myocardium (63.8 ± 18.1) (p infarcted myocardium, compared to the remote myocardium. The T2 maps showed that T2 values in the infarcted myocardium had mostly increased, regardless of group, with values of 71 ± 9 ms in group 1, 64.9 ± 7.4 ms in group 2, and 61.4 ± 8.5 ms in group 3. T2 mapping is superior to T2WI for detecting areas of high SI in the infarcted myocardium. Therefore, quantitative T2 mapping sequences may be more useful and reliable in identifying myocardial edema in the infarcted myocardium than T2WI.

  4. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR.

    Directory of Open Access Journals (Sweden)

    Nicolas Chemidlin Prévost-Bouré

    Full Text Available Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR. The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1/FF390. This in silico analysis of the specificity of FR1/FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1/FF390 for Fungi was validated in vitro by cloning--sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.

  5. International Cartilage Repair Society (ICRS) Recommended Guidelines for Histological Endpoints for Cartilage Repair Studies in Animal Models and Clinical Trials.

    Science.gov (United States)

    Hoemann, Caroline; Kandel, Rita; Roberts, Sally; Saris, Daniel B F; Creemers, Laura; Mainil-Varlet, Pierre; Méthot, Stephane; Hollander, Anthony P; Buschmann, Michael D

    2011-04-01

    Cartilage repair strategies aim to resurface a lesion with osteochondral tissue resembling native cartilage, but a variety of repair tissues are usually observed. Histology is an important structural outcome that could serve as an interim measure of efficacy in randomized controlled clinical studies. The purpose of this article is to propose guidelines for standardized histoprocessing and unbiased evaluation of animal tissues and human biopsies. Methods were compiled from a literature review, and illustrative data were added. In animal models, treatments are usually administered to acute defects created in healthy tissues, and the entire joint can be analyzed at multiple postoperative time points. In human clinical therapy, treatments are applied to developed lesions, and biopsies are obtained, usually from a subset of patients, at a specific time point. In striving to standardize evaluation of structural endpoints in cartilage repair studies, 5 variables should be controlled: 1) location of biopsy/sample section, 2) timing of biopsy/sample recovery, 3) histoprocessing, 4) staining, and 5) blinded evaluation with a proper control group. Histological scores, quantitative histomorphometry of repair tissue thickness, percentage of tissue staining for collagens and glycosaminoglycan, polarized light microscopy for collagen fibril organization, and subchondral bone integration/structure are all relevant outcome measures that can be collected and used to assess the efficacy of novel therapeutics. Standardized histology methods could improve statistical analyses, help interpret and validate noninvasive imaging outcomes, and permit cross-comparison between studies. Currently, there are no suitable substitutes for histology in evaluating repair tissue quality and cartilaginous character.

  6. Validation of quantitative {sup 1}H NMR method for the analysis of pharmaceutical formulations; Validacao de metodo quantitativo por RMN de {sup 1}H para analises de formulacoes farmaceuticas

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Maiara da S. [Universidade de Sao Paulo (USP), Sao Carlos, SP (Brazil). Instituto de Quimica; Colnago, Luiz Alberto, E-mail: luiz.colnago@embrapa.br [Embrapa Instrumentacao, Sao Carlos, SP (Brazil)

    2013-09-01

    The need for effective and reliable quality control in products from pharmaceutical industries renders the analyses of their active ingredients and constituents of great importance. This study presents the theoretical basis of Superscript-One H NMR for quantitative analyses and an example of the method validation according to Resolution RE N. 899 by the Brazilian National Health Surveillance Agency (ANVISA), in which the compound paracetamol was the active ingredient. All evaluated parameters (selectivity, linearity, accuracy, repeatability and robustness) showed satisfactory results. It was concluded that a single NMR measurement provides structural and quantitative information of active components and excipients in the sample. (author)

  7. Cellular Consequences of Telomere Shortening in Histologically Normal Breast Tissues

    Science.gov (United States)

    2013-09-01

    in Figure 1, telomere shortening occurs specifically in luminal epithelial cells, but not in myoepithelial cells, in histologically normal terminal...the adjacent myoepithelial cells (panel A). In contrast, some TDLUs demonstrate dim telomere signals in the luminal cells when compared to the...adjacent myoepithelial cells (panel B). Through digital image analysis, quantitative determination of the telomere FISH signals confirms this moderated

  8. Fast hydrodynamic model for medium- and long-term dispersion in seawater in the English Channel and southern North Sea, qualitative and quantitative validation by radionuclide tracers

    Science.gov (United States)

    du Bois, P. Bailly; Dumas, F.

    The database for medium- and long-term model validation using 125Sb released by the La Hague reprocessing plant includes 1400 measurements performed between 1987 and 1994 in the English Channel and the North Sea and data for each release since 1982. Antimony-125 has a conservative behaviour in water masses over a period of several years. These data can be used qualitatively and quantitatively to compare the measured concentrations with the calculated ones and quantities of tracers. Tritium measurements are also available for model calibration. A two-dimensional hydrodynamic model has been developed to allow repetitive long-term simulations. This model uses a database of residual tidal currents calculated using the Lagrangian barycentric method [Salomon, J.C., Guéguéniat, P., Orbi, A., Baron, Y., 1988. A Lagrangian model for long-term tidally induced transport and mixing. Verification by artificial radionuclide concentrations. In: Guary, J.C., Guéguéniat, P., Pentreath, R.J. (Eds.), Radionuclides: A Tool for Oceanography, Cherbourg 1-5 June, 1987. Elsevier Applied Science Publishers, London, New York, pp. 384-394]. The area covered by the model includes the English Channel, the southern North Sea and the Irish Sea with a mesh size of 1 km. The main adjustment parameters of this model are the sources of wind data used and the calculation method for evaluating wind stress at the sea surface. With these parameters, the fluxes of radionuclides and water masses in the English Channel and the North Sea were balanced for the whole period of field measurements (1987-1994). The correlation factor between individual measurements in seawater and calculation results is 0.88 with an average error of ±54%, the error attributable to the measurement process being 15% on average. The mean flux through the Dover Strait is 126,000 m 3 s -1, close from the one obtained from previous studies [Salomon, J.C., Breton, M., Guéguéniat, P. 1993. Computed residual flow through the Dover

  9. Meningeal tumors histologically mimicking meningioma.

    Science.gov (United States)

    Barresi, Valeria; Caffo, Maria; Branca, Giovanni; Caltabiano, Rosario; Tuccari, Giovanni

    2012-10-15

    A number of meningeal neoplastic lesions may radiologically and clinically simulate meningioma. In the present paper, we review meningeal non-meningothelial tumors which may also mimic different histotypes of meningioma at the histological examination. Awareness that these lesions exist may facilitate their recognition and correct diagnosis, which is of fundamental importance for prognosis and an appropriate therapeutic approach. Histological and immunohistochemical clues for the differential diagnosis are discussed.

  10. Rapid, sensitive, and validated UPLC/Q-TOF-MS method for quantitative determination of vasicine in Adhatoda vasica and its in vitro culture

    Directory of Open Access Journals (Sweden)

    Garg Madhukar

    2014-01-01

    Full Text Available Background: Adhatoda vasica a perennial herb has been used in Ayurvedic and Unani system of medicines since last 2000 years and has been employed for the treatment of respiratory tract ailments. Objective: To develop and validate new, rapid, and highly sensitive high throughput ultra-performance liquid chromatography/quadrupole-time-of-flight mass-spectrometry (UPLC/Q-TOF-MS method for the quantitative estimation of vasicine in the leaves and to establish in vitro cultures of Adhatoda vasica for production of vasicine. Materials and Methods: The chromatographic separation was achieved on a Waters ACQUITY UPLC TM BEH C8 (100.0 × 2.1 mm; 1.7 μm column packing using isocratic mobile phase consisting of acetonitrile: 20 mM ammonium acetate (90:10; v/v in a multiple reactions monitoring mode using the transitions m/z 189.09 → 171.08 for vasicine. Results: The vasicine was eluted at 2.58 ± 0.05 min and established a dynamic range of linearity over the concentration range of 1-1000 ng/ml (r2 = 0.999 ± 0.0005. The lower limit of detection and quantification was 0.68 and 1.0 ng/ml, respectively. There was no significant difference observed in the content of vasicine (0.92-1.04%w/w among the eleven samples collected from different locations of India. The in vitro cultures developed showed that addition of extra 28 mM KNO 3 and 100 mM NaCl in MS medium supplemented with 2,4-dichlorophenoxyacetic acid (2,4-D + benzyladenine (BA + indole acetic acid (IAA (1 ppm each produces faster biomass and higher amount of quinazoline alkaloids. Conclusion: Rapid, efficient, and sensitive UPLC/Q-TOF-MS method was developed for the estimation of vasicine and an efficient protocol for development of in vitro cultures was proposed, which can be used at large scale for industrial production of vasicine using bioreactors.

  11. Selection and validation of a set of reliable reference genes for quantitative RT-PCR studies in the brain of the Cephalopod Mollusc Octopus vulgaris

    Directory of Open Access Journals (Sweden)

    Biffali Elio

    2009-07-01

    Full Text Available Abstract Background Quantitative real-time polymerase chain reaction (RT-qPCR is valuable for studying the molecular events underlying physiological and behavioral phenomena. Normalization of real-time PCR data is critical for a reliable mRNA quantification. Here we identify reference genes to be utilized in RT-qPCR experiments to normalize and monitor the expression of target genes in the brain of the cephalopod mollusc Octopus vulgaris, an invertebrate. Such an approach is novel for this taxon and of advantage in future experiments given the complexity of the behavioral repertoire of this species when compared with its relatively simple neural organization. Results We chose 16S, and 18S rRNA, actB, EEF1A, tubA and ubi as candidate reference genes (housekeeping genes, HKG. The expression of 16S and 18S was highly variable and did not meet the requirements of candidate HKG. The expression of the other genes was almost stable and uniform among samples. We analyzed the expression of HKG into two different set of animals using tissues taken from the central nervous system (brain parts and mantle (here considered as control tissue by BestKeeper, geNorm and NormFinder. We found that HKG expressions differed considerably with respect to brain area and octopus samples in an HKG-specific manner. However, when the mantle is treated as control tissue and the entire central nervous system is considered, NormFinder revealed tubA and ubi as the most suitable HKG pair. These two genes were utilized to evaluate the relative expression of the genes FoxP, creb, dat and TH in O. vulgaris. Conclusion We analyzed the expression profiles of some genes here identified for O. vulgaris by applying RT-qPCR analysis for the first time in cephalopods. We validated candidate reference genes and found the expression of ubi and tubA to be the most appropriate to evaluate the expression of target genes in the brain of different octopuses. Our results also underline the

  12. Validation of reference genes for gene expression studies in the dinoflagellateAkashiwo sanguinea by quantitative real-time RT-PCR

    Institute of Scientific and Technical Information of China (English)

    DENG Yunyan; HU Zhangxi; MA Zhaopeng; TANG Ying Zhong

    2016-01-01

    The accurate measurement of gene expression via quantitative real-time reverse transcription PCR (qRT-PCR) heavily relies on the choice of valid reference gene(s) for data normalization. Resting cyst is the dormant stage in the life cycle of dinoflagellate, which plays crucial roles in HAB-forming dinoflagellate ecology. However, only limited investigations have been conducted on the reference gene selection in dinoflagellates. Gap remained in our knowledge about appropriate HKGs for normalizing gene expression in different life stages, which laid obstacles for the application of qRT-PCR to the HAB-forming group. In this study, six candidate reference genes, 18S ribosomal RNA (18S), glyceraldehyde-3-phosphate dehydrogenase (GAPDH),α-tubulin (TUA),β-tubulin (TUB), actin (ACT) and cytochrome oxidase subunit 1 (COX1), were evaluated for their expression stability with qRT-PCR and three statistical algorithms (GeNorm, NormFinder, and BestKeeper) for the cosmopolitan, harmful algal bloom-forming dinoflagellateAkashiwo sanguinea. Expression patterns were observed across 18 biological samples, including cells at resting stages (resting cysts), different growth stages, in darkness, exposed to abscisic acid (ABA) and exposed to temperature stress. The results indicated thatTUA,18S andGAPDH were relatively stable across all tested scenarios. While the best-recommended reference genes differed across experimental groups, the pairs ofACT andTUA,18S andGAPDH were the most reliable for cells at different growth stages and darkness treatment. The combination ofTUA andTUB was the best choice for normalization in resting cysts and in ABA treatment, respectively. The pair ofACT andCOX1 was suitable for temperature treatments. This study was the first to investigate the stable internal reference genes in dinoflagellates at different stages of life cycle, particularly in resting cysts. Our results provided useful information for selection of reference genes in dinoflagellates

  13. Validation of quantitative computed tomography-derived areal bone mineral density with dual energy X-ray absorptiometry in an elderly Chinese population

    Institute of Scientific and Technical Information of China (English)

    Cheng Xiaoguang; Wang Ling; Wang Qianqian; Ma Yimin; Su Yongbin; Li Kai

    2014-01-01

    Background The performance of computed tomography X-ray absorptiometry (CTXA) against the dual energy X-ray absorptiometry (DXA) as standard has not been studied in Chinese population.The aim of this study was to evaluate the precision of this measurement and validate the value of quantitative computed tomography (QCT) by comparing CTXA results with DXA results in an elderly Chinese population.Methods One hundred and three females of 46 to 76 years old and 49 males of 52 to 76 years old were recruited from the Prospective Urban Rural Epidemiology study.All subjects underwent hip scans by both QCT and DXA on the same day.For precision determination,30 subjects had duplicate DXA hip scans.The hip QCT data of a subset of 27 subjects were separately analyzed by two observers and reanalyzed by one observer at a different time.The inter-and intra-observer variations of CTXA measurement were assessed,and the difference and correlation between CTXA and DXA results were analyzed.Results The inter-and intra-observer variations of CTXA were 0.070 and 0.024 g/cm2 in the femoral neck (FN),and 0.030 and 0.012 g/cm2 in the total hip (TH),which were comparable to the DXA inter-scan variations (0.013 g/cm2 for FN and 0.014 g/cm2 for TH).The results of CTXA bone mineral density (BMD) were highly correlated with those of DXA (R2 =0.810 for FN and R2=0.878 for TH).The BMD values of CTXA in FN and TH were lower than those of DXA by 21.0% and 17.8% (P<0.05),respectively.However,after appropriate transformation,the difference was eliminated and a comparable T score could be obtained.Conclusions CTXA shows good agreement with DXA for the measurement of BMD in the proximal femur,which makes QCT suitable for the quantification of bone mineral content in the hip and helpful for the diagnosis of osteoporosis.

  14. High reproducibility of histological characterization by whole virtual slide quantification; an example using carotid plaque specimens.

    Directory of Open Access Journals (Sweden)

    Joyce E P Vrijenhoek

    Full Text Available Tissue biobanks are an important source for discovery and validation studies aiming for new proteins that are causally related with disease development. There is an increasing demand for accurate and reproducible histological characterization, especially for subsequent analysis and interpretation of data in association studies. We assessed reproducibility of one semiquantative and two quantitative methods for histological tissue characterization. We introduce a new automated method for whole digital slide quantification. Carotid atherosclerotic plaques were used to test reproducibility.50 atherosclerotic plaques that were obtained during carotid endarterectomy were analysed. For the semiquantitative analysis, 6 different plaque characteristics were scored in categories by two independent observers, and Cohen's κ was used to test intra- and interobserver reproducibility. The computer-aided method (assessed by two independent observers and automated method were tested on CD68 (for macrophages and α smooth muscle actin (for smooth muscle cells stainings. Agreement for these two methods (done on a continuous scale was assessed by intraclass correlation coefficients (ICCs.For the semiquantitative analysis, κ values ranged from 0.55 to 0.69 for interobserver variability, and were slightly higher for intraobserver reproducibility in both observers. The computer-aided method yielded intra- and interobserver ICCs between 0.6 and 0.9. The new automated method performed most optimal regarding reproducibility, with ICCs ranging from 0.92 to 0.97.The analysis of performance of three methods for histological slide characterization on carotid atherosclerotic plaques showed high precision and agreement in repeated measurements for the automated method for whole digital slide quantification. We suggest that this method can fulfill the need for reproducible histological quantification.

  15. Development and validation of an ICP-OES method for quantitation of elemental impurities in tablets according to coming US pharmacopeia chapters

    DEFF Research Database (Denmark)

    Jensen, Celina Støving; Jensen, Henrik; Gammelgaard, Bente

    2013-01-01

    for quantitation of As, Cd, Cu, Cr, Fe, Hg, Ir, Mn, Mo, Ni, Os, Pb, Pd, Pt, Rh, Ru, V and Zn in tablets according to the new USP chapters was developed. Sample preparation was performed by microwave-assisted acid digestion using a mixture of 65% HNO3 and 37% HCl (3:1, v/v). Limits of detection and quantitation...

  16. Validity and sensitivity to change of the semi-quantitative OMERACT ultrasound scoring system for tenosynovitis in patients with rheumatoid arthritis

    DEFF Research Database (Denmark)

    Ammitzbøll-Danielsen, Mads; Østergaard, Mikkel; Naredo, Esperanza;

    2016-01-01

    OBJECTIVES: The aim was to evaluate the metric properties of the semi-quantitative OMERACT US scoring system vs a novel quantitative US scoring system for tenosynovitis, by testing its intra- and inter-reader reliability, sensitivity to change and comparison with clinical tenosynovitis scoring in...

  17. Assessment of simpler calibration models in the development and validation of a fast postmortem multi-analyte LC-QTOF quantitation method in whole blood with simultaneous screening capabilities using SWATH acquisition.

    Science.gov (United States)

    Elmiger, Marco P; Poetzsch, Michael; Steuer, Andrea E; Kraemer, Thomas

    2017-08-29

    In postmortem toxicology, fast methods can provide a triage to avoid unnecessary autopsies. Usually, this requires multiple qualitative and quantitative analytical methods. The aim of the present study was to develop a postmortem LC-QTOF method for simultaneous screening and quantitation using easy sample preparation and reduced alternative calibration models. Hence, a method for 24 highly relevant substances in forensic toxicology was fully validated using the following calibration models: one-point external, one-point internal via corresponding deuterated standards, multi-point external daily calibration, and multi-point external weekly calibration. Two hundred microliters of postmortem blood were spiked with internal deuterated standard mixture and extracted by acetonitrile protein precipitation. Analysis was performed on a Sciex 6600 QTOF instrument with ESI+ mode using data-independent acquisition (DIA) namely sequential window acquisition of all theoretical mass spectra (SWATH). Validation of the different calibration models included selectivity, autosampler stability, recovery, matrix effects, accuracy, and precision for 24 substances. In addition, corresponding deuterated analogs of 52 substances were included to the internal standard mix for semi-quantitative concentration assessment. The simple protein precipitation provided recoveries higher than 55 and 75% for all analytes at low and high concentrations, respectively. Accuracy and precision criteria (bias and imprecision ± 15 and ± 20% near the limit of quantitation) were fulfilled by the different calibration models for most analytes. The validated method was successfully applied to more than 100 authentic postmortem samples and 3 proficiency tests. Furthermore, the one-point internal calibration via corresponding deuterated standard proved to be a considerably time saving technique for 76 analytes. Graphical abstract One-point and multi-point calibration and the resulting beta

  18. Histological analysis of surgical lumbar intervertebral disc tissue provides evidence for an association between disc degeneration and increased body mass index

    Directory of Open Access Journals (Sweden)

    Weiler Christoph

    2011-11-01

    Full Text Available Abstract Background Although histopathological grading systems for disc degeneration are frequently used in research, they are not yet integrated into daily care routine pathology of surgical samples. Therefore, data on histopathological changes in surgically excised disc material and their correlation to clinical parameters such as age, gender or body mass index (BMI is limited to date. The current study was designed to correlate major physico-clinical parameters from a population of orthopaedic spine center patients (gender, age and BMI with a quantitative histologic degeneration score (HDS. Methods Excised lumbar disc material from 854 patients (529 men/325 women/mean age 56 (15-96 yrs. was graded based on a previously validated histologic degeneration score (HDS in a cohort of surgical disc samples that had been obtained for the treatment of either disc herniation or discogenic back pain. Cases with obvious inflammation, tumor formation or congenital disc pathology were excluded. The degree of histological changes was correlated with sex, age and BMI. Results The HDS (0-15 points showed significantly higher values in the nucleus pulposus (NP than in the annulus fibrosus (AF (Mean: NP 11.45/AF 7.87, with a significantly higher frequency of histomorphological alterations in men in comparison to women. Furthermore, the HDS revealed a positive significant correlation between the BMI and the extent of histological changes. No statistical age relation of the degenerative lesions was seen. Conclusions This study demonstrated that histological disc alterations in surgical specimens can be graded in a reliable manner based on a quantitative histologic degeneration score (HDS. Increased BMI was identified as a positive risk factor for the development of symptomatic, clinically significant disc degeneration.

  19. Histology-directed MALDI mass spectrometry for the diagnostic pathology

    Science.gov (United States)

    Kim, Hark Kyun; Kim, In-Hoo

    2012-10-01

    With the advent of targeted agents, it has become clinically important to distinguish histologic types of non-small cell lung cancers (NSCLCs) using biopsy samples. We investigated whether direct tissue matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) analysis on lipid may classify histology of NSCLCs. Twentyone pairs of frozen, resected NSCLCs were analyzed using histology-directed, MALDI MS. 2,5-dihydroxybenzoic acid/α-cyano-4-hydroxycinnamic acid were manually deposited on areas of each tissue section enriched in epithelial cells to identify lipid profiles, and mass spectra were acquired using a MALDI-time of flight instrument. Squamous cell carcinomas and adenocarcinomas, two major histologic types of NSCLC, were found to have different lipid profiles. Discriminatory lipids correctly classified the histology of 80.4% of independent NSCLC surgical tissue samples (41 out of 51) in validation set, suggesting that lipid profiles can classify NSCLCs according to the histologic type. We also found that protein and lipid MALDI MS profiles can classify 30 breast cancers according to the intrinsic subtypes. Immunohistochemistry-defined, luminal, HER2+, and triple-negative tumors demonstrated different protein and lipid profiles, as evidenced by cross validation P values < 0.01. Discriminatory proteins and lipids classified tumors according to the intrinsic subtype with median prediction accuracies of 80.0-81.3% in 100 random test sets. Potential advantages of this label-free approach may include small tissue requirement, relatively rapid procedure, and low reagent cost. Day-today variation of this technology is also acceptable, with the Pearson correlation of 0.95. Taken together, these results suggest the possible clinical utility of histology-directed, lipid and protein MALDI MS.

  20. Development and validation of a LC-MS/MS method for quantitative analysis of uraemic toxins p-cresol sulphate and indoxyl sulphate in saliva.

    Science.gov (United States)

    Giebułtowicz, Joanna; Korytowska, Natalia; Sankowski, Bartłomiej; Wroczyński, Piotr

    2016-04-01

    p-Cresol sulphate (pCS) and indoxyl sulphate (IS) are uraemic toxins, the concentration of which in serum correlate with the stage of renal failure. The aim of this study was to develop and validate a high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the analysis of pCS and IS in saliva. This is the first time, to our knowledge, that such a method has been developed using saliva. Unstimulated, fasting saliva was collected from healthy volunteers in the morning and pooled for validation assay. The method was validated for linearity, precision, accuracy, stability (freeze/thaw stability, stability in autosampler, short- and long-term stability, stock solution stability), dilution integrity and matrix effect. The analysed validation criteria were fulfilled. No influence of salivary flow (pCS: p=0.678; IS: p=0.238) nor type of swab in the Salivette device was detected. Finally, using the novel validated method, the saliva samples of healthy people (n=70) of various ages were analysed. We observed a tendency for an increase of concentration of toxins in saliva in the elderly. This could be a result of age-related diseases, e.g., diabetes and kidney function decline. We can conclude that the novel LC-MS/MS method can be used for the determination of pCS and IS in human saliva. The results encourage the validation of saliva as a clinical sample for monitoring toxin levels in organisms.

  1. Reordering Histology to Enhance Engagement

    Science.gov (United States)

    Amerongen, Helen

    2011-01-01

    In redesigning the preclinical curriculum and shifting from a discipline-based approach to an organ system-based approach, faculty at the University of Arizona College of Medicine in Tucson took the opportunity to restructure the sequence of introductory histology content to make it more engaging and relevant. In this article, the author describes…

  2. Reordering Histology to Enhance Engagement

    Science.gov (United States)

    Amerongen, Helen

    2011-01-01

    In redesigning the preclinical curriculum and shifting from a discipline-based approach to an organ system-based approach, faculty at the University of Arizona College of Medicine in Tucson took the opportunity to restructure the sequence of introductory histology content to make it more engaging and relevant. In this article, the author describes…

  3. A validated procedure for detection and quantitation of salvinorin a in pericardial fluid, vitreous humor, whole blood and plasma using solid phase extraction and gas chromatography-mass spectrometry.

    Science.gov (United States)

    Margalho, Cláudia; Gallardo, Eugenia; Castanheira, Alice; Vieira, Duarte Nuno; López-Rivadulla, Manuel; Real, Francisco Corte

    2013-08-23

    The use of vitreous humor and pericardial fluid as alternative matrices to blood and plasma in the field of forensic toxicology is described to quantitate low levels of Salvinorin A using ethion as internal standard. The method was optimized and fully validated using international accepted guidelines. The developed methodology utilizes a solid phase extraction procedure coupled to gas chromatography mass spectrometry operated in the selected ion monitoring mode. The method was linear in the range of 5.0-100ng/mL with determination coefficients higher than 0.99 in 100μL of vitreous humor and in 250μL of each matrix pericardial fluid, whole blood and plasma. The limits of detection and quantitation were experimentally determined as 5.0ng/mL, intra-day precision, intermediate precision and accuracy were in conformity with the criteria normally accepted in bioanalytical method validation. The sample cleanup step presented mean efficiencies between 80 and 106% in the different biological specimens analyzed. According to the low volumes of samples used, and the low limits achieved using a single quadrupole mass spectrometer, which is available in most laboratories, we can conclude that the validated methodology is sensitive and simple and is suitable for the application in forensic toxicology laboratories for the routine analysis of Salvinorin A in both conventional and unconventional biological samples.

  4. Comparison of the quantitative performances and measurement uncertainty estimates obtained during method validation versus routine applications of a novel hydrophilic interaction chromatography method for the determination of cidofovir in human plasma.

    Science.gov (United States)

    Lecomte, F; Hubert, C; Demarche, S; De Bleye, C; Dispas, A; Jost, M; Frankenne, F; Ceccato, A; Rozet, E; Hubert, Ph

    2012-01-05

    Method validation is essential to ensure that an analytical method is fit for its intended purpose. Additionally, it is advisable to estimate measurement uncertainty in order to allow a correct interpretation of the results generated by analytical methods. Measurement uncertainty can be efficiently estimated during method validation as a top-down approach. However, method validation predictions of the quantitative performances of the assay and estimations of measurement uncertainty may be far away from the real performances obtained during the routine application of this assay. In this work, the predictions of the quantitative performances and measurement uncertainty estimations obtained from a method validation are compared to those obtained during routine applications of a bioanalytical method. For that purpose, a new hydrophilic interaction chromatography (HILIC) method was used. This method was developed for the determination of cidofovir, an antiviral drug, in human plasma. Cidofovir (CDV) is a highly polar molecule presenting three ionizable functions. Therefore, it is an interesting candidate for determination by HILIC mode. CDV is an acyclic cytidine monophosphate analog that has a broad antiviral spectrum and is currently undergoing evaluation in clinical trials as a topical agent for treatment of papillomavirus infections. The analytical conditions were optimized by means of design of experiments approach in order to obtain robust analytical conditions. These ones were absolutely necessary to enable the comparisons mentioned above. After a sample clean-up by means of solid phase extraction, the chromatographic analysis was performed on bare silica stationary phase using a mixture of acetonitrile-ammonium hydrogen carbonate (pH 7.0; 20mM) (72:28, v/v) as mobile phase. This newly developed bioanalytical method was then fully validated according to FDA (Food and Drug Administration) requirements using a total error approach that guaranteed that each future

  5. Development and validation of quantitative polymerase chain reaction protocols targeting the ‘L’, ‘M’, and ‘S’ ribonucleic acid of Soybean vein necrosis virus

    Science.gov (United States)

    Soybean vein necrosis virus (SVNV) was first reported in Wisconsin in 2012. SVNV is a new member of the Tospovirus family and is becoming more frequent in occurrence in the north central region USA. New real-time reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) protocols were d...

  6. The Historical Foundation of Learning Disabilities: A Quantitative Synthesis Assessing the Validity of Strauss and Werner's Exogenous versus Endogenous Distinction of Mental Retardation.

    Science.gov (United States)

    Kavale, Kenneth A.; Forness, Steven R.

    1985-01-01

    The paper reviews research of A. Strauss and H. Werner on behavioral differences between exogeneous (brain injured) and endogeneous (familial-cultural) mental retardation using quantitative methods of research synthesis. Findings offer little empirical support for the presumed behavioral differences and reveal considerable overlap among the…

  7. Comparison of visual scoring and quantitative planimetry methods for estimation of global infarct size on delayed enhanced cardiac MRI and validation with myocardial enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Mewton, Nathan, E-mail: nmewton@gmail.com [Hopital Cardiovasculaire Louis Pradel, 28, Avenue Doyen Lepine, 69677 Bron cedex, Hospices Civils de Lyon (France); CREATIS-LRMN (Centre de Recherche et d' Applications en Traitement de l' Image et du Signal), Universite Claude Bernard Lyon 1, UMR CNRS 5220, U 630 INSERM (France); Revel, Didier [Hopital Cardiovasculaire Louis Pradel, 28, Avenue Doyen Lepine, 69677 Bron cedex, Hospices Civils de Lyon (France); CREATIS-LRMN (Centre de Recherche et d' Applications en Traitement de l' Image et du Signal), Universite Claude Bernard Lyon 1, UMR CNRS 5220, U 630 INSERM (France); Bonnefoy, Eric [Hopital Cardiovasculaire Louis Pradel, 28, Avenue Doyen Lepine, 69677 Bron cedex, Hospices Civils de Lyon (France); Ovize, Michel [Hopital Cardiovasculaire Louis Pradel, 28, Avenue Doyen Lepine, 69677 Bron cedex, Hospices Civils de Lyon (France); INSERM Unite 886 (France); Croisille, Pierre [Hopital Cardiovasculaire Louis Pradel, 28, Avenue Doyen Lepine, 69677 Bron cedex, Hospices Civils de Lyon (France); CREATIS-LRMN (Centre de Recherche et d' Applications en Traitement de l' Image et du Signal), Universite Claude Bernard Lyon 1, UMR CNRS 5220, U 630 INSERM (France)

    2011-04-15

    Purpose: Although delayed enhanced CMR has become a reference method for infarct size quantification, there is no ideal method to quantify total infarct size in a routine clinical practice. In a prospective study we compared the performance and post-processing time of a global visual scoring method to standard quantitative planimetry and we compared both methods to the peak values of myocardial biomarkers. Materials and methods: This study had local ethics committee approval; all patients gave written informed consent. One hundred and three patients admitted with reperfused AMI to our intensive care unit had a complete CMR study with gadolinium-contrast injection 4 {+-} 2 days after admission. A global visual score was defined on a 17-segment model and compared with the quantitative planimetric evaluation of hyperenhancement. The peak values of serum Troponin I (TnI) and creatine kinase (CK) release were measured in each patient. Results: The mean percentage of total left ventricular myocardium with hyperenhancement determined by the quantitative planimetry method was (20.1 {+-} 14.6) with a range of 1-68%. There was an excellent correlation between quantitative planimetry and visual global scoring for the hyperenhancement extent's measurement (r = 0.94; y = 1.093x + 0.87; SEE = 1.2; P < 0.001) The Bland-Altman plot showed a good concordance between the two approaches (mean of the differences = 1.9% with a standard deviation of 4.7). Mean post-processing time for quantitative planimetry was significantly longer than visual scoring post-processing time (23.7 {+-} 5.7 min vs 5.0 {+-} 1.1 min respectively, P < 0.001). Correlation between peak CK and quantitative planimetry was r = 0.82 (P < 0.001) and r = 0.83 (P < 0.001) with visual global scoring. Correlation between peak Troponin I and quantitative planimetry was r = 0.86 (P < 0.001) and r = 0.85 (P < 0.001) with visual global scoring. Conclusion: A visual approach based on a 17-segment model allows a rapid

  8. Effectiveness of quantitative MAA SPECT/CT for the definition of vascularized hepatic volume and dosimetric approach: phantom validation and clinical preliminary results in patients with complex hepatic vascularization treated with yttrium-90-labeled microspheres.

    Science.gov (United States)

    Garin, Etienne; Lenoir, Laurence; Rolland, Yan; Laffont, Sophie; Pracht, Marc; Mesbah, Habiba; Porée, Philippe; Ardisson, Valérie; Bourguet, Patrick; Clement, Bruno; Boucher, Eveline

    2011-12-01

    The goal of this study was to assess the use of quantitative single-photon emission computed tomography/computed tomography (SPECT/CT) analysis for vascularized volume measurements in the use of the yttrium-90-radiolabeled microspheres (TheraSphere). A phantom study was conducted for the validation of SPECT/CT volume measurement. SPECT/CT quantitative analysis was used for the measurement of the volume of distribution of the albumin macroaggregates (MAA; i.e., the vascularized volume) in the liver and the tumor, and the total activity contained in the liver and the tumor in four consecutive patients presenting with a complex liver vascularization referred for a treatment with TheraSphere. SPECT/CT volume measurement proved to be accurate (mean error data, instead of angiography and CT data, results in modifying the activity injected for three treatments of eight. Moreover, quantitative analysis of SPECT/CT allows us to calculate the absorbed dose in the tumor and in the healthy liver, leading to doubling of the injected activity for one treatment of eight. MAA SPECT/CT is accurate for volume measurements. It provides a valuable contribution to the therapeutic planning of patients presenting with complex hepatic vascularization, in particular for calculating the vascularized liver volume, the activity to be injected and the absorbed doses. Studies should be conducted to assess the role of quantitative MAA/SPECT CT in therapeutic planning.

  9. Development and validation of a real-time two-step RT-qPCR TaqMan(®) assay for quantitation of Sacbrood virus (SBV) and its application to a field survey of symptomatic honey bee colonies

    DEFF Research Database (Denmark)

    Blanchard, Philippe; Guillot, Sylvain; Antùnez, Karina

    2014-01-01

    Sacbrood virus (SBV) is the causal agent of a disease of honey bee larvae, resulting in failure to pupate and causing death. The typical clinical symptom of SBV is an accumulation of SBV-rich fluid in swollen sub-cuticular pouches, forming the characteristic fluid-filled sac that gives its name...... bees. A two-step real-time RT-PCR assay, based on TaqMan(®) technology using a fluorescent probe (FAM-TAMRA) was therefore developed to quantify Sacbrood virus in larvae, pupae and adult bees from symptomatic apiaries. This assay was first validated according to the recent XP-U47-600 standard issued...... with individuals without clinical signs. The SBV quantitation revealed that, in symptomatic larvae, the virus load was significantly higher than in samples without clinical signs. Combining quantitation with clinical data, a threshold of SBV viral load related to an overt disease was proposed (10(10) SBV genome...

  10. Academic and Nonacademic Validating Agents on Latinas Mathematics and Science Self Concept A Quantitative Study Utilizing the High School Longitudinal Study of 2009

    Science.gov (United States)

    Garza, Jennifer M.

    The purpose of this study is to inform and further the discussion of academic (i.e. teachers and school counselors) and non-academic (i.e. parents, family, friends, etc.) validating agents on Latina students' mathematics and science self-concepts. This study found a relationship between Latina students' interactions with academic and non-academic validating agents and their math and science self-concept at the K-12 level. Through the review of the literature the researcher addresses identifiable factors and strategies that inform the field of education in the areas of validation theory, family characteristics, and access to STEM fields for Latina students. The researcher used an established instrument designed, administered, and validated through the National Center for Education Statistics (NCES). For purposes of this study, a categorical subset of participants who self-identified as being a Latina student was used. As a result, the total subset number in this study was N=1,882. To determine if academic and non-academic validating agents had an observable statistically significant relationship with Latina students' math and science self-concept, a series of one-way ANOVAs were calculated to compare differences in students' math and science self-concept based on academic and non-academic validating agents for the weighted sample of Latinas for the HLS:09 survey. A path analysis was also employed to assess the factors involved in Latina students' math and science self-concepts. The findings are consistent with previous research involving the influence that academic and non-academic validating agents have on the math and science self-concept of Latina students. The results indicated that students who had teachers that believed in the students, regardless of family background, social economic status or home environment influences had higher math and science self concepts than those who did not. Similarly, it was found that students who had counselors that set high

  11. Comparative histology of mouse, rat, and human pelvic ligaments.

    Science.gov (United States)

    Iwanaga, Ritsuko; Orlicky, David J; Arnett, Jameson; Guess, Marsha K; Hurt, K Joseph; Connell, Kathleen A

    2016-11-01

    The uterosacral (USL) and cardinal ligaments (CL) provide support to the uterus and pelvic organs, and the round ligaments (RL) maintain their position in the pelvis. In women with pelvic organ prolapse (POP), the connective tissue, smooth muscle, vasculature, and innervation of the pelvic support structures are altered. Rodents are commonly used animal models for POP research. However, the pelvic ligaments have not been defined in these animals. In this study, we hypothesized that the gross anatomy and histological composition of pelvic ligaments in rodents and humans are similar. We performed an extensive literature search for anatomical and histological descriptions of the pelvic support ligaments in rodents. We also performed anatomical dissections of the pelvis to define anatomical landmarks in relation to the ligaments. In addition, we identified the histological components of the pelvic ligaments and performed quantitative analysis of the smooth muscle bundles and connective tissue of the USL and RL. The anatomy of the USL, CL, and RL and their anatomical landmarks are similar in mice, rats, and humans. All species contain the same cellular components and have similar histological architecture. However, the cervical portion of the mouse USL and RL contain more smooth muscle and less connective tissue compared with rat and human ligaments. The pelvic support structures of rats and mice are anatomically and histologically similar to those of humans. We propose that both mice and rats are appropriate, cost-effective models for directed studies in POP research.

  12. Donkey dental anatomy. Part 2: Histological and scanning electron microscopic examinations.

    Science.gov (United States)

    Du Toit, N; Kempson, S A; Dixon, P M

    2008-06-01

    Ten normal cheek teeth (CT) were extracted at post mortem from donkeys that died or were euthanased for humane reasons. Decalcified histology was performed on three sections (sub-occlusal, mid-tooth and pre-apical) of each tooth, and undecalcified histology undertaken on sub-occlusal sections of the same teeth. The normal histological anatomy of primary, regular and irregular secondary dentine was found to be similar to that of the horse, with no tertiary dentine present. Undecalcified histology demonstrated the normal enamel histology, including the presence of enamel spindles. Scanning electron microscopy was performed on mid-tooth sections of five maxillary CT, five mandibular CT and two incisors. The ultrastructural anatomy of primary and secondary dentine, and equine enamel types-1, -2 and -3 (as described in horses) were identified in donkey teeth. Histological and ultrastructural donkey dental anatomy was found to be very similar to equine dental anatomy with only a few quantitative differences observed.

  13. Anal anatomy and normal histology.

    Science.gov (United States)

    Pandey, Priti

    2012-12-01

    The focus of this article is the anatomy and histology of the anal canal, and its clinical relevance to anal cancers. The article also highlights the recent histological and anatomical changes to the traditional terminology of the anal canal. The terminology has been adopted by the American Joint Committee on Cancer, separating the anal region into the anal canal, the perianal region and the skin. This paper describes the gross anatomy of the anal canal, along with its associated blood supply, venous and lymphatic drainage, and nerve supply. The new terminology referred to in this article may assist clinicians and health care providers to identify lesions more precisely through naked eye observation and without the need for instrumentation. Knowledge of the regional anatomy of the anus will also assist in management decisions.

  14. Histological Value of Duodenal Biopsies

    Directory of Open Access Journals (Sweden)

    Limci Gupta

    2005-01-01

    Full Text Available This study was performed to see the value of histopathological diagnosis in management of patients with duodenal biopsies; to look for correlation of histology and serology in suspected cases of coeliac disease; the reasons for taking duodenal biopsies and whether proper adequate histories are provided on the forms sent with request for histopathological view on duodenal biopsies. Here are the observations of the study followed by the discussion.

  15. Adapting lean to histology laboratories.

    Science.gov (United States)

    Buesa, René J

    2009-10-01

    Histology laboratories (histolabs) can increase productivity and reduce turnaround time and errors by using any one of several available management tools. After a few years of operation, all histolabs develop workflow problems. Histology laboratories handling more than 20,000 cases per year benefit the most from implementing management tools, as occurred in the 25 facilities summarized in this article. Discontinuous workflow, lack of "pulling" between steps, accepting unavoidable waiting times while working with small batches within work cells, and a workflow with an uneven rate of completion, are some of the adaptations required by the Lean system when it is used in histology because 70% of the tasks are manual and the flow has to be interrupted to add value to the pieces of tissue during tissue processing, no matter how short that step is. After all these adaptations are incorporated, the histolab becomes as "Lean" as it can be, and the qualifier is also a recognition of the effort and personnel involvement in the implementation. Given its service nature, productivity increments do not expand the histolab customer base and could lead to staffing reductions. This is one of the causes of reluctance by some employees for implementing these techniques which are mostly driven by cost reductions sought by insurance companies and administrators, and not necessarily because of a real medical need to reduce the turnaround time. Finally, any histolab wanting to improve its workflow can follow some easy steps presented here as a guide to accomplish that objective. These steps stress the need for the supervisors to insure that the personnel in the histology laboratory are being paid at a comparable rate as other histolabs in the area.

  16. Anatomical analysis of an aye-aye brain (Daubentonia madagascariensis, primates: Prosimii) combining histology, structural magnetic resonance imaging, and diffusion-tensor imaging.

    Science.gov (United States)

    Kaufman, Jason A; Ahrens, Eric T; Laidlaw, David H; Zhang, Song; Allman, John M

    2005-11-01

    This report presents initial results of a multimodal analysis of tissue volume and microstructure in the brain of an aye-aye (Daubentonia madagascariensis). The left hemisphere of an aye-aye brain was scanned using T2-weighted structural magnetic resonance imaging (MRI) and diffusion-tensor imaging (DTI) prior to histological processing and staining for Nissl substance and myelinated fibers. The objectives of the experiment were to estimate the volume of gross brain regions for comparison with published data on other prosimians and to validate DTI data on fiber anisotropy with histological measurements of fiber spread. Measurements of brain structure volumes in the specimen are consistent with those reported in the literature: the aye-aye has a very large brain for its body size, a reduced volume of visual structures (V1 and LGN), and an increased volume of the olfactory lobe. This trade-off between visual and olfactory reliance is likely a reflection of the nocturnal extractive foraging behavior practiced by Daubentonia. Additionally, frontal cortex volume is large in the aye-aye, a feature that may also be related to its complex foraging behavior and sensorimotor demands. Analysis of DTI data in the anterior cingulum bundle demonstrates a strong correlation between fiber spread as measured from histological sections and fiber spread as measured from DTI. These results represent the first quantitative comparison of DTI data and fiber-stained histology in the brain.

  17. Development and Validation of a Semi-Quantitative Food Frequency Questionnaire to Assess Dietary Intake of Turkish School-Aged Children

    Directory of Open Access Journals (Sweden)

    Güneş Fatma Esra

    2016-06-01

    Full Text Available The aim of this study was to develop and validate a food frequency questionnaire (FFQ on the dietary intake of Turkish school-aged children. Fifty randomly selected students aged 7–12 from urban areas of Istanbul were included in this study. An FFQ, containing a list of 138 frequently consumed foods was developed. Dietary records (DRs including three days, and FFQs were collected during autumn and spring. Daily consumption of each food group was assessed and the nutrient compositions of diet were calculated. The Pearson correlation coefficient, weighted kappa, the Bland-Altman scatter plots between averages of the reported (FFQ and the references method (DR were used as validity coefficient.

  18. Development and validation of an RP-HPLC method for the quantitation of odanacatib in rat and human plasma and its application to a pharmacokinetic study.

    Science.gov (United States)

    Police, Anitha; Gurav, Sandip; Dhiman, Vinay; Zainuddin, Mohd; Bhamidipati, Ravi Kanth; Rajagopal, Sriram; Mullangi, Ramesh

    2015-11-01

    A simple, specific, sensitive and reproducible high-performance liquid chromatography (HPLC) assay method has been developed and validated for the estimation of odanacatib in rat and human plasma. The bioanalytical procedure involves extraction of odanacatib and itraconazole (internal standard, IS) from a 200 μL plasma aliquot with simple liquid-liquid extraction process. Chromatographic separation was achieved on a Symmetry Shield RP18 using an isocratic mobile phase at a flow rate of 0.7 mL/min. The UV detection wave length was 268 nm. Odanacatib and IS eluted at 5.5 and 8.6 min, respectively with a total run time of 10 min. Method validation was performed as per US Food and Drug Administration guidelines and the results met the acceptance criteria. The calibration curve was linear over a concentration range of 50.9-2037 ng/mL (r(2) = 0.994). The intra- and inter-day precisions were in the range of 2.06-5.11 and 5.84-13.1%, respectively, in rat plasma and 2.38-7.90 and 6.39-10.2%, respectively, in human plasma. The validated HPLC method was successfully applied to a pharmacokinetic study in rats.

  19. Quantitative impurity analysis of monoclonal antibody size heterogeneity by CE-LIF: example of development and validation through a quality-by-design framework.

    Science.gov (United States)

    Michels, David A; Parker, Monica; Salas-Solano, Oscar

    2012-03-01

    This paper describes the framework of quality by design applied to the development, optimization and validation of a sensitive capillary electrophoresis-sodium dodecyl sulfate (CE-SDS) assay for monitoring impurities that potentially impact drug efficacy or patient safety produced in the manufacture of therapeutic MAb products. Drug substance or drug product samples are derivatized with fluorogenic 3-(2-furoyl)quinoline-2-carboxaldehyde and nucleophilic cyanide before separation by CE-SDS coupled to LIF detection. Three design-of-experiments enabled critical labeling parameters to meet method requirements for detecting minor impurities while building precision and robustness into the assay during development. The screening design predicted optimal conditions to control labeling artifacts while two full factorial designs demonstrated method robustness through control of temperature and cyanide parameters within the normal operating range. Subsequent validation according to the guidelines of the International Committee of Harmonization showed the CE-SDS/LIF assay was specific, accurate, and precise (RSD ≤ 0.8%) for relative peak distribution and linear (R > 0.997) between the range of 0.5-1.5 mg/mL with LOD and LOQ of 10 ng/mL and 35 ng/mL, respectively. Validation confirmed the system suitability criteria used as a level of control to ensure reliable method performance.

  20. Establishment and Validation of a Non-Radioactive Method for In Vitro Transcription Assay Using Primer Extension and Quantitative Real Time PCR.

    Science.gov (United States)

    Wang, Juan; Zhao, Shasha; Zhou, Ying; Wei, Yun; Deng, Wensheng

    2015-01-01

    Primer extension-dependent in vitro transcription assay is one of the most important approaches in the research field of gene transcription. However, conventional in vitro transcription assays incorporates radioactive isotopes that cause environmental and health concerns and restricts its scope of application. Here we report a novel non-radioactive method for in vitro transcription analysis by combining primer extension with quantitative real time PCR (qPCR). We show that the DNA template within the transcription system can be effectively eliminated to a very low level by our specially designed approach, and that the primers uniquely designed for primer extension and qPCR can specifically recognize the RNA transcripts. Quantitative PCR data demonstrate that the novel method has successfully been applied to in vitro transcription analyses using the adenovirus E4 and major late promoters. Furthermore, we show that the TFIIB recognition element inhibits transcription of TATA-less promoters using both conventional and nonradioactive in vitro transcription assays. Our method will benefit the laboratories that need to perform in vitro transcription but either lack of or choose to avoid radioactive facilities.

  1. Construction and Experimental Validation of a Quantitative Kinetic Model of Nitric Oxide Stress in Enterohemorrhagic Escherichia coli O157:H7

    Directory of Open Access Journals (Sweden)

    Jonathan L. Robinson

    2016-02-01

    Full Text Available Enterohemorrhagic Escherichia coli (EHEC are responsible for large outbreaks of hemorrhagic colitis, which can progress to life-threatening hemolytic uremic syndrome (HUS due to the release of Shiga-like toxins (Stx. The presence of a functional nitric oxide (NO· reductase (NorV, which protects EHEC from NO· produced by immune cells, was previously found to correlate with high HUS incidence, and it was shown that NorV activity enabled prolonged EHEC survival and increased Stx production within macrophages. To enable quantitative study of EHEC NO· defenses and facilitate the development of NO·-potentiating therapeutics, we translated an existing kinetic model of the E. coli K-12 NO· response to an EHEC O157:H7 strain. To do this, we trained uncertain model parameters on measurements of [NO·] and [O2] in EHEC cultures, assessed parametric and prediction uncertainty with the use of a Markov chain Monte Carlo approach, and confirmed the predictive accuracy of the model with experimental data from genetic mutants lacking NorV or Hmp (NO· dioxygenase. Collectively, these results establish a methodology for the translation of quantitative models of NO· stress in model organisms to pathogenic sub-species, which is a critical step toward the application of these models for the study of infectious disease.

  2. Validation of housekeeping genes as internal controls for studying the gene expression in Pyropia haitanensis (Bangiales, Rhodophyta) by quantitative real-time PCR

    Institute of Scientific and Technical Information of China (English)

    LI Bing; CHEN Changsheng; XU Yan; JI Dehua; XIE Chaotian

    2014-01-01

    Pyropia haitanensis is an economically important mariculture crop in China and has a high research value for several life phenomena, for example environmental tolerance. To explore the mechanisms underlying these characteristics, gene expression has been investigated at the whole transcriptome level. Gene expres-sion studies using quantitative real-time PCR should start by selecting an appropriate internal control gene;therefore, the absolute expression abundance of six housekeeping genes (18S rRNA (18S), ubiquitin-conju-gating enzyme (UBC), actin (ACT),β-tubulin (TUB), elongation factors 2 (EF2), and glyceraldehyde-3-phos-phate dehydrogenase (GAPDH) examined by the quantitative real-time PCR in samples corresponding to different strains, life-cycle stages and abiotic stress treatments. Their expression stabilities were assessed by the comparative cycle threshold (Ct) method and by two different software packages:geNorm and Norm-Finder. The most stable housekeeping gene is UBC and the least stable housekeeping is GADPH. Thus, it is proposed that the most appropriate internal control gene for expression analyses in P. haitanensis is UBC. The results pave the way for further gene expression analyses of different aspects of P. haitanensis biology including different strains, life-history stages and abiotic stress responses.

  3. Quantitative analysis of boldine alkaloid in natural extracts by cyclic voltammetry at a liquid-liquid interface and validation of the method by comparison with high performance liquid chromatography.

    Science.gov (United States)

    Cámara, C I; Bornancini, C A; Cabrera, J L; Ortega, M G; Yudi, L M

    2010-12-15

    The quantitative determination of boldine alkaloid in boldo leaf extracts by employing cyclic voltammetry, at a liquid/liquid interface as well as the validation of this methodology against the reference method, high performance liquid chromatography (HPLC), are reported in the present paper. The voltammetric analysis was performed successfully and economically using two kinds of liquid/liquid interfaces: water/1,2-dicholoroethane and water/PVC (polyvinyl chloride)-gelled 1,2-dichloroethane. Linear calibration curves in the concentration range of 1.04 × 10(-5)mol L(-1) to 5.19 × 10(-4)mol L(-1) were obtained with a detection limit equal to (6.1 ± 0.7) × 10(-5)mol L(-1) and the quantitative determination of this alkaloid, in complex matrixes such as boldo leaf extracts, by the electrochemical technique proposed was found to be equal to the values obtained using the standard HPLC method. The validation analysis of this methodology against HPLC demonstrated that accuracy, linearity, limit of detection (LOD), limit of quantification (LOQ), specificity and precision are acceptable. The electroanalytical technique proposed is economical and selective, involves simple equipment and can be applied for the quantitative determination of boldine alkaloid in complex matrixes such as leaf extracts without special drug separation. Moreover, cyclic voltammetry (CV) experiments applied at the liquid/liquid interface under different experimental conditions allowed us to study the transfer mechanism of boldine, and determine a value of pK(a)(w)=6.90 for protonated boldine, from the variation of voltammetric peak current with pH.

  4. Optimization of solid phase extraction clean up and validation of quantitative determination of corticosteroids in urine by liquid chromatography-tandem mass spectrometry

    DEFF Research Database (Denmark)

    Andersen, Jens Hinge; Hansen, Lene Gram; Pedersen, Mikael

    2008-01-01

    A solid phase extraction (SPE) method for extraction and clean up of 9 synthetic corticosteroids was optimized for quantification by reversed-phase high-performance liquid chromatography/negative electrospray ionisation mass spectrometry. Clean up was accomplished using a mixed mode polymeric...... strong anion exchange SPE column. The final method was validated according to EU regulations for determination of residues of veterinarian drugs in products of animal origin. Initial results showed a large difference in ion suppression between samples of porcine and bovine urine. The aim of optimisation...

  5. Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.

    Science.gov (United States)

    Christensen, Geoff A; Wymore, Ann M; King, Andrew J; Podar, Mircea; Hurt, Richard A; Santillan, Eugenio U; Soren, Ally; Brandt, Craig C; Brown, Steven D; Palumbo, Anthony V; Wall, Judy D; Gilmour, Cynthia C; Elias, Dwayne A

    2016-10-01

    Two genes, hgcA and hgcB, are essential for microbial mercury (Hg) methylation. Detection and estimation of their abundance, in conjunction with Hg concentration, bioavailability, and biogeochemistry, are critical in determining potential hot spots of methylmercury (MeHg) generation in at-risk environments. We developed broad-range degenerate PCR primers spanning known hgcAB genes to determine the presence of both genes in diverse environments. These primers were tested against an extensive set of pure cultures with published genomes, including 13 Deltaproteobacteria, nine Firmicutes, and nine methanogenic Archaea genomes. A distinct PCR product at the expected size was confirmed for all hgcAB(+) strains tested via Sanger sequencing. Additionally, we developed clade-specific degenerate quantitative PCR (qPCR) primers that targeted hgcA for each of the three dominant Hg-methylating clades. The clade-specific qPCR primers amplified hgcA from 64%, 88%, and 86% of tested pure cultures of Deltaproteobacteria, Firmicutes, and Archaea, respectively, and were highly specific for each clade. Amplification efficiencies and detection limits were quantified for each organism. Primer sensitivity varied among species based on sequence conservation. Finally, to begin to evaluate the utility of our primer sets in nature, we tested hgcA and hgcAB recovery from pure cultures spiked into sand and soil. These novel quantitative molecular tools designed in this study will allow for more accurate identification and quantification of the individual Hg-methylating groups of microorganisms in the environment. The resulting data will be essential in developing accurate and robust predictive models of Hg methylation potential, ideally integrating the geochemistry of Hg methylation to the microbiology and genetics of hgcAB IMPORTANCE: The neurotoxin methylmercury (MeHg) poses a serious risk to human health. MeHg production in nature is associated with anaerobic microorganisms. The recent

  6. Schneckenbecken dysplasia, radiology, and histology

    Energy Technology Data Exchange (ETDEWEB)

    Nikkels, P.G. [Rijksuniversiteit Utrecht (Netherlands). Dept. of Pathology; Stigter, R.H. [Div. of Neonatology and Obstetrics, University Medical Centre Utrecht (Netherlands); Knol, I.E. [Div. of Medical Genetics, University Medical Centre Utrecht (Netherlands); Harten, H.J. van der [Dept. of Pathology, Free University Amsterdam (Netherlands)

    2001-01-01

    To our knowledge this is the first report of Schneckenbecken dysplasia with the development of hydrops early in the second trimester. The radiological findings showed the typical hypoplastic iliac bones with medial extension and very flattened, on lateral view, oval-shaped vertebral bodies and short long bones. The histology showed hypercellular and hypervascular cartilage with chondrocytes with centrally located nucleus. The absence of the lacunar space as described before was also observed in some chondrocytes in our case. This male fetus was the product of consanguineous parents of Mediterranean origin compatible with autosomal recessive inheritance. (orig.)

  7. Selection and validation of candidate reference genes for quantitative real-time PCR studies in the shrimp Penaeus vannamei under viral infection.

    Science.gov (United States)

    Valenzuela-Castillo, Adán; Mendoza-Cano, Fernando; Enríquez-Espinosa, Tania; Grijalva-Chon, José Manuel; Sánchez-Paz, Arturo

    2017-06-01

    The decapod Penstyldensovirus 1 (PstDV-1) represents one of the most serious threats for penaeid shrimp farming. Studies aimed at defining relevant molecular effects of this virus over its host are imperative in the attempt to increase our understanding of its pathogenesis. Unfortunately, few studies have focused on the definition of the expression profile of reference genes in shrimp challenged with a pathogen. As a result, there are no studies on the selection of reference genes for the normalization of target gene expression changes yielding reliable data of the effects following PstDV-1 infection in shrimp. Therefore, the aim of the present study was to evaluate and validate the appropriateness of four candidate reference genes (ef1-α, gapdh, rpl8 and β-tubulin) for their use as reference genes to normalize qPCR data in gene expression studies of PstDV-1-shrimp interactions. By analyzing the expression profile of those genes, gapdh was validated as a suitable reference gene to normalize expression data gathered from a PstDV1-challenge, while ef1-α, β-tubulin, and rpl8 were identified as unstably expressed during the infectious process. The suitability of gapdh as a common reference gene in studies of host gene response to viral infections is underlined. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Optimisation and validation of ultra-high performance liquid chromatographic-tandem mass spectrometry method for qualitative and quantitative analysis of potato steroidal alkaloids.

    Science.gov (United States)

    Hossain, Mohammad B; Rai, Dilip K; Brunton, Nigel P

    2015-08-01

    An ultra-high performance liquid chromatographic-tandem mass spectrometry (UHPLC-MS/MS) method for quantification of potato steroidal alkaloids, namely α-solanine, α-chaconine, solanidine and demissidine was developed and validated. Three different column chemistries, i.e. ethylene bridged hybrid (BEH) C18, hydrophilic lipophilic interaction and amide columns, were assessed. The BEH C18 column showed best separation and sensitivity for the alkaloids. Validation data (inter-day and intra-day combined) for accuracy and recovery ranged from 94.3 to 107.7% and 97.0 to 103.5%, respectively. The accuracy data were within the acceptable range of 15% as outlined in the United States Food and Drug Administration (USFDA) guidelines. The recovery data were consistent and reproducible with a coefficient of variation (CV) ranging from 6.2 to 9.7%. In addition, precision of the method also met the criteria of the USFDA with CV values lower than 15% even at lower limit of quantification (LLOQ), while the permissible variation is considered acceptable below 20%. The limit of detection and LLOQ of the four alkaloids were in the range of 0.001-0.004μg/mL whereas the linearities of the standard curves were between 0.980 and 0.995.

  9. Development and validation of sensitive and rapid UPLC-MS/MS method for quantitative determination of daclatasvir in human plasma: Application to a bioequivalence study.

    Science.gov (United States)

    Rezk, Mamdouh R; Bendas, Ehab R; Basalious, Emad B; Karim, Iman A

    2016-09-05

    A rapid and sensitive UPLC-MS/MS method was developed and validated for determination of daclatasvir (DAC) in human plasma using sofosbuvir (SOF) as an internal standard (IS). The Xevo TQD LC-MS/MS was operated under the multiple-reaction monitoring mode using electrospray ionization. Precipitation with acetonitrile was used in sample preparation. The prepared samples were chromatographed on Acquity UPLC HSS C18 (50×2.1mm, 1.8μm) column by pumping 10mM ammonium formate (pH 3.5) and acetonitrile in an isocratic mode at a flow rate of 0.30ml/min. Method validation was performed as per the FDA guidelines and the standard curves were found to be linear in the range of 5-4000ng/ml for DAC. The intra-day and inter-day precision and accuracy results were within the acceptable limits. A very short run time of 1.2min made it possible to analyze more than 500 human plasma samples per day. The wider range of quantification of DAC allowed the applicability of the developed method for its determination in a bioequivalence study in human volunteers.

  10. Development and Validation of a New Stability-Indicating RP-UPLC Method for the Quantitative Determination of Bromfenac Sodium and Its Impurities in an Ophthalmic Dosage Form.

    Science.gov (United States)

    Koppala, Srinivasarao; Reddy, V Ranga; Anireddy, Jaya Shree

    2016-06-06

    A new rapid stability-indicating reversed-phase UPLC method was developed and validated for the determination of Bromfenac sodium and its impurities in Bromfenac ophthalmic solution. During literature search, only a few publications were found about Bromfenac sodium. There is no official monograph in the pharmacopoeias about Bromfenac sodium. Chromatographic separation has been achieved on a polar-embedded Waters Acquity BEH Shield RP18 (100 mm × 2.1 mm, 1.7 μm) column under gradient elution by using a binary mixture of potassium dihydrogen phosphate (0.01 M, pH 3.3) and acetonitrile (ACN) at a flow rate of 0.5 mL/min. Chromatogram was monitored at 265 nm using a photodiode array detector (PDA). The drug and its related impurities are eluted within 13 min. Resolution of Bromfenac sodium and all eight potential impurities have been achieved greater than 4.0 for all pairs of compounds. To prove the stability-indicating power of the method, the drug was subjected to hydrolytic (acid, alkaline and water), oxidative, photolytic and thermal stress, and the major degradation products were identified based on LC-MS analysis. The developed method was validated as per ICH guidelines with respect to specificity, linearity, limit of detection, limit of quantification, precision, accuracy and robustness.

  11. Quantitative Analysis of Norfloxacin in β-Cyclodextrin Inclusion Complexes--Development and Validation of a Stability-indicating HPLC Method.

    Science.gov (United States)

    Mendes, Cassiana; Buttchevitz, Aline; Kruger, Jéssica Henriques; Bernardi, Larissa Sakis; Oliveira, Paulo Renato; Silva, Marcos Antônio Segatto

    2015-01-01

    The aim of this study was to develop and validate a simple liquid-chromatography method, with good accuracy, reproducibility and sensitivity, for the quantification of norfloxacin in β-cyclodextrin inclusion complexes. In the method validation, the parameters evaluated were linearity, limits of detection and quantification, specificity, accuracy, precision and robustness. The stability-indication property of the method was evaluated through studies on the degradation under stress conditions. A method employing a simple mobile phase consisting of phosphate buffer (pH 3.0) and acetonitrile (86:14 v/v) was developed. Fluorescence detection was employed to minimize the influence of degradation products, due to its high sensitivity, selectivity and specificity. The method was specific, linear in the concentration range of 1 - 30 μg/mL, robust, precise and accurate. The proposed method was successfully applied in the determination of norfloxacin in inclusion complexes, thus aiding quality-control analysis in the future development of drug delivery systems.

  12. Heterogeneous patterns of DNA methylation-based field effects in histologically normal prostate tissue from cancer patients.

    Science.gov (United States)

    Møller, Mia; Strand, Siri Hundtofte; Mundbjerg, Kamilla; Liang, Gangning; Gill, Inderbir; Haldrup, Christa; Borre, Michael; Høyer, Søren; Ørntoft, Torben Falck; Sørensen, Karina Dalsgaard

    2017-01-13

    Prostate cancer (PC) diagnosis is based on histological evaluation of prostate needle biopsies, which have high false negative rates. Here, we investigated if cancer-associated epigenetic field effects in histologically normal prostate tissue may be used to increase sensitivity for PC. We focused on nine genes (AOX1, CCDC181 (C1orf114), GABRE, GAS6, HAPLN3, KLF8, MOB3B, SLC18A2, and GSTP1) known to be hypermethylated in PC. Using quantitative methylation-specific PCR, we analysed 66 malignant and 134 non-malignant tissue samples from 107 patients, who underwent ultrasound-guided prostate biopsy (67 patients had at least one cancer-positive biopsy, 40 had exclusively cancer-negative biopsies). Hypermethylation was detectable for all genes in malignant needle biopsy samples (AUC: 0.80 to 0.98), confirming previous findings in prostatectomy specimens. Furthermore, we identified a four-gene methylation signature (AOX1xGSTP1xHAPLN3xSLC18A2) that distinguished histologically non-malignant biopsies from patients with vs. without PC in other biopsies (AUC = 0.65; sensitivity = 30.8%; specificity = 100%). This signature was validated in an independent patient set (59 PC, 36 adjacent non-malignant, and 9 normal prostate tissue samples) analysed on Illumina 450 K methylation arrays (AUC = 0.70; sensitivity = 40.6%; specificity = 100%). Our results suggest that a novel four-gene signature may be used to increase sensitivity for PC diagnosis through detection of epigenetic field effects in histologically non-malignant prostate tissue samples.

  13. Development & validation of a quantitative anti-protective antigen IgG enzyme linked immunosorbent assay for serodiagnosis of cutaneous anthrax

    Directory of Open Access Journals (Sweden)

    N Ghosh

    2015-01-01

    Full Text Available Background & objectives: Anthrax caused by Bacillus anthracis is primarily a disease of herbivorous animals, although several mammals are vulnerable to it. ELISA is the most widely accepted serodiagnostic assay for large scale surveillance of cutaneous anthrax. The aims of this study were to develop and evaluate a quantitative ELISA for determination of IgG antibodies against B. anthracis protective antigen (PA in human cutaneous anthrax cases. Methods: Quantitative ELISA was developed using the recombinant PA for coating and standard reference serum AVR801 for quantification. A total of 116 human test and control serum samples were used in the study. The assay was evaluated for its precision, accuracy and linearity. Results: The minimum detection limit and lower limit of quantification of the assay for anti-PA IgG were 3.2 and 4 µg/ml, respectively. The serum samples collected from the anthrax infected patients were found to have anti-PA IgG concentrations of 5.2 to 166.3 µg/ml. The intra-assay precision per cent CV within an assay and within an operator ranged from 0.99 to 7.4 per cent and 1.7 to 3.9 per cent, respectively. The accuracy of the assay was high with a per cent error of 6.5 - 24.1 per cent. The described assay was found to be linear between the range of 4 to 80 ng/ml (R [2] =0.9982; slope=0.9186; intercept = 0.1108. Interpretation & conclusions: The results suggested that the developed assay could be a useful tool for quantification of anti-PA IgG response in human after anthrax infection or vaccination.

  14. Development & validation of a quantitative anti-protective antigen IgG enzyme linked immunosorbent assay for serodiagnosis of cutaneous anthrax.

    Science.gov (United States)

    Ghosh, N; Gunti, D; Lukka, H; Reddy, B R; Padmaja, Jyothi; Goel, A K

    2015-08-01

    Anthrax caused by Bacillus anthracis is primarily a disease of herbivorous animals, although several mammals are vulnerable to it. ELISA is the most widely accepted serodiagnostic assay for large scale surveillance of cutaneous anthrax. The aims of this study were to develop and evaluate a quantitative ELISA for determination of IgG antibodies against B. anthracis protective antigen (PA) in human cutaneous anthrax cases. Quantitative ELISA was developed using the recombinant PA for coating and standard reference serum AVR801 for quantification. A total of 116 human test and control serum samples were used in the study. The assay was evaluated for its precision, accuracy and linearity. The minimum detection limit and lower limit of quantification of the assay for anti-PA IgG were 3.2 and 4 µg/ml, respectively. The serum samples collected from the anthrax infected patients were found to have anti-PA IgG concentrations of 5.2 to 166.3 µg/ml. The intra-assay precision per cent CV within an assay and within an operator ranged from 0.99 to 7.4 per cent and 1.7 to 3.9 per cent, respectively. The accuracy of the assay was high with a per cent error of 6.5 - 24.1 per cent. The described assay was found to be linear between the range of 4 to 80 ng/ml (R [2] = 0.9982; slope = 0.9186; intercept = 0.1108). The results suggested that the developed assay could be a useful tool for quantification of anti-PA IgG response in human after anthrax infection or vaccination.

  15. Validity of using a 3-dimensional PET scanner during inhalation of 15O-labeled oxygen for quantitative assessment of regional metabolic rate of oxygen in man.

    Science.gov (United States)

    Hori, Yuki; Hirano, Yoshiyuki; Koshino, Kazuhiro; Moriguchi, Tetsuaki; Iguchi, Satoshi; Yamamoto, Akihide; Enmi, Junichiro; Kawashima, Hidekazu; Zeniya, Tsutomu; Morita, Naomi; Nakagawara, Jyoji; Casey, Michael E; Iida, Hidehiro

    2014-09-21

    Use of 15O labeled oxygen (15O2) and positron emission tomography (PET) allows quantitative assessment of the regional metabolic rate of oxygen (CMRO2) in vivo, which is essential to understanding the pathological status of patients with cerebral vascular and neurological disorders. The method has, however, been challenging, when a 3D PET scanner is employed, largely attributed to the presence of gaseous radioactivity in the trachea and the inhalation system, which results in a large amount of scatter and random events in the PET assessment. The present study was intended to evaluate the adequacy of using a recently available commercial 3D PET scanner in the assessment of regional cerebral radioactivity distribution during an inhalation of 15O2. Systematic experiments were carried out on a brain phantom. Experiments were also performed on a healthy volunteer following a recently developed protocol for simultaneous assessment of CMRO2 and cerebral blood flow, which involves sequential administration of 15O2 and C15O2. A particular intention was to evaluate the adequacy of the scatter-correction procedures. The phantom experiment demonstrated that errors were within 3% at the practically maximum radioactivity in the face mask, with the greatest radioactivity in the lung. The volunteer experiment demonstrated that the counting rate was at peak during the 15O gas inhalation period, within a verified range. Tomographic images represented good quality over the entire FOV, including the lower part of the cerebral structures and the carotid artery regions. The scatter-correction procedures appeared to be important, particularly in the process to compensate for the scatter originating outside the FOV. Reconstructed images dramatically changed if the correction was carried out using inappropriate procedures. This study demonstrated that accurate reconstruction could be obtained when the scatter compensation was appropriately carried out. This study also suggested the

  16. Validation of housekeeping genes for quantitative real-time PCR in in-vivo and in-vitro models of cerebral ischaemia

    Directory of Open Access Journals (Sweden)

    Serena Joaquín

    2009-06-01

    Full Text Available Abstract Background Studies of gene expression in experimental cerebral ischaemia models can contribute to understanding the pathophysiology of brain ischaemia and to identifying prognostic markers and potential therapeutic targets. The normalization of relative qRT-PCR data using a suitable reference gene is a crucial prerequisite for obtaining reliable conclusions. No validated housekeeping genes have been reported for the relative quantification of the mRNA expression profile activated in in-vitro ischaemic conditions, whereas for the in-vivo model different reference genes have been used. The present study aims to determine the expression stability of ten housekeeping genes (Gapdh, β2m, Hprt, Ppia, Rpl13a, Oaz1, 18S rRNA, Gusb, Ywhaz and Sdha to establish their suitability as control genes for in-vitro and in-vivo cerebral ischaemia models. Results The expression stability of the candidate reference genes was evaluated using the 2-ΔC'T method and ANOVA followed by Dunnett's test. For the in-vitro model using primary cultures of rat astrocytes, all genes analysed except for Rpl13a and Sdha were found to have significantly different levels of mRNA expression. These different levels were also found in the case of the in-vivo model of pMCAO in rats except for Hprt, Sdha and Ywhaz mRNA, where the expression did not vary. Sdha and Ywhaz were identified by geNorm and NormFinder as the two most stable genes. Conclusion We have validated endogenous control genes for qRT-PCR analysis of gene expression in in-vitro and in-vivo cerebral ischaemia models. For normalization purposes, Rpl13a and Sdha are found to be the most suitable genes for the in-vitro model and Sdha and Ywhaz for the in-vivo model. Genes previously used as housekeeping genes for the in-vivo model in the literature were not validated as good control genes in the present study, showing the need for careful evaluation for each new experimental setup.

  17. Histology of the first fish

    Science.gov (United States)

    Smith, M.P.; Sansom, I.J.; Repetski, J.E.

    1996-01-01

    THE first description of Anatolepis Bockelie & Fortey was from early Ordovician sediments of Ny Friesland, Spitsbergen1,2, but the genus is now known from many localities in North America and Greenland, ranging in age from the Late Cambrian period to the Early Ordovician3-6. Although initially interpreted as an agnathan fish2,3 that predated other representatives7, this has been widely disputed because the available histological data were unconvincing6,8-10 and the scales fell outside the known morphological range of other accepted early vertebrates9-11. Further doubt was cast upon the vertebrate affinity of Anatolepis when specimens from East Greenland were interpreted as the cuticular fragments of aglaspid arthropods6, although this interpretation has also been refuted12. Here we report on the morphology and histology of large collections of Anatolepis, and demonstrate the presence of dentine, a tissue unique to vertebrates, confirming that the taxon is both a vertebrate and the oldest known fish.

  18. A histological study of prostate

    Directory of Open Access Journals (Sweden)

    Ashfaq U. Hassan

    2013-08-01

    Full Text Available The work of anatomists and pathologists in the role of study of prostate has been significant. Starting from earlier times till modern time, the study of prostate has been a dynamic one and the basic anatomical knowledge of the prostate has undergone much change apart from the new techniques, micro invasive procedures and the chemotherapeutic approach for various disorders of the gland. The present study was based on the microscopic examination of Prostatic tissue of individuals with individual tissues of different age groups. The present study involved 40 cases which were further subdivided into various age groups and characteristic histological changes were noted. The study presents an assessment of age changes in prostate in elderly in Kashmiri population with pathological significance. Besides the histological study is of great importance in staging of diseases of prostate and especially in modern era where the incidence and prevalence of prostatic diseases is on rise. [Int J Res Med Sci 2013; 1(4.000: 557-562

  19. Validation and application of a quantitative real-time PCR assay to detect common wheat adulteration of durum wheat for pasta production.

    Science.gov (United States)

    Carloni, Elisa; Amagliani, Giulia; Omiccioli, Enrica; Ceppetelli, Veronica; Del Mastro, Michele; Rotundo, Luca; Brandi, Giorgio; Magnani, Mauro

    2017-06-01

    Pasta is the Italian product par excellence and it is now popular worldwide. Pasta of a superior quality is made with pure durum wheat. In Italy, addition of Triticum aestivum (common wheat) during manufacturing is not allowed and, without adequate labeling, its presence is considered an adulteration. PCR-related techniques can be employed for the detection of common wheat contaminations. In this work, we demonstrated that a previously published method for the detection of T. aestivum, based on the gliadin gene, is inadequate. Moreover, a new molecular method, based on DNA extraction from semolina and real-time PCR determination of T. aestivum in Triticum spp., was validated. This multiplex real-time PCR, based on the dual-labeled probe strategy, guarantees target detection specificity and sensitivity in a short period of time. Moreover, the molecular analysis of common wheat contamination in commercial wheat and flours is described for the first time.

  20. Development and Validation of UV-Visible Spectrophotometric Baseline Manipulation Method for Simultaneous Quantitation of Tenofovir Disoproxil Fumarate and Emtricitabine in Pharmaceutical Dosage Form

    Directory of Open Access Journals (Sweden)

    Vishnu P. Choudhari

    2013-01-01

    Full Text Available A simple, economical, precise, and accurate new UV-visible spectrophotometric baseline manipulation method for simultaneous determination of tenofovir disoproxil fumarate (TE and emtricitabine (EM in combined tablet dosage form has been developed. The method is based on baseline manipulation (difference spectroscopy where amplitudes at 261 and 289.9 nm were selected to determine TE and EM, respectively, in combined formulation, and distilled water was used as solvent. Both drugs obey Beer’s law in the concentration ranges of 4–20 μg/mL for TE and 6–30 μg/mL for EM. The results of analysis have been validated statistically, and recovery studies confirmed the accuracy of the proposed method which was carried out by following the ICH guidelines.

  1. Novel Selectivity-Based Forensic Toxicological Validation of a Paper Spray Mass Spectrometry Method for the Quantitative Determination of Eight Amphetamines in Whole Blood

    Science.gov (United States)

    Teunissen, Sebastiaan F.; Fedick, Patrick W.; Berendsen, Bjorn J. A.; Nielen, Michel W. F.; Eberlin, Marcos N.; Graham Cooks, R.; van Asten, Arian C.

    2017-09-01

    Paper spray tandem mass spectrometry is used to identify and quantify eight individual amphetamines in whole blood in 1.3 min. The method has been optimized and fully validated according to forensic toxicology guidelines, for the quantification of amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine (MDA), 3,4-methylenedioxy-N-methylamphetamine (MDMA), 3,4-methylenedioxy-N-ethylamphetamine (MDEA), para-methoxyamphetamine (PMA), para-methoxymethamphetamine (PMMA), and 4-fluoroamphetamine (4-FA). Additionally, a new concept of intrinsic and application-based selectivity is discussed, featuring increased confidence in the power to discriminate the amphetamines from other chemically similar compounds when applying an ambient mass spectrometric method without chromatographic separation. Accuracy was within ±15% and average precision was better than 15%, and better than 20% at the LLOQ. Detection limits between 15 and 50 ng/mL were obtained using only 12 μL of whole blood. [Figure not available: see fulltext.

  2. ACA-Pro: calibration protocol for quantitative diffuse reflectance spectroscopy. Validation on contact and noncontact probe- and CCD-based systems

    Science.gov (United States)

    Sorgato, Veronica; Berger, Michel; Emain, Charlotte; Vever-Bizet, Christine; Dinten, Jean-Marc; Bourg-Heckly, Geneviève; Planat-Chrétien, Anne

    2016-06-01

    We have developed an adaptive calibration algorithm and protocol (ACA-Pro) that corrects from the instrumental response of various spatially resolved diffuse reflectance spectroscopy (DRSsr) systems to enable the quantification of absorption and scattering properties based on a Monte Carlo-based look-up-table approach. The protocol involves the use of a calibration reference base built with measurements of a range of different diffusive intralipid phantoms. Moreover, an advanced strategy was established to take into account the experimental variations with an additional measurement of a common solid material, allowing the use of a single calibration reference base for all experiments. The ACA-Pro is validated in contact and noncontact probe-based DRSsr systems. Furthermore, the first results of a setup replacing the probe with a CCD detector are shown to confirm the robustness of the approach.

  3. Quantitative Ultrasound for Staging of Hepatic Steatosis in Patients on Home Parenteral Nutrition Validated with Magnetic Resonance Spectroscopy: A Feasibility Study.

    Science.gov (United States)

    Weijers, Gerrit; Wanten, Geert; Thijssen, Johan M; van der Graaf, Marinette; de Korte, Chris L

    2016-03-01

    Patients on home parenteral nutrition are at risk for developing liver dysfunction, which is due partly to the accumulation of lipids in the liver (steatosis) and may progress to end-stage liver disease with overt liver failure. Therefore, a timely diagnosis with easy access to repeated assessment of the degree of liver steatosis is of great importance. A pilot study was performed in 14 patients on long-term home parenteral nutrition using the computer-aided ultrasound method. Ultrasound radio frequency data were acquired using a phased array transducer and were converted into conventional B-mode images. All patients were subjected to proton magnetic resonance spectroscopy measurement of liver fat content for reference. Computer-aided ultrasound parameters similar to those in a previous validation study in cows revealed significant correlations with fat content measured by magnetic resonance spectroscopy. The most significant parameters were the residual attenuation coefficient (R = 0.95, p ultrasound for staging of hepatic steatosis.

  4. A simple validated RP-HPLC bioanalytical method for the quantitative determination of a novel valproic acid arylamide derivative in rat hepatic microsomes.

    Science.gov (United States)

    Silva-Trujillo, Arianna; Correa-Basurto, José; Romero-Castro, Aurelio; Albores, Arnulfo; Mendieta-Wejebe, Jessica Elena

    2015-04-01

    A simple and specific bioanalytical method based on reversed-phase high-performance liquid chromatography (RP-HPLC) coupled with ultraviolet detection was developed and validated for the determination of a novel valproic acid arylamide, N-(2-hydroxyphenyl)-2-propylpentanamide (HO-AAVPA) in rat hepatic microsomes (a subcellular fraction containing phase I enzymes, especially cytochrome P450). The chromatographic separation was achieved using a reversed-phase Zorbax SB-C18 column and a mobile phase of acetic acid in water (0.2% v/v) and acetonitrile (40:60 v/v) with a flow rate of 0.5 mL/min. The calibration curve was linear over the range of 882-7060 ng/mL (r(2)  = 0.9987), and the lower limit of quantification and the lower limit of determination were found to be 882 and 127.99 ng/mL, respectively. The method was validated with excellent sensitivity, and intra-day accuracy and precision varied from 93.79 to 93.12%, and from 2.12 to 4.36%, respectively. The inter-day accuracy and precision ranged from 93.29 to 97.30% and from 0.68 to 3.60%, respectively. The recovery of HO-AAVPA was measured between 91.36 and 97.98%. The assay was successfully applied to the analysis of kinetic metabolism and pharmacokinetic parameters in vitro by a substrate depletion approach.

  5. Reliability and validity in research.

    Science.gov (United States)

    Roberts, Paula; Priest, Helena

    This article examines reliability and validity as ways to demonstrate the rigour and trustworthiness of quantitative and qualitative research. The authors discuss the basic principles of reliability and validity for readers who are new to research.

  6. Comparative validation using quantitative real-time PCR (qPCR and conventional PCR of bovine semen centrifuged in continuous density gradient

    Directory of Open Access Journals (Sweden)

    M.V. Resende

    2011-06-01

    Full Text Available The objective of the present study was to determine the sperm enrichment with X-bearing spermatozoa, after one centrifugation in a Percoll or OptiPrep continuous density gradient, using quantitative real-time polymerase chain reaction (qPCR of sperm DNA and resultant in vitro-produced bovine embryos by PCR. Frozen/thawed sperm was layered on density gradients and the tubes were centrifuged. Supernatants were gently aspirated and the sperm recovered from the bottom of the tubes. Cleavage and blastocyst rates were determined through in vitro production of embryos and PCR was performed to identify the embryos' genetic sex. A difference in blastocyst rate was found in the Percoll treatment compared to OptiPrep (P<0.05. The percentage of female embryos in the Percoll and OptiPrep groups was 62.0% and 47.1%, respectively. These results were confirmed by qPCR of spermatozoa DNA and underestimation was seen only in the Percoll group. It was possible to sexing sperm using simple approach.

  7. Validation of housekeeping genes as an internal control for gene expression studies in Giardia lamblia using quantitative real-time PCR.

    Science.gov (United States)

    Marcial-Quino, Jaime; Fierro, Francisco; De la Mora-De la Mora, Ignacio; Enríquez-Flores, Sergio; Gómez-Manzo, Saúl; Vanoye-Carlo, America; Garcia-Torres, Itzhel; Sierra-Palacios, Edgar; Reyes-Vivas, Horacio

    2016-04-25

    The analysis of transcript levels of specific genes is important for understanding transcriptional regulation and for the characterization of gene function. Real-time quantitative reverse transcriptase PCR (RT-qPCR) has become a powerful tool to quantify gene expression. The objective of this study was to identify reliable housekeeping genes in Giardia lamblia. Twelve genes were selected for this purpose, and their expression was analyzed in the wild type WB strain and in two strains with resistance to nitazoxanide (NTZ) and metronidazole (MTZ), respectively. RefFinder software analysis showed that the expression of the genes is different in the three strains. The integrated data from the four analyses showed that the NADH oxidase (NADH) and aldolase (ALD) genes were the most steadily expressed genes, whereas the glyceraldehyde-3-phosphate dehydrogenase gene was the most unstable. Additionally, the relative expression of seven genes were quantified in the NTZ- and MTZ-resistant strains by RT-qPCR, using the aldolase gene as the internal control, and the results showed a consistent differential pattern of expression in both strains. The housekeeping genes found in this work will facilitate the analysis of mRNA expression levels of other genes of interest in G. lamblia.

  8. Screening and Validation of Housekeeping Genes of the Root and Cotyledon of Cunninghamia lanceolata under Abiotic Stresses by Using Quantitative Real-Time PCR

    Directory of Open Access Journals (Sweden)

    Wenlong Bao

    2016-07-01

    Full Text Available Cunninghamia lanceolata (Chinese fir is a fast-growing and commercially important conifer of the Cupressaceae family. Due to the unavailability of complete genome sequences and relatively poor genetic background information of the Chinese fir, it is necessary to identify and analyze the expression levels of suitable housekeeping genes (HKGs as internal reference for precise analysis. Based on the results of database analysis and transcriptome sequencing, we have chosen five candidate HKGs (Actin, GAPDH, EF1a, 18S rRNA, and UBQ with conservative sequences in the Chinese fir and related species for quantitative analysis. The expression levels of these HKGs in roots and cotyledons under five different abiotic stresses in different time intervals were measured by qRT-PCR. The data were statistically analyzed using the following algorithms: NormFinder, BestKeeper, and geNorm. Finally, RankAggreg was applied to merge the sequences generated from three programs and rank these according to consensus sequences. The expression levels of these HKGs showed variable stabilities under different abiotic stresses. Among these, Actin was the most stable internal control in root, and GAPDH was the most stable housekeeping gene in cotyledon. We have also described an experimental procedure for selecting HKGs based on the de novo sequencing database of other non-model plants.

  9. Selection and validation of reference genes for quantitative gene expression studies in Erythroxylum coca [v1; ref status: indexed, http://f1000r.es/y1

    Directory of Open Access Journals (Sweden)

    Teresa Docimo

    2013-02-01

    Full Text Available Real-time quantitative PCR is a powerful technique for the investigation of comparative gene expression, but its accuracy and reliability depend on the reference genes used as internal standards. Only genes that show a high level of expression stability are suitable for use as reference genes, and these must be identified on a case-by-case basis. Erythroxylum coca produces and accumulates high amounts of the pharmacologically active tropane alkaloid cocaine (especially in the leaves, and is an emerging model for the investigation of tropane alkaloid biosynthesis. The identification of stable internal reference genes for this species is important for its development as a model species, and would enable comparative analysis of candidate biosynthetic genes in the different tissues of the coca plant. In this study, we evaluated the expression stability of nine candidate reference genes in E. coca (Ec6409, Ec10131, Ec11142, Actin, APT2, EF1α, TPB1, Pex4, Pp2aa3. The expression of these genes was measured in seven tissues (flowers, stems, roots and four developmental leaf stages and the stability of expression was assessed using three algorithms (geNorm, NormFinder and BestKeeper. From our results we conclude that Ec10131 and TPB1 are the most appropriate internal reference genes in leaves (where the majority of cocaine is produced, while Ec10131 and Ec6409 are the most suitable internal reference genes across all of the tissues tested.

  10. Development, evaluation, and in-vivo validation of two non-invasive methods for quantitation of activity and dosimetry of monoclonal antibodies in humans

    Energy Technology Data Exchange (ETDEWEB)

    Hammond, N.D.; Moldofsky, P.J.; Exten, R.E.; Gatenby, R.A.; Broder, G.J.

    1985-05-01

    The authors have applied both a conjugate view imaging method and a first pass study for quantitation of absolute I-131 activity in lesions and normal tissue of patients with colon carcinoma in order to study biological clearance of the I-131 F(ab)'/sub 2/ fragments of mouse monoclonal antibody and the resultant dosimetry. Both methods require a transmission scan for determining patient attenuation and measurement of patient lesion or organ size in the region of interest. The conjugate view method is analyzed for both SPECT and planar imaging. The percent error of both methods relates to lesion size and absolute activity when compared to actual well-counter assayed samples of malignant and normal tissue obtained from CT-guided needle biopsies or surgical specimens. Dosimetric evaluation was based on determination of activity, clearance from computer-generated time-activity curves and lesion or organ volumes from volumetric CT scan data. The dose to the thyroid gland was calculated for one population receiving Lugol's solution 3 days prior and for the other who received Lugol's at the time of administration. Data showed no significant difference in absorbed thyroid dose. Lastly, the absolute uptake of I-131, lesion to background ratios, and the dosimetry data were compared for three different monoclonal antibody fragments.

  11. Selection and validation of reference genes for quantitative real-time PCR in buckwheat (Fagopyrum esculentum) based on transcriptome sequence data.

    Science.gov (United States)

    Demidenko, Natalia V; Logacheva, Maria D; Penin, Aleksey A

    2011-05-12

    Quantitative reverse transcription PCR (qRT-PCR) is one of the most precise and widely used methods of gene expression analysis. A necessary prerequisite of exact and reliable data is the accurate choice of reference genes. We studied the expression stability of potential reference genes in common buckwheat (Fagopyrum esculentum) in order to find the optimal reference for gene expression analysis in this economically important crop. Recently sequenced buckwheat floral transcriptome was used as source of sequence information. Expression stability of eight candidate reference genes was assessed in different plant structures (leaves and inflorescences at two stages of development and fruits). These genes are the orthologs of Arabidopsis genes identified as stable in a genome-wide survey gene of expression stability and a traditionally used housekeeping gene GAPDH. Three software applications--geNorm, NormFinder and BestKeeper--were used to estimate expression stability and provided congruent results. The orthologs of AT4G33380 (expressed protein of unknown function, Expressed1), AT2G28390 (SAND family protein, SAND) and AT5G46630 (clathrin adapter complex subunit family protein, CACS) are revealed as the most stable. We recommend using the combination of Expressed1, SAND and CACS for the normalization of gene expression data in studies on buckwheat using qRT-PCR. These genes are listed among five the most stably expressed in Arabidopsis that emphasizes utility of the studies on model plants as a framework for other species.

  12. Selection and validation of reference genes for quantitative real-time PCR in buckwheat (Fagopyrum esculentum based on transcriptome sequence data.

    Directory of Open Access Journals (Sweden)

    Natalia V Demidenko

    Full Text Available Quantitative reverse transcription PCR (qRT-PCR is one of the most precise and widely used methods of gene expression analysis. A necessary prerequisite of exact and reliable data is the accurate choice of reference genes. We studied the expression stability of potential reference genes in common buckwheat (Fagopyrum esculentum in order to find the optimal reference for gene expression analysis in this economically important crop. Recently sequenced buckwheat floral transcriptome was used as source of sequence information. Expression stability of eight candidate reference genes was assessed in different plant structures (leaves and inflorescences at two stages of development and fruits. These genes are the orthologs of Arabidopsis genes identified as stable in a genome-wide survey gene of expression stability and a traditionally used housekeeping gene GAPDH. Three software applications--geNorm, NormFinder and BestKeeper--were used to estimate expression stability and provided congruent results. The orthologs of AT4G33380 (expressed protein of unknown function, Expressed1, AT2G28390 (SAND family protein, SAND and AT5G46630 (clathrin adapter complex subunit family protein, CACS are revealed as the most stable. We recommend using the combination of Expressed1, SAND and CACS for the normalization of gene expression data in studies on buckwheat using qRT-PCR. These genes are listed among five the most stably expressed in Arabidopsis that emphasizes utility of the studies on model plants as a framework for other species.

  13. Development and validation of a novel stability-indicating HPLC method for the quantitative determination of eleven related substances in ezetimibe drug substance and drug product.

    Science.gov (United States)

    Luo, Zhiqiang; Deng, Zhongqing; Liu, Yang; Wang, Guopeng; Yang, Wenning; Hou, Chengbo; Tang, Minming; Yang, Ruirui; Zhou, Huaming

    2015-07-01

    Ezetimibe is a novel lipid-lowering agent that inhibits intestinal absorption of dietary and biliary cholesterol. In the present work, a simple, sensitive and reproducible gradient reverse phase high performance liquid chromatographic (RP-HPLC) method for separation and determination of the related substances of ezetimibe was developed and validated. Eleven potential process-related impurities (starting materials, (3S,4S,3'S)-isomer, degradants and byproducts) were identified in the crude samples. Tentative structures for all the impurities were assigned primarily based on comparison of their retention time and mass spectrometric data with that of available standards and references. This method can be applied to routine analysis in quality control of both bulk drugs and commercial tablets. Separation of all these compounds was performed on a Phenomenex Luna Phenyl-Hexyl (100mm×4.6mm, 5μm) analytical column. The mobile phase-A consists of acetonitrile-water (pH adjusted to 4.0 with phosphoric acid)-methanol at 15:75:10 (v/v/v), and mobile phase-B contains acetonitrile. The eluted compounds were monitored at 210nm. Ezetimibe was subjected to hydrolytic, acid, base, oxidative, photolytic and thermal stress conditions as per ICH serves to generate degradation products that can be used as a worst case to assess the analytical method performance. The drug showed extensive degradation in thermal, acid, oxidative, base and hydrolytic stress conditions, while it was stable to photolytic degradation conditions. The main degradation product formed under thermal, acid, oxidative, base and hydrolytic stress conditions corresponding to (2R,3R,6S)-N, 6-bis(4-fluorophenyl)-2-(4-hydroxyphenyl)-oxane-3-carboxamide (Ezetimibe tetrahydropyran impurity) was characterized by LC-MS/MS analysis. The degradation products were well resolved from the main peak and its impurities, thus proved the stability-indicating power of the method. The developed method was validated as per

  14. Bone histology in chronic kidney disease-related mineral and bone disorder.

    Science.gov (United States)

    Kazama, Junichiro James

    2011-06-01

    A quantitative histological analysis of biopsied bone samples is currently regarded as the gold standard for a diagnosing procedure for bone diseases associated with chronic kidney disease-related mineral and bone disorder. Conventionally, "bone cell activities" and "bone mineralization" are applied as two independent assessment axes, and the histology results are classified into five categories according to these axes. Recently, a new bone histology classification system called the Turnover-Mineralization-Volume system, which applied "cancellous bone volume" as another major assessing axis, was advocated; however, both classification systems have many unsolved problems. Clinicians must realize the limitations in evaluating bone metabolism by bone histology. We will need to establish a new classification method for renal bone diseases independent of histological findings.

  15. Validated liquid chromatography-tandem mass spectrometry method for quantitative determination of dauricine in human plasma and its application to pharmacokinetic study.

    Science.gov (United States)

    Liu, Xiaoying; Liu, Qian; Wang, Dongmei; Wang, Xueya; Zhang, Peng; Xu, Haiyan; Zhao, Hui; Zhao, Huaiqing

    2010-05-01

    A highly sensitive and selective LC-MS/MS method was developed and validated for the determination of dauricine in human plasma, using protopine as internal standard (IS). The analyte and IS were extracted by liquid-liquid extraction and analyzed by LC-MS/MS. Chromatographic separation was performed on Agilent TC-C(18) column with a mobile phase of methanol-water-glacial acetic acid (60:40:0.8, v/v/v) at a flow rate of 0.7 mL/min. Detection was performed on a triple quadrupole tandem mass spectrum by multiple reaction monitoring (MRM) mode using the electrospray ionization technique in positive mode. The method was linear over the concentration range of 1-200 ng/mL. The lower limit of quantification (LLOQ) was 1 ng/mL in human plasma with acceptable precision and accuracy. The intra- and inter-day precision was less than 5.9% determined from quality control (QC) samples at concentrations of 2.0, 20.0 and 160 ng/mL, and the accuracy was within +/-9.9%. This method was successfully applied for the evaluation of pharmacokinetics of dauricine after oral doses of 100, 300 and 600 mg phenolic alkaloids of menispermum dauricum tablet (PAMDT) to 12 Chinese healthy volunteers.

  16. Validation of the World Health Organization Enzyme-Linked Immunosorbent Assay for the Quantitation of Immunoglobulin G Serotype-Specific Anti-Pneumococcal Antibodies in Human Serum.

    Science.gov (United States)

    Lee, Hyunju; Lim, Soo Young; Kim, Kyung Hyo

    2017-10-01

    The World Health Organization (WHO) enzyme-linked immunosorbent assay (ELISA) guideline is currently accepted as the gold standard for the evaluation of immunoglobulin G (IgG) antibodies specific to pneumococcal capsular polysaccharide. We conducted validation of the WHO ELISA for 7 pneumococcal serotypes (4, 6B, 9V, 14, 18C, 19F, and 23F) by evaluating its specificity, precision (reproducibility and intermediate precision), accuracy, spiking recovery test, lower limit of quantification (LLOQ), and stability at the Ewha Center for Vaccine Evaluation and Study, Seoul, Korea. We found that the specificity, reproducibility, and intermediate precision were within acceptance ranges (reproducibility, coefficient of variability [CV] ≤ 15%; intermediate precision, CV ≤ 20%) for all serotypes. Comparisons between the provisional assignments of calibration sera and the results from this laboratory showed a high correlation > 94% for all 7 serotypes, supporting the accuracy of the ELISA. The spiking recovery test also fell within an acceptable range. The quantification limit, calculated using the LLOQ, for each of the serotypes was 0.05-0.093 μg/mL. The freeze-thaw stability and the short-term temperature stability were also within an acceptable range. In conclusion, we showed good performance using the standardized WHO ELISA for the evaluation of serotype-specific anti-pneumococcal IgG antibodies; the WHO ELISA can evaluate the immune response against pneumococcal vaccines with consistency and accuracy. © 2017 The Korean Academy of Medical Sciences.

  17. Validation of Simultaneous Quantitative Method of HIV Protease Inhibitors Atazanavir, Darunavir and Ritonavir in Human Plasma by UPLC-MS/MS

    Directory of Open Access Journals (Sweden)

    Tulsidas Mishra

    2014-01-01

    Full Text Available Objectives. HIV protease inhibitors are used in the treatment of patients suffering from AIDS and they act at the final stage of viral replication by interfering with the HIV protease enzyme. The paper describes a selective, sensitive, and robust method for simultaneous determination of three protease inhibitors atazanavir, darunavir and ritonavir in human plasma by ultra performance liquid chromatography-tandem mass spectrometry. Materials and Methods. The sample pretreatment consisted of solid phase extraction of analytes and their deuterated analogs as internal standards from 50 μL human plasma. Chromatographic separation of analytes was performed on Waters Acquity UPLC C18 (50 × 2.1 mm, 1.7 μm column under gradient conditions using 10 mM ammonium formate, pH 4.0, and acetonitrile as the mobile phase. Results. The method was established over a concentration range of 5.0–6000 ng/mL for atazanavir, 5.0–5000 ng/mL for darunavir and 1.0–500 ng/mL for ritonavir. Accuracy, precision, matrix effect, recovery, and stability of the analytes were evaluated as per US FDA guidelines. Conclusions. The efficiency of sample preparation, short analysis time, and high selectivity permit simultaneous estimation of these inhibitors. The validated method can be useful in determining plasma concentration of these protease inhibitors for therapeutic drug monitoring and in high throughput clinical studies.

  18. Development and validation of a stability-indicating RP-UPLC method for the quantitative analysis of nabumetone in tablet dosage form.

    Science.gov (United States)

    Sethi, Neha; Anand, Ankit; Chandrul, Kaushal K; Jain, Garima; Srinivas, Kona S

    2012-02-01

    High efficiency and less run time are the basic requirements of high-speed chromatographic separations. To fulfill these requirements, a new separation technique, ultra-performance liquid chromatography (UPLC), has shown promising developments. A rapid, specific, sensitive, and precise reverse-phase UPLC method is developed for the determination of nabumetone in tablet dosage form. In this work, a new isocratic chromatographic method is developed. The newly developed method is applicable for assay determination of the active pharmaceutical ingredient. The chromatographic separation is achieved on a Waters Acquity BEH column (100 mm, i.d., 2.1 mm, 1.7 µm) within a short runtime of 2 min using a mobile phase of 5 mM ammonium acetate-acetonitrile (25:75, v/v), at a flow rate of 0.3 mL/min at an ambient temperature. Quantification is achieved with photodiode array detection at 230 nm, over the concentration range of 0.05-26 µg/mL. Forced degradation studies are also performed for nabumetone bulk drug samples to demonstrate the stability-indicating power of the UPLC method. Comparison of system performance with conventional high-performance liquid chromatography is made with respect to analysis time, efficiency, and sensitivity. The method is validated according to the ICH guidelines and is applied successfully for the determination of nabumetone in tablets.

  19. A comparison of histological and chemical analysis in mechanically separated meat

    OpenAIRE

    Petr Komrska; Bohuslava Tremlová; Pavel Štarha; Jana Simeonovová; Zdenka Randulová

    2011-01-01

    The aim of this study was evaluation of quality of mechanically separated chicken meat (MSCM) samples obtained by three different separators, by means of a histological (qualitative and quantitative) and chemical examination. Histological examinations used Green Trichrome and Alizarine red staining. The examination was focused on the evaluation of muscle, fat, collagenous connective tissue, bone fragment and calcium content and on the degree of damage to the muscle fibres. Chemical analysis w...

  20. Selection and Validation of Reference Genes for Real-Time Quantitative PCR in Hyperaccumulating Ecotype of Sedum alfredii under Different Heavy Metals Stresses

    Science.gov (United States)

    Liu, Mingying; Qiao, Guirong; Jiang, Jing; Zhuo, Renying

    2013-01-01

    Real-time Quantitative PCR (RT-qPCR) has become an effective method for accurate analysis of gene expression in several biological systems as well as under different experimental conditions. Although with high sensitivity, specificity and broad dynamic range, this method requires suitable reference genes for transcript normalization in order to guarantee reproducible and meaningful results. In the present study, we evaluated five traditional housekeeping genes and five novel reference genes in Hyperaccumulating ecotype of Sedum alfredii, a well known hyperaccumulator for heavy metals phytoremediation, under Cd, Pb, Zn and Cu stresses of seven different durations. The expression stability of these ten candidates were determined with three programs - geNorm, NormFinder and BestKeeper. The results showed that all the selected reference genes except for SAND could be used for RT-qPCR normalization. Among them UBC9 and TUB were ranked as the most stable candidates across all samples by three programs together. For the least stable reference genes, however, BestKeeper produced different results compared with geNorm and NormFinder. Meanwhile, the expression profiles of PCS under Cd, Pb, Zn and Cu stresses were assessed using UBC9 and TUB respectively, and similar trends were obtained from the results of the two groups. The distinct expression patterns of PCS indicated that various strategies could be taken by plants in adaption to different heavy metals stresses. This study will provide appropriate reference genes for further gene expression quantification using RT-qPCR in Hyperaccumulator S. alfredii. PMID:24340067

  1. Testing and validation of numerical models of groundwater flow, solute transport and chemical reactions in fractured granites: A quantitative study of the hydrogeological and hydrochemical impact produced

    Energy Technology Data Exchange (ETDEWEB)

    Molinero Huguet, J.

    2001-07-01

    This work deals with numerical modeling of groundwater flow, solute transport and chemical reactions through fractured media. These models have been developed within the framework of research activities founded by ENRESA , the Spanish Company for Nuclear Waste Management. This project is the result of a collaborative agreement between ENRESA and his equivalent Swedish Company (SKB) through the research project Task Force 5 of the Aspo Underground Laboratory. One of the objectives of this project is to assess quantitatively th hydrogeological and hydrochemical impact produced by the construction of a Deep Geological Repository in fractured granites. This is important because the new conditions altered construction impact will constitute the initial conditions for the repository closure stage. A second goo l of this work deals with testing the ability of current numerical tools to cope simultaneously with the complex hydrogeological and hydrochemical settlings, which are expected to take place in actual nuclear waste underground repositories constructed in crystalline fractured bed racks. This study has been undertaken through the performance of numerical models, which have subsequently been applied to simulate the hydrogeological and hydrochemical behavior of a granite massif, at a kilo metrical scale, during construction of the Aspo Hard Rock Underground Laboratory (Sweden). The Aspo Hard Rock Laboratory is a prototype, full-scale underground facility launched and operated by SKB. The main aim of the laboratory is to provide an opportunity for research, development and demonstration in a realistic rock environment down to the depth planned for the future deep repository. The framework of this underground facility provides a unique opportunity to attempt the objectives of the present dissertation. (Author)

  2. Efficient, validated method for detection of mycobacterial growth in liquid culture media by use of bead beating, magnetic-particle-based nucleic acid isolation, and quantitative PCR.

    Science.gov (United States)

    Plain, Karren M; Waldron, Anna M; Begg, Douglas J; de Silva, Kumudika; Purdie, Auriol C; Whittington, Richard J

    2015-04-01

    Pathogenic mycobacteria are difficult to culture, requiring specialized media and a long incubation time, and have complex and exceedingly robust cell walls. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease, a chronic wasting disease of ruminants, is a typical example. Culture of MAP from the feces and intestinal tissues is a commonly used test for confirmation of infection. Liquid medium offers greater sensitivity than solid medium for detection of MAP; however, support for the BD Bactec 460 system commonly used for this purpose has been discontinued. We previously developed a new liquid culture medium, M7H9C, to replace it, with confirmation of growth reliant on PCR. Here, we report an efficient DNA isolation and quantitative PCR methodology for the specific detection and confirmation of MAP growth in liquid culture media containing egg yolk. The analytical sensitivity was at least 10(4)-fold higher than a commonly used method involving ethanol precipitation of DNA and conventional PCR; this may be partly due to the addition of a bead-beating step to manually disrupt the cell wall of the mycobacteria. The limit of detection, determined using pure cultures of two different MAP strains, was 100 to 1,000 MAP organisms/ml. The diagnostic accuracy was confirmed using a panel of cattle fecal (n=54) and sheep fecal and tissue (n=90) culture samples. This technique is directly relevant for diagnostic laboratories that perform MAP cultures but may also be applicable to the detection of other species, including M. avium and M. tuberculosis.

  3. Identification and validation of reference genes for quantification of target gene expression with quantitative real-time PCR for tall fescue under four abiotic stresses.

    Directory of Open Access Journals (Sweden)

    Zhimin Yang

    Full Text Available Tall fescue (Festuca arundinacea Schreb. is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41 was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species.

  4. Selection and validation of reference genes for quantitative real-time PCR studies during Saccharomyces cerevisiae alcoholic fermentation in the presence of sulfite.

    Science.gov (United States)

    Nadai, Chiara; Campanaro, Stefano; Giacomini, Alessio; Corich, Viviana

    2015-12-23

    Sulfur dioxide is extensively used during industrial fermentations and contributes to determine the harsh conditions of winemaking together with low pH, high sugar content and increasing ethanol concentration. Therefore the presence of sulfite has to be considered in yeast gene expression studies to properly understand yeast behavior in technological environments such as winemaking. A reliable expression pattern can be obtained only using an appropriate reference gene set that is constitutively expressed regardless of perturbations linked to the experimental conditions. In this work we tested 15 candidate reference genes suitable for analysis of gene expression during must fermentation in the presence of sulfite. New reference genes were selected from a genome-wide expression experiment, obtained by RNA sequencing of four Saccharomyces cerevisiae wine strains grown in enological conditions. Their performance was compared to that of the most common genes used in previous studies. The most popular software based on different statistical approaches (geNorm, NormFinder and BestKeeper) were chosen to evaluate expression stability of the candidate reference genes. Validation was obtained using other wine strains by comparing normalized gene expression data with transcriptome quantification both in the presence and absence of sulfite. Among 15 reference genes tested ALG9, FBA1, UBC6 and PFK1 appeared to be the most reliable while ENO1, PMA1, DED1 and FAS2 were the worst. The most popular reference gene ACT1, widely used for S. cerevisiae gene expression studies, showed a stability level markedly lower than those of our selected reference genes. Finally, as the expression of the new reference gene set remained constant over the entire fermentation process, irrespective of the perturbation due to sulfite addition, our results can be considered also when no sulfite is added to the must.

  5. Development and validation of an ion-pair liquid chromatographic method for the quantitation of sodium cromoglycate in urine following inhalation.

    Science.gov (United States)

    Aswania, O A; Corlett, S A; Chrystyn, H

    1997-03-07

    An ion-pair liquid high-performance chromatography method with solid-phase extraction for measuring urinary concentrations of sodium cromoglycate following inhalation has been developed and validated. Sodium cromoglycate was extracted from urine on a 100-mg phenyl cartridge (Isolute, Jones Chromatography) and then quantified on a 25-cm C8 Spherisorb 5 microns stationary phase with a mobile phase of methanol-0.045 M phosphate buffer-0.05 M dodecyl triethyl ammonium phosphate (550:447.6:2.4, v/v) pH 2.3, at 0.85 ml min-1 using nedocromil sodium as an internal standard and UV detection at 238 nm. The inter- and intra-day reproducibilities were 8.33 and 13.63%, respectively, at 0.25 mg l-1. The limit of determination for sodium cromoglycate was 0.25 mg l-1 (with a signal-to-noise ratio of greater than 10:1). Following oral and inhaled administration of 20 mg of sodium cromoglycate to eight healthy volunteers, the mean and S.D. of sodium cromoglycate excreted in the urine at 0.5, 1 and 24 h post-dose were 0.02, 0.05 and 0.33%, and 0.16, 0.30 and 1.55% of the dose, respectively. The urinary recovery of sodium cromoglycate at 0.5 and 1 h following inhalation can therefore be used to compare the amount of drug reaching the respiratory tract using different sodium cromoglycate inhaled products or inhalation methods.

  6. Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses.

    Science.gov (United States)

    Galli, Vanessa; Borowski, Joyce Moura; Perin, Ellen Cristina; Messias, Rafael da Silva; Labonde, Julia; Pereira, Ivan dos Santos; Silva, Sérgio Delmar Dos Anjos; Rombaldi, Cesar Valmor

    2015-01-10

    The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

    Directory of Open Access Journals (Sweden)

    Richard B Lanman

    Full Text Available Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999% enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

  8. Validation and dissection of quantitative trait loci for leaf traits in interval RM4923-RM402 on the short arm of rice chromosome 6

    Indian Academy of Sciences (India)

    Bo Shen; Wei-Dong Yu; Jing-Hong Du; Ye-Yang Fan; Ji-Rong Wu; Jie-Yun Zhuang

    2011-04-01

    Validation and dissection of a QTL region for leaf traits in rice which has been reported in a number of independent studies were conducted. Three sets of near isogenic lines (NILs) were originated from a residual heterozygous line derived the indica cross Zhenshan 97B/Milyang 46. They were overlapping and totally covered a 4.2-Mb heterogenous region extending from RM4923 to RM402 on the short arm of rice chromosome 6. Each NIL set consisted of 10 maternal lines and 10 paternal lines. They were measured for the length, width, perimeter and area of the top three leaves and the number of spikelets per panicle, number of grains per panicle and grain weight per panicle. In NIL sets 6-4 and 6-7, differing in intervals RM4923-RM225 and RM19410-RM6119, respectively, significant variations with the enhancing alleles from the female parent ZS97 were shown for the length, perimeter and area except for the area of the third leaf from top in 6-4, but the effects were lower in 6-4 than in 6-7. No significant effects were detected for the three traits in the remaining NIL set. It was shown that flag leaf length (FLL) is the primary target of the QTLs detected. Two QTLs for FLL linked in repulsion phase were resolved, of which qFLL6.2 located in the 1.19-Mb interval RM3414-RM6917 had a major effect with the enhancing allele from Zhenshan 97B, and qFLL6.1 located in the 946.8-kb interval RM19350-RM19410 had a smaller effect with the enhancing allele from Milyang 46. The two QTLs also exerted pleiotropic effects on the yield traits.

  9. Development and validation of an in-house quantitative analysis method for cylindrospermopsin using hydrophilic interaction liquid chromatography-tandem mass spectrometry: Quantification demonstrated in 4 aquatic organisms.

    Science.gov (United States)

    Esterhuizen-Londt, Maranda; Kühn, Sandra; Pflugmacher, Stephan

    2015-12-01

    The cyanobacterial toxin cylindrospermopsin (CYN) is of great concern in aquatic environments because of its incidence, multiple toxicity endpoints, and, therefore, the severity of health implications. It may bioaccumulate in aquatic food webs, resulting in high exposure concentrations to higher-order trophic levels, particularly humans. Because of accumulation at primary levels resulting from exposure to trace amounts of toxin, a sensitive analytical technique with proven aquatic applications is required. In the present study, a hydrophilic interaction liquid chromatographic-tandem mass spectrometric method with a lower limit of detection of 200 fg on column (signal-to-noise ratio = 3, n = 9) and a lower limit of quantification of 1 pg on column (signal-to-noise ratio = 11, n = 9) with demonstrated application in 4 aquatic organisms is described. The analytical method was optimized and validated with a linear range (r(2) = 0.999) from 0.1 ng mL(-1) to 100 ng mL(-1) CYN. Mean recovery of the extraction method was 98 ± 2%. Application of the method was demonstrated by quantifying CYN uptake in Scenedesmus subspicatus (green algae), Egeria densa (Brazilian waterweed), Daphnia magna (water flea), and Lumbriculus variegatus (blackworm) after 24 h of static exposure to 50 μg L(-1) CYN. Uptake ranged from 0.05% to 0.11% of the nominal CYN exposure amount. This constitutes a sensitive and reproducible method for extraction and quantification of unconjugated CYN with demonstrated application in 4 aquatic organisms, which can be used in further aquatic toxicological investigations.

  10. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA

    Science.gov (United States)

    Zill, Oliver A.; Sebisanovic, Dragan; Lopez, Rene; Blau, Sibel; Collisson, Eric A.; Divers, Stephen G.; Hoon, Dave S. B.; Kopetz, E. Scott; Lee, Jeeyun; Nikolinakos, Petros G.; Baca, Arthur M.; Kermani, Bahram G.; Eltoukhy, Helmy; Talasaz, AmirAli

    2015-01-01

    Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital SequencingTM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing. PMID:26474073

  11. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

    Science.gov (United States)

    Lanman, Richard B; Mortimer, Stefanie A; Zill, Oliver A; Sebisanovic, Dragan; Lopez, Rene; Blau, Sibel; Collisson, Eric A; Divers, Stephen G; Hoon, Dave S B; Kopetz, E Scott; Lee, Jeeyun; Nikolinakos, Petros G; Baca, Arthur M; Kermani, Bahram G; Eltoukhy, Helmy; Talasaz, AmirAli

    2015-01-01

    Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

  12. Histological variability in fossil and recent alligatoroid osteoderms: systematic and functional implications.

    Science.gov (United States)

    Burns, Michael E; Vickaryous, Matthew K; Currie, Philip J

    2013-06-01

    Statements about morphological variation in extinct taxa often suffer from insufficient sampling that can be remedied by taking advantage of larger sample sizes provided by related, extant taxa. This analysis quantitatively and qualitatively examines histological and morphological variation of osteoderms from extant and extinct alligatoroid specimens. Statistically significant differences were correlated with changes in osteoderm size and shape. These differences are independent of position on the body, taxonomy, or evolution. Histological variation in alligatoroid osteoderms is due to morphological constraints on the elements themselves, and not taxonomic differences. This has implications for the recognition of histological characters in the osteoderms of extinct archosaur groups that lack extant representatives.

  13. Atlas-guided correction of brain histology distortion

    Directory of Open Access Journals (Sweden)

    Xi Qiu

    2011-01-01

    Full Text Available Histological tissue preparation stages (e.g., cutting, sectioning, etc. often introduce tissue distortions that prevent a smooth 3D reconstruction from being built. In this paper, we propose a method to correct histology distortions by running a piecewise registration scheme. It takes the information of several consecutive slices in a neighborhood into account. In order to achieve an accurate anatomic presentation, we run the method iteratively with the assistance from a pre-segmented brain atlas. The registration parameters are optimized to accommodate different brain sub-regions, e.g., cerebellum, hippocampus, etc. The results are evaluated by both visual and quantitative approaches. The proposed method has been proved to be robust enough for reconstructing an accurate and smooth mouse brain volume.

  14. A two-step genetic study on quantitative precursors of coronary artery disease in a homogeneous Indian population: Case–control association discovery and validation by transmission-disequilibrium test

    Indian Academy of Sciences (India)

    Sanjukta Mallik; Partha P Majumder

    2011-12-01

    In spite of its strong familiality, gene identification for coronary artery disease (CAD) has not yielded a consistent picture. One major reason for this is that families or cases and controls were not recruited from a homogeneous population. We, therefore, attempted to map genes underlying 10 quantitative traits (QTs) that are known precursors of CAD in a homogeneous population (Marwari) of India. The QTs are apolipoprotein B (ApoB), C-reactive protein (CRP), fibrinogen (FBG), homocysteine (HCY), lipoprotein (a) (LPA), cholesterol – total (CHOL-T), cholesterol – HDL (CHOL-H), cholesterol – LDL (CHOL-L), cholesterol – VLDL (CHOL-V) and triglyceride (TG). We assayed 209 SNPs in 31 genes among members of Marwari families. After log-transformation and covariate-adjustment of the QTs, a two-step analysis was performed. In Step-1, data on unrelated individuals were analysed for association with the SNPs. In Step-2, for validation of Step-1 results, a quantitative transmission-disequilibrium test on parent–offspring data was performed for each SNP found to be significantly associated with a QT in Step-1 on an independent sample set drawn from the same population. Statistically significant results found for the various QTs and SNPs were: rs3774933, rs230528, rs230521, rs1005819 and rs1609798 (intronic, NFKB1) with APOB; rs5361 (Missense, R > S, SELE) and rs4648004 (Intronic, NFKB1) with FBG; rs4220 (Missense, K > R, FGB) with HCY; and rs3025035 (Intronic, VEGFA) with CHOL-H. SNPs in SELE, VEGFA, FGB and NFKB1 genes impact significantly on levels of quantitative precursors of CAD in Marwaris.

  15. Validation of housekeeping genes as internal controls for studying gene expression during Pacific oyster (Crassostrea gigas) development by quantitative real-time PCR.

    Science.gov (United States)

    Du, Yishuai; Zhang, Linlin; Xu, Fei; Huang, Baoyu; Zhang, Guofan; Li, Li

    2013-03-01

    Hatchery-reared larvae of the Pacific oyster (Crassostrea gigas) often suffer from massive mortality induced by Ostreid herpesvirus 1 (OsHV-1) infection, indicating the importance of better understanding of oyster immune defense systems. The accuracy of measurements of gene expression levels based on quantitative real-time PCR assays relies on the use of housekeeping genes as internal controls; however, few studies have focused on the selection of such internal controls. In this study, we conducted a comprehensive investigation of internal control genes during oyster development in virus-infected and uninfected samples. Transcriptome data for 38 developmental stages were downloaded and the gene expression patterns were classified into 30 clusters. A total of 317 orthologs of classical housekeeping genes in the oyster genome were annotated. After combining the expression profiles and oyster housekeeping gene dataset, 14 candidate internal controls were selected for further investigation: Elongation factor-1α (EF-1α), 18S rRNA (18S), 28S rRNA (28S), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β-actin (ACT), Ribosomal protein L7 (RL7), Ribosomal protein L27 (RL27), Ribosomal protein L36 (RL36), Ribosomal protein S18 (RS18), Heterogeneous nuclear ribonucleoprotein A2/B1 (RO21), Eukaryotic translation elongation factor 2 (EF2), Ubiquitin-conjugating enzyme E2D2 (UBCD1), S-phase kinase-associated protein 1 (SKP1) and Heterogeneous nuclear ribonucleoprotein Q (HNRPQ). RNA was extracted from oyster larvae infected with OsHV-1 (group A; GA), and OsHV-1 free larvae (group B; GB). The expression levels of the 14 candidate internal controls were studied in GA and GB larvae by real-time PCR. Their expression stabilities were further analyzed using the GeNorm program. RL7 and RS18 were the most stable genes in both OsHV-1 infected (GA) and uninfected (GB) larvae. These results suggest that RL7 and RS18 could be used as internal controls for studying gene expression in

  16. Validation of reference genes as internal control for studying viral infections in cereals by quantitative real-time RT-PCR

    Directory of Open Access Journals (Sweden)

    Kundu Jiban K

    2010-07-01

    Full Text Available Abstract Background Reference genes are commonly used as the endogenous normalisation measure for the relative quantification of target genes. The appropriate application of quantitative real-time PCR (RT-qPCR, however, requires the use of reference genes whose level of expression is not affected by the test, by general physiological conditions or by inter-individual variability. For this purpose, seven reference genes were investigated in tissues of the most important cereals (wheat, barley and oats. Titre of Barley yellow dwarf virus (BYDV was determined in oats using relative quantification with different reference genes and absolute quantification, and the results were compared. Results The expression of seven potential reference genes was evaluated in tissues of 180 healthy, physiologically stressed and virus-infected cereal plants. These genes were tested by RT-qPCR and ranked according to the stability of their expression using three different methods (two-way ANOVA, GeNorm and NormFinder tools. In most cases, the expression of all genes did not depend on abiotic stress conditions or virus infections. All the genes showed significant differences in expression among plant species. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, beta-tubulin (TUBB and 18S ribosomal RNA (18S rRNA always ranked as the three most stable genes. On the other hand, elongation factor-1 alpha (EF1A, eukaryotic initiation factor 4a (EIF4A, and 28S ribosomal RNA (28S rRNA for barley and oat samples; and alpha-tubulin (TUBA for wheat samples were consistently ranked as the less reliable controls. The BYDV titre was determined in two oat varieties by RT-qPCR using three different quantification approaches. There were no significant differences between the absolute and relative quantifications, or between quantification using GAPDH + TUBB + TUBA +18S rRNA and EF1A + EIF4A + 28S rRNA. However, there were discrepancies between the results of individual assays

  17. Histologic analysis of postmeniscectomy osteonecrosis.

    Science.gov (United States)

    Higuchi, Hiroshi; Kobayashi, Yasukazu; Kobayashi, Atsushi; Hatayama, Kazuhisa; Kimura, Masashi

    2013-05-01

    Bone marrow signal changes on magnetic resonance imaging (MRI) after meniscectomy have been reported as evidence of postmeniscectomy osteonecrosis, but this pathology is unclear. We conducted a study to follow-up cases with bone marrow signal changes on MRI after meniscectomy and investigate the pathology of underlying lesions. Of 136 patients with no presurgical evidence of osteonecrosis, 29 had juxta-articular bone marrow signal changes on MRI after arthroscopic meniscectomy and subsequently underwent conservative therapy. In 6 of these 29 patients, clinical symptoms and radiographic changes began deteriorating. Based on the Koshino classification, 4 of the 6 patients had Stage-2 knee osteonecrosis and 2 had Stage-3. Arthroscopic and pathologic examinations were performed. Arthroscopic findings were fibrillation (all 6 cases), fissuring (4), ulceration (2), and eburnation (2). Histologic analysis confirmed subchondral bone fractures in all 6 cases, but osteonecrotic lesions were detected only in 2 cases with obvious radiologic deterioration. Postmeniscectomy osteonecrosis might result from subchondral bone fractures. Fracture healing is worse in patients with comorbidities than in those without it; comorbidities might be a risk factor for osteonecrosis.

  18. Esquemas de histología

    OpenAIRE

    1982-01-01

    Cuarenta y siete diagramas de estructuras histológicas extraídas de un atlas de histología, obra de Radivoj Vase Krstić. Forty-seven diagrams of histological structures from an atlas of histiology by Radivoj Vase Krstić.

  19. [Calcifying periarthropathy (radiologic-histological synopsis, terminology)].

    Science.gov (United States)

    Dihlmann, W

    1981-01-01

    On the basis of a case of radiologically and histologically investigated calcifying periarthropathy in the tendon of the glutaeus medius muscle the histological appearance and the pathogenesis of pain associated with this process is considered. The transformation of tendon tissue into fibrous cartilage is emphasized.

  20. Validation of a quantitative 12-multigene expression assay (Oncotype DX® Colon Cancer Assay in Korean patients with stage II colon cancer: implication of ethnic differences contributing to differences in gene expression

    Directory of Open Access Journals (Sweden)

    Jeong DH

    2015-12-01

    Full Text Available Duck Hyoun Jeong,1 Woo Ram Kim,1 Byung Soh Min,1 Young Wan Kim,2 Mi Kyung Song,3 Nam Kyu Kim1 1Department of Surgery, Yonsei University College of Medicine, Seoul, 2Department of Surgery, Wonju College of Medicine, Wonju, 3Department of Research Affairs, Biostatistics Collaboration Unit, Yonsei University College of Medicine, Seoul, Korea Purpose: To evaluate the Recurrence Score® of the quantitative 12-multigene expression assay and to determine risk groups based on the continuous Recurrence Score® in Korean patients.Method: A total of 95 patients with pathological T3N0 tumors and mismatch repair-proficient tumors were enrolled. The Recurrence Score® was used to classify risk groups (low risk, <30; intermediate risk, 30–40; high risk, ≥41.Results: Fifty-four patients (56.8% were aged over 70 years. There were 49 men (51.6% and 56 cases of right-sided colon cancer (58.9%. Eight cases (8.4% had well-differentiated tumors, and 86 cases (90.5% showed moderate differentiation. Only one case (1.1% had a poorly differentiated tumor. Three patients (3.2% had lymphovascular invasion. Sixty-one patients were identified as low risk (64.2% and 34 patients as intermediate risk (35.8%. There were no high-risk patients. Although not significant, the 3-year recurrence risk increased with the Recurrence Score®.Conclusion: Distribution patterns of risk groups based on the Recurrence Score®, particularly the absence of a high-risk group, were different from the prior validation studies. These findings suggest that ethnic differences between Koreans and Western patients are potential contributing factors for different gene expressions in the quantitative 12-multigene expression assay. Keywords: colonic neoplasms, gene expression, adjuvant chemotherapy, ethnic groups

  1. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Mingyao [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri (United States); Bzdusek, Karl [Philips Healthcare, Fitchburg, Wisconsin (United States); Brink, Carsten [Institute of Clinical Research, University of Southern Denmark, Odense (Denmark); Laboratory of Radiation Physics, Odense University Hospital, Odense (Denmark); Eriksen, Jesper Grau [Department of Oncology, Odense University Hospital, Odense (Denmark); Hansen, Olfred [Institute of Clinical Research, University of Southern Denmark, Odense (Denmark); Department of Oncology, Odense University Hospital, Odense (Denmark); Jensen, Helle Anita [Department of Oncology, Odense University Hospital, Odense (Denmark); Gay, Hiram A.; Thorstad, Wade [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri (United States); Widder, Joachim; Brouwer, Charlotte L.; Steenbakkers, Roel J.H.M.; Vanhauten, Hubertus A.M. [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Cao, Jeffrey Q.; McBrayne, Gail [London Regional Cancer Centre, Ontario (Canada); Patel, Salil H. [Department of Radiation Oncology, Rhode Island Hospital, Providence, Rhode Island (United States); Cannon, Donald M. [Department of Human Oncology, University of Wisconsin—Madison (United States); Hardcastle, Nicholas [Department of Physical Science, Peter MacCallum Cancer Centre, Melbourne (Australia); Tomé, Wolfgang A. [Montefiore Medical Center and Institute of Onco-Physics, Albert Einstein College of Medicine, Bronx, New York (United States); Guckenberg, Matthias [University of Würzburg, Department of Radiation Oncology, Würzburg (Germany); Parikh, Parag J., E-mail: pparikh@radonc.wustl.edu [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri (United States)

    2013-11-15

    Purpose: Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE). Methods and Materials: CT images of 125 treated patients (32 head and neck [HN], 40 thorax, 23 liver, and 30 prostate) in 7 independent institutions were autosegmented using SPICE and computational times were recorded. The number of structures autocontoured were 25 for the HN, 7 for the thorax, 3 for the liver, and 6 for the male pelvis regions. Using the clinical contours as reference, autocontours of 22 selected structures were quantitatively evaluated using Dice Similarity Coefficient (DSC) and Mean Slice-wise Hausdorff Distance (MSHD). All 40 autocontours were evaluated by a radiation oncologist from the institution that treated the patients. Results: The mean computational times to autosegment all the structures using SPICE were 3.1 to 11.1 minutes per patient. For the HN region, the mean DSC was >0.70 for all evaluated structures, and the MSHD ranged from 3.2 to 10.0 mm. For the thorax region, the mean DSC was 0.95 for the lungs and 0.90 for the heart, and the MSHD ranged from 2.8 to 12.8 mm. For the liver region, the mean DSC was >0.92 for all structures, and the MSHD ranged from 5.2 to 15.9 mm. For the male pelvis region, the mean DSC was >0.76 for all structures, and the MSHD ranged from 4.8 to 10.5 mm. Out of the 40 autocontoured structures reviews by experts, 25 were scored useful as autocontoured or with minor edits for at least 90% of the patients and 33 were scored useful autocontoured or with minor edits for at least 80% of the patients. Conclusions: Compared with manual contouring, autosegmentation using SPICE for the HN, thorax, liver, and male pelvis regions is efficient and shows significant promise for clinical utility.

  2. Quantitative autonomic testing.

    Science.gov (United States)

    Novak, Peter

    2011-07-19

    Disorders associated with dysfunction of autonomic nervous system are quite common yet frequently unrecognized. Quantitative autonomic testing can be invaluable tool for evaluation of these disorders, both in clinic and research. There are number of autonomic tests, however, only few were validated clinically or are quantitative. Here, fully quantitative and clinically validated protocol for testing of autonomic functions is presented. As a bare minimum the clinical autonomic laboratory should have a tilt table, ECG monitor, continuous noninvasive blood pressure monitor, respiratory monitor and a mean for evaluation of sudomotor domain. The software for recording and evaluation of autonomic tests is critical for correct evaluation of data. The presented protocol evaluates 3 major autonomic domains: cardiovagal, adrenergic and sudomotor. The tests include deep breathing, Valsalva maneuver, head-up tilt, and quantitative sudomotor axon test (QSART). The severity and distribution of dysautonomia is quantitated using Composite Autonomic Severity Scores (CASS). Detailed protocol is provided highlighting essential aspects of testing with emphasis on proper data acquisition, obtaining the relevant parameters and unbiased evaluation of autonomic signals. The normative data and CASS algorithm for interpretation of results are provided as well.

  3. Bibliometrics for Social Validation

    Science.gov (United States)

    2016-01-01

    This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion. PMID:28005974

  4. Bibliometrics for Social Validation.

    Science.gov (United States)

    Hicks, Daniel J

    2016-01-01

    This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion.

  5. Grade Validity of Online Quantitative Courses

    Science.gov (United States)

    Faurer, Judson C.

    2013-01-01

    Are prospective employers getting "quality" educated, degreed applicants and are academic institutions that offer online degree programs ensuring the quality control of the courses/programs offered? The issue specifically addressed in this paper is not with all institutions offering degrees through online programs or even with all online…

  6. Structure Function Estimated From Histological Tissue Sections.

    Science.gov (United States)

    Han, Aiguo; O'Brien, William D

    2016-09-01

    Ultrasonic scattering is determined by not only the properties of individual scatterers but also the correlation among scatterer positions. The role of scatterer spatial correlation is significant for dense medium, but has not been fully understood. The effect of scatterer spatial correlation may be modeled by the structure function as a frequency-dependent factor in the backscatter coefficient (BSC) expression. The structure function has been previously estimated from the BSC data. The aim of this study is to estimate the structure function from histology to test if the acoustically estimated structure function is indeed caused by the scatterer spatial distribution. Hematoxylin and eosin stained histological sections from dense cell pellet biophantoms were digitized. The scatterer positions were determined manually from the histological images. The structure function was calculated from the extracted scatterer positions. The structure function obtained from histology showed reasonable agreement in the shape but not in the amplitude, compared with the structure function previously estimated from the backscattered data. Fitting a polydisperse structure function model to the histologically estimated structure function yielded relatively accurate cell radius estimates ([Formula: see text]). Furthermore, two types of mouse tumors that have similar cell size and shape but distinct cell spatial distributions were studied, where the backscattered data were shown to be related to the cell spatial distribution through the structure function estimated from histology. In conclusion, the agreement between acoustically estimated and histologically estimated structure functions suggests that the acoustically estimated structure function is related to the scatterer spatial distribution.

  7. The virtual histology intravascular ultrasound appearance of newly placed drug-eluting stents.

    Science.gov (United States)

    Kim, Sang-Wook; Mintz, Gary S; Hong, Young-Joon; Pakala, Rajbabu; Park, Kyung-Sook; Pichard, Augusto D; Satler, Lowell F; Kent, Kenneth M; Suddath, William O; Waksman, Ron; Weissman, Neil J

    2008-11-01

    Intravascular ultrasound (IVUS) is used before and after intervention and at follow-up to assess the quality of the acute result as well as the long-term effects of stent implantation. Virtual histology (VH) IVUS classifies tissue into fibrous and fibrofatty plaque, dense calcium, and necrotic core. Although most interventional procedures include stent implantation, VH IVUS classification of stent metal has not been validated. In this study, the VH IVUS appearance of acutely implanted stents was assessed in 27 patients (30 lesions). Most stent struts (80%) appeared white (misclassified as "calcium") surrounded by red (misclassified as "necrotic core"); 2% appeared just white, and 17% were not detectable (compared with grayscale IVUS because of the software-imposed gray medial stripe). The rate of "white surrounded by red" was similar over the lengths of the stents; however, undetectable struts were mostly at the distal edges (31%). Quantitatively, including the struts within the regions of interest increased the amount of "calcium" from 0.23 +/- 0.35 to 1.07 +/- 0.66 mm(2) (p stents have an appearance that can be misclassified by VH IVUS as "calcium with or without necrotic core." It is important not to overinterpret VH IVUS studies of chronically implanted stents when this appearance is observed at follow-up. A separate classification for stent struts is necessary to avoid these misconceptions and misclassifications.

  8. Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, Plant Height, and Heading Date in Rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Touming Liu; Haiyang Liu; Huang Zhan; Yongzhong Xing

    2013-01-01

    A quantitative trait locus (QTL) that affects heading date (HD) and the number of spikelets per panicle (SPP) was previously identified in a small region on chromosome 7 in rice (Oryza sativa L.). In order to further characterize the QTL region, near isogenic lines (NILs) were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height (PH), SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9%of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.

  9. SE Marine Mammal Histology/Tissue data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tissue samples are collected from stranded marine mammals in the Southeastern United States. These tissue samples are examined histologically and evaluated to...

  10. [Histological findings in an irradiated choroidal melanoma].

    Science.gov (United States)

    Koinzer, S; Hasselbach, H; Bräsen, J H; Leuschner, I; Roider, J

    2011-06-01

    Histological findings of choroidal melanomas after proton beam irradiation have been reported for complicated cases after enucleation. We present specimens of a tumor after transretinal probe excision. One year after irradiation, the biopsy was examined histologically. The specimens showed pigmented, spindle-shaped cells staining positively for Melan-A and HMB-45. Ki-67 showed low proliferation. Caspase-3 staining was normal. The melanoma still contained vital and even single proliferating cells, but regressed afterwards without additional therapy.

  11. Quantitative micro-CT based coronary artery profiling using interactive local thresholding and cylindrical coordinates.

    Science.gov (United States)

    Panetta, Daniele; Pelosi, Gualtiero; Viglione, Federica; Kusmic, Claudia; Terreni, Marianna; Belcari, Nicola; Guerra, Alberto Del; Athanasiou, Lambros; Exarchos, Themistoklis; Fotiadis, Dimitrios I; Filipovic, Nenad; Trivella, Maria Giovanna; Salvadori, Piero A; Parodi, Oberdan

    2015-01-01

    Micro-CT is an established imaging technique for high-resolution non-destructive assessment of vascular samples, which is gaining growing interest for investigations of atherosclerotic arteries both in humans and in animal models. However, there is still a lack in the definition of micro-CT image metrics suitable for comprehensive evaluation and quantification of features of interest in the field of experimental atherosclerosis (ATS). A novel approach to micro-CT image processing for profiling of coronary ATS is described, providing comprehensive visualization and quantification of contrast agent-free 3D high-resolution reconstruction of full-length artery walls. Accelerated coronary ATS has been induced by high fat cholesterol-enriched diet in swine and left coronary artery (LCA) harvested en bloc for micro-CT scanning and histologic processing. A cylindrical coordinate system has been defined on the image space after curved multiplanar reformation of the coronary vessel for the comprehensive visualization of the main vessel features such as wall thickening and calcium content. A novel semi-automatic segmentation procedure based on 2D histograms has been implemented and the quantitative results validated by histology. The potentiality of attenuation-based micro-CT at low kV to reliably separate arterial wall layers from adjacent tissue as well as identify wall and plaque contours and major tissue components has been validated by histology. Morphometric indexes from histological data corresponding to several micro-CT slices have been derived (double observer evaluation at different coronary ATS stages) and highly significant correlations (R2 > 0.90) evidenced. Semi-automatic morphometry has been validated by double observer manual morphometry of micro-CT slices and highly significant correlations were found (R2 > 0.92). The micro-CT methodology described represents a handy and reliable tool for quantitative high resolution and contrast agent free full length

  12. Diagnostic dry bone histology in human paleopathology.

    Science.gov (United States)

    de Boer, H H Hans; Van der Merwe, A E Lida

    2016-10-01

    Paleopathology is the study of trauma and disease as may be observed in ancient (human) remains. In contrast to its central role in current medical practice, microscopy plays a rather modest role in paleopathology. This is at least partially due to the differences between fresh and decomposed (i.e., skeletonized or "dry bone") tissue samples. This review discusses these differences and describes how they affect the histological analysis of paleopathological specimens. First, we provide a summary of some general challenges related to the histological analysis of palaeopathological specimens. Second, the reader is introduced in bone tissue histology and bone tissue dynamics. The remainder of the paper is dedicated to the diagnostic value of dry bone histology. Its value and limitations are illustrated by comparing several well-studied paleopathological cases with similar contemporary, clinical cases. This review illustrates that due to post-mortem loss of soft tissue, a limited number of disorders display pathognomonic features during histological analysis of skeletonized human remains. In the remainder of cases, histology may help to narrow down the differential diagnosis or is diagnostically unspecific. A comprehensive, multidisciplinary diagnostic approach therefore remains essential. Clin. Anat. 29:831-843, 2016. © 2016 Wiley Periodicals, Inc.

  13. Development and proof-of-concept of three-dimensional lung histology volumes

    Science.gov (United States)

    Mathew, Lindsay; Alabousi, Mostafa; Wheatley, Andrew; Aladl, Usaf; Slipetz, Deborah; Hogg, James C.; Fenster, Aaron; Parraga, Grace

    2012-03-01

    Most medical imaging is inherently three-dimensional (3D) but for validation of pathological findings, histopathology is commonly used and typically histopathology images are acquired as twodimensional slices with quantitative analysis performed in a single dimension. Histopathology is invasive, labour-intensive, and the analysis cannot be performed in real time, yet it remains the gold standard for the pathological diagnosis and validation of clinical or radiological diagnoses of disease. A major goal worldwide is to improve medical imaging resolution, sensitivity and specificity to better guide therapy and biopsy and to one day delay or replace biopsy. A key limitation however is the lack of tools to directly compare 3D macroscopic imaging acquired in patients with histopathology findings, typically provided in a single dimension (1D) or in two dimensions (2D). To directly address this, we developed methods for 2D histology slice visualization/registration to generate 3D volumes and quantified tissue components in the 3D volume for direct comparison to volumetric micro-CT and clinical CT. We used the elastase-instilled mouse emphysema lung model to evaluate our methods with murine lungs sectioned (5 μm thickness/10 μm gap) and digitized with 2μm in-plane resolution. 3D volumes were generated for wildtype and elastase mouse lung sections after semi-automated registration of all tissue slices. The 1D mean linear intercept (Lm) for wildtype (WT) (47.1 μm +/- 9.8 μm) and elastase mouse lung (64.5 μm +/- 14.0 μm) was significantly different (p<.001). We also generated 3D measurements based on tissue and airspace morphometry from the 3D volumes and all of these were significantly different (p<.0001) when comparing elastase and WT mouse lung. The ratio of the airspace-to-lung volume for the entire lung volume was also significantly and strongly correlated with Lm.

  14. Towards in vivo focal cortical dysplasia phenotyping using quantitative MRI.

    Science.gov (United States)

    Adler, Sophie; Lorio, Sara; Jacques, Thomas S; Benova, Barbora; Gunny, Roxana; Cross, J Helen; Baldeweg, Torsten; Carmichael, David W

    2017-01-01

    Focal cortical dysplasias (FCDs) are a range of malformations of cortical development each with specific histopathological features. Conventional radiological assessment of standard structural MRI is useful for the localization of lesions but is unable to accurately predict the histopathological features. Quantitative MRI offers the possibility to probe tissue biophysical properties in vivo and may bridge the gap between radiological assessment and ex-vivo histology. This review will cover histological, genetic and radiological features of FCD following the ILAE classification and will explain how quantitative voxel- and surface-based techniques can characterise these features. We will provide an overview of the quantitative MRI measures available, their link with biophysical properties and finally the potential application of quantitative MRI to the problem of FCD subtyping. Future research linking quantitative MRI to FCD histological properties should improve clinical protocols, allow better characterisation of lesions in vivo and tailored surgical planning to the individual.

  15. Development and validation of a real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay for investigation of wild poliovirus type 1-South Asian (SOAS) strain reintroduced into Israel, 2013 to 2014.

    Science.gov (United States)

    Hindiyeh, M Y; Moran-Gilad, J; Manor, Y; Ram, D; Shulman, L M; Sofer, D; Mendelson, E

    2014-02-20

    In February 2013, wild poliovirus type 1 (WPV1) was reintroduced into southern Israel and resulted in continuous silent circulation in the highly immune population. As a part of the public health emergency response, a novel real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was developed, to allow for the sensitive and specific detection of the circulatingWPV1-South Asian (SOAS) strain. Specific primers and probes derived from the VP-1 region were designed, based on sequenced sewage isolates, and used to simultaneously amplify this WPV1-SOAS sequence together with bacteriophage MS-2 as internal control. High titre WPV1-SOAS stock virus was used for assay optimisation and 50 processed sewage samples collected from southern Israel and tested by reference culture based methods were used for analytical validation of the assay’s performance. The limit of detection of the multiplex qRT-PCR (SOAS/MS-2) assay was 0.1 plaque-forming unit (pfu)/reaction (20 pfu/mL) for WPV1-SOAS RNA with 100% sensitivity, specificity, positive and negative predictive values when compared to the culture based method. The turnaround time was rapid, providing results for environmental samples within 24 to 48 hours from completion of sewage processing, instead of five to seven days by culture-based analysis. Direct sewage testing by qRT-PCR assay proved to be a useful tool for rapid detection and environmental surveillance of WPV1-SOAS circulating strain during emergency response. Application of the approach for detection of WPV1-SOAS in stool samples obtained during acute flaccid paralysis (AFP) surveillance or field surveys should be further evaluated.

  16. Development of three quantitative real-time PCR assays for the detection of Rickettsia raoultii, Rickettsia slovaca, and Rickettsia aeschlimannii and their validation with ticks from the country of Georgia and the Republic of Azerbaijan.

    Science.gov (United States)

    Jiang, Ju; You, Brian J; Liu, Evan; Apte, Anisha; Yarina, Tamasin R; Myers, Todd E; Lee, John S; Francesconi, Stephen C; O'Guinn, Monica L; Tsertsvadze, Nikoloz; Vephkhvadze, Nino; Babuadze, Giorgi; Sidamonidze, Ketevan; Kokhreidze, Maka; Donduashvili, Marina; Onashvili, Tinatin; Ismayilov, Afrail; Agayev, Nigar; Aliyev, Mubariz; Muttalibov, Nizam; Richards, Allen L

    2012-12-01

    A previous surveillance study of human pathogens within ticks collected in the country of Georgia showed a relatively high infection rate for Rickettsia raoultii, R. slovaca, and R. aeschlimannii. These 3 spotted fever group rickettsiae are human pathogens: R. raoultii and R. slovaca cause tick-borne lymphadenopathy (TIBOLA), and R. aeschlimannii causes an infection characterized by fever and maculopapular rash. Three quantitative real-time polymerase chain reaction (qPCR) assays, Rraoul, Rslov, and Raesch were developed and optimized to detect R. raoultii, R. slovaca, and R. aeschlimannii, respectively, by targeting fragments of the outer membrane protein B gene (ompB) using species-specific molecular beacon or TaqMan probes. The 3 qPCR assays showed 100% specificity when tested against a rickettsiae DNA panel (n=20) and a bacteria DNA panel (n=12). The limit of detection was found to be at least 3 copies per reaction for all assays. Validation of the assays using previously investigated tick nucleic acid preparations, which included Rickettsia-free tick samples, tick samples that contain R. raoultii, R. slovaca, R. aeschlimannii, and other Rickettsia spp., gave 100% sensitivity for all 3 qPCR assays. In addition, a total of 65 tick nucleic acid preparations (representing 259 individual ticks) collected from the country of Georgia and the Republic of Azerbaijan in 2009 was tested using the 3 qPCR assays. R. raoultii, R. slovaca, and R. aeschlimannii were not detected in any ticks (n=31) from the Republic of Azerbaijan, but in the ticks from the country of Georgia (n=228) the minimal infection rate for R. raoultii and R. slovaca in Dermacentor marginatus was 10% and 4%, respectively, and for R. aeschlimannii in Haemaphysalis sulcata and Hyalomma spp. it was 1.9% and 20%, respectively.

  17. Development and validation of a sensitive, simple, and rapid method for simultaneous quantitation of atorvastatin and its acid and lactone metabolites by liquid chromatography-tandem mass spectrometry (LC-MS/MS).

    Science.gov (United States)

    Macwan, Joyce S; Ionita, Ileana A; Dostalek, Miroslav; Akhlaghi, Fatemeh

    2011-04-01

    The aim of the proposed work was to develop and validate a simple and sensitive assay for the analysis of atorvastatin (ATV) acid, ortho- and para-hydroxy-ATV, ATV lactone, and ortho- and para-hydroxy-ATV lactone in human plasma using liquid chromatography-tandem mass spectrometry. All six analytes and corresponding deuterium (d5)-labeled internal standards were extracted from 50 μL of human plasma by protein precipitation. The chromatographic separation of analytes was achieved using a Zorbax-SB Phenyl column (2.1 mm × 100 mm, 3.5 μm). The mobile phase consisted of a gradient mixture of 0.1% v/v glacial acetic acid in 10% v/v methanol in water (solvent A) and 40% v/v methanol in acetonitrile (solvent B). All analytes including ortho- and para-hydroxy metabolites were baseline-separated within 7.0 min using a flow rate of 0.35 mL/min. Mass spectrometry detection was carried out in positive electrospray ionization mode, with multiple-reaction monitoring scan. The calibration curves for all analytes were linear (R(2) ≥ 0.9975, n = 3) over the concentration range of 0.05-100 ng/mL and with lower limit of quantitation of 0.05 ng/mL. Mean extraction recoveries ranged between 88.6-111%. Intra- and inter-run mean percent accuracy were between 85-115% and percent imprecision was ≤ 15%. Stability studies revealed that ATV acid and lactone forms were stable in plasma during bench top (6 h on ice-water slurry), at the end of three successive freeze and thaw cycles and at -80 °C for 3 months. The method was successfully applied in a clinical study to determine concentrations of ATV and its metabolites over 12 h post-dose in patients receiving atorvastatin.

  18. Development and validation of a liquid chromatography-tandem mass spectrometry method for the quantitation of synthetic cannabinoids of the aminoalkylindole type and methanandamide in serum and its application to forensic samples.

    Science.gov (United States)

    Dresen, Sebastian; Kneisel, Stefan; Weinmann, Wolfgang; Zimmermann, Ralf; Auwärter, Volker

    2011-02-01

    After the discovery of synthetic cannabimimetic substances in 'Spice'-like herbal mixtures marketed as 'incense' or 'plant fertilizer' the active compounds have been declared as controlled substances in several European countries. As expected, a monitoring of new herbal mixtures which continue to appear on the market revealed that shortly after control measures have been taken by legal authorities, other compounds were added to existing mixtures and to new products. Several compounds of the aminoalkylindole type have been detected so far in herbal mixtures but still their consumption cannot be detected by commonly used drug-screening procedures, encouraging drug users to substitute cannabis with those products. There is a increasing demand on the part of police authorities, hospitals and psychiatrists for detection and quantification of synthetic cannabinoids in biological samples originating from psychiatric inpatients, emergency units or assessment of fitness to drive. Therefore, a liquid chromatography-tandem mass spectrometry method after liquid-liquid extraction for the quantitation of JWH-015, JWH-018, JWH-073, JWH-081, JWH 200, JWH-250, WIN 55,212-2 and methanandamide and the detection of JWH-019 and JWH-020 in human serum has been developed and fully validated according to guidelines for forensic toxicological analyses. The method was successfully applied to 101 serum samples from 80 subjects provided by hospitals, detoxification and therapy centers, forensic psychiatric centers and police authorities. Fifty-seven samples or 56.4% were found positive for at least one aminoalkylindole. JWH-019, JWH-020, JWH-200, WIN 55,212-2 and methanandamide were not detected in any of the analyzed samples.

  19. 利用荧光定量PCR验证与比较豇豆耐旱表达谱%Validation and comparison of drought-responsive microarray with real-time fluorescent quantitative PCR in asparagus bean

    Institute of Scientific and Technical Information of China (English)

    王莎; 徐沛; 汪宝根; 吴晓花; 黄芸萍; 鲁忠富; 刘永华; 李国景

    2013-01-01

    Originating from Africa and domesticated in Asia, asparagus bean [ Vigna unguiculata ssp. sesquipediailis ( L. ) Verdc ] is an important vegetable crop in China. Drought is an important environmental factor restricting the safety of asparagus bean production; therefore it is fundamental to identify drought tolerance genes from the asparagus bean germplasms. Fluorescence quantitative PCR is a useful tool for quantitative assay of gene expression. In this study, we validated and compared expression pattern of a subset of 11 genes from an in-house cowpea cDNA microarray with fluorescence quantitative PCR. It turned out that in roots and leaves of two different asparagus bean cultivars subject to drought stress, qPCR and microarray generally got similar results. The gene/tissue combinations showed congruent expression regulations between the two methods included 27 up-regulated and 7 down-regulated genes, relative to 10 inconsistently observed combinations, giving a rate of consistence of 0. 773. This experiment verified the confidence of high-throughput cDNA microarray in monitoring drought-related gene expressions, which lays a foundation for mining and utilizing drought-tolerant genes in asparagus bean. The causes of differential gene expression patterns between the two methods were discussed.%豇豆[Vigna unguiculata(L.)Walp]起源于非洲,是我国重要的蔬菜作物.干旱是制约长豇豆生产的重要因素,研究和挖掘长豇豆种质中蕴含的耐旱基因是改良长豇豆耐旱性的必要基础.荧光定量PCR是定量检测基因表达的重要手段之一.本实验室前期开发了首张豇豆cDNA表达谱芯片,并利用该芯片研究了长豇豆耐旱表达谱.在此基础上,利用荧光定量PCR对其中11个基因的表达模式进行了验证和比较.试验结果表明,在干旱处理的长豇豆2个品种的根和叶中,供试基因的表达谱芯片分析和qPCR结果一致的共计34组,其中上调27组,下调7

  20. Echocardiographic versus histologic findings in Marfan syndrome.

    Science.gov (United States)

    Gu, Xiaoyan; He, Yihua; Li, Zhian; Han, Jiancheng; Chen, Jian; Nixon, J V Ian

    2015-02-01

    This retrospective study attempted to establish the prevalence of multiple-valve involvement in Marfan syndrome and to compare echocardiographic with histopathologic findings in Marfan patients undergoing valvular or aortic surgery. We reviewed echocardiograms of 73 Marfan patients who underwent cardiovascular surgery from January 2004 through October 2009. Tissue histology was available for comparison in 29 patients. Among the 73 patients, 66 underwent aortic valve replacement or the Bentall procedure. Histologic findings were available in 29 patients, all of whom had myxomatous degeneration. Of 63 patients with moderate or severe aortic regurgitation as determined by echocardiography, 4 had thickened aortic valves. The echocardiographic findings in 18 patients with mitral involvement included mitral prolapse in 15. Of 11 patients with moderate or severe mitral regurgitation as determined by echocardiography, 4 underwent mitral valve repair and 7 mitral valve replacement. Histologic findings among mitral valve replacement patients showed thickened valve tissue and myxomatous degeneration. Tricuspid involvement was seen echocardiographically in 8 patients, all of whom had tricuspid prolapse. Two patients had severe tricuspid regurgitation, and both underwent repair. Both mitral and tricuspid involvement were seen echocardiographically in 7 patients. Among the 73 patients undergoing cardiac surgery for Marfan syndrome, 66 had moderate or severe aortic regurgitation, although their valves manifested few histologic changes. Eighteen patients had mitral involvement (moderate or severe mitral regurgitation, prolapse, or both), and 8 had tricuspid involvement. Mitral valves were most frequently found to have histologic changes, but the tricuspid valve was invariably involved.

  1. Clinical and Histologic Mimickers of Celiac Disease.

    Science.gov (United States)

    Kamboj, Amrit K; Oxentenko, Amy S

    2017-08-17

    Celiac disease is an autoimmune disorder of the small bowel, classically associated with diarrhea, abdominal pain, and malabsorption. The diagnosis of celiac disease is made when there are compatible clinical features, supportive serologic markers, representative histology from the small bowel, and response to a gluten-free diet. Histologic findings associated with celiac disease include intraepithelial lymphocytosis, crypt hyperplasia, villous atrophy, and a chronic inflammatory cell infiltrate in the lamina propria. It is important to recognize and diagnose celiac disease, as strict adherence to a gluten-free diet can lead to resolution of clinical and histologic manifestations of the disease. However, many other entities can present with clinical and/or histologic features of celiac disease. In this review article, we highlight key clinical and histologic mimickers of celiac disease. The evaluation of a patient with serologically negative enteropathy necessitates a carefully elicited history and detailed review by a pathologist. Medications can mimic celiac disease and should be considered in all patients with a serologically negative enteropathy. Many mimickers of celiac disease have clues to the underlying diagnosis, and many have a targeted therapy. It is necessary to provide patients with a correct diagnosis rather than subject them to a lifetime of an unnecessary gluten-free diet.

  2. A clinical prediction rule for histological chorioamnionitis in preterm newborns.

    Directory of Open Access Journals (Sweden)

    Jasper V Been

    Full Text Available BACKGROUND: Histological chorioamnionitis (HC is an intrauterine inflammatory process highly associated with preterm birth and adverse neonatal outcome. HC is often clinically silent and diagnosed postnatally by placental histology. Earlier identification could facilitate treatment individualisation to improve outcome in preterm newborns. AIM: Develop a clinical prediction rule at birth for HC and HC with fetal involvement (HCF in preterm newborns. METHODS: Clinical data and placental pathology were obtained from singleton preterm newborns (gestational age ≤ 32.0 weeks born at Erasmus UMC Rotterdam from 2001 to 2003 (derivation cohort; n = 216 or Máxima MC Veldhoven from 2009 to 2010 (validation cohort; n = 206. HC and HCF prediction rules were developed with preference for high sensitivity using clinical variables available at birth. RESULTS: HC and HCF were present in 39% and 24% in the derivation cohort and in 44% and 22% in the validation cohort, respectively. HC was predicted with 87% accuracy, yielding an area under ROC curve of 0.95 (95%CI = 0.92-0.98, a positive predictive value of 80% (95%CI = 74-84%, and a negative predictive value of 93% (95%CI = 88-96%. Corresponding figures for HCF were: accuracy 83%, area under ROC curve 0.92 (95%CI = 0.88-0.96, positive predictive value 59% (95%CI = 52-62%, and negative predictive value 97% (95%CI = 93-99%. External validation expectedly resulted in some loss of test performance, preferentially affecting positive predictive rather than negative predictive values. CONCLUSION: Using a clinical prediction rule composed of clinical variables available at birth, HC and HCF could be predicted with good test characteristics in preterm newborns. Further studies should evaluate the clinical value of these rules to guide early treatment individualisation.

  3. Histology image search using multimodal fusion.

    Science.gov (United States)

    Caicedo, Juan C; Vanegas, Jorge A; Páez, Fabian; González, Fabio A

    2014-10-01

    This work proposes a histology image indexing strategy based on multimodal representations obtained from the combination of visual features and associated semantic annotations. Both data modalities are complementary information sources for an image retrieval system, since visual features lack explicit semantic information and semantic terms do not usually describe the visual appearance of images. The paper proposes a novel strategy to build a fused image representation using matrix factorization algorithms and data reconstruction principles to generate a set of multimodal features. The methodology can seamlessly recover the multimodal representation of images without semantic annotations, allowing us to index new images using visual features only, and also accepting single example images as queries. Experimental evaluations on three different histology image data sets show that our strategy is a simple, yet effective approach to building multimodal representations for histology image search, and outperforms the response of the popular late fusion approach to combine information.

  4. [Histological aspects of naso-ethmoidal tumors].

    Science.gov (United States)

    Carnot, F

    1997-01-01

    Among malignant neoplasms of the sino-nasal tract, tumors of the nasal vault have special features: their higher incidence in woodworkers, their frequent local recurrence and invasiveness in the skull base. Histologically too, they are peculiar by the predominance of the glandular tumors, of colonic or enteric type especially. Microscopic examination allows histological grading of these adenocarcinoma. Squamous carcinoma and adenoid cystic carcinoma are less frequent than in other parts of the sinonasal tract. Rare other tumors, often undifferentiated, can be diagnosed by immuno-staining as esthesioneuroblastomas, malignant melanomas, neuro-endocrine carcinomas, malignant lymphomas or sarcomas. A retrospective study of 147 patients yielded similar data.

  5. Histological classification of mesial temporal sclerosis

    Directory of Open Access Journals (Sweden)

    D. V. Dmitrenko

    2016-01-01

    Full Text Available Mesial temporal sclerosis (MTS is the most common histopathology occurring in patients with drug-resistant temporal lobe epilepsy. Over the past decades, there have been various attempts to classify the variants of hippocampal neuronal cell loss in relation to postoperative outcome. However, no consensus on the common international definition and classification of MTS has been reached. The article describes the modern histological classification based on a semiquantitative hippocampal cell loss model. The publications dealing with the histological classification of mesial temporal sclerosis are reviewed. 

  6. 3D reconstruction of multiple stained histology images

    Directory of Open Access Journals (Sweden)

    Yi Song

    2013-01-01

    Full Text Available Context: Three dimensional (3D tissue reconstructions from the histology images with different stains allows the spatial alignment of structural and functional elements highlighted by different stains for quantitative study of many physiological and pathological phenomena. This has significant potential to improve the understanding of the growth patterns and the spatial arrangement of diseased cells, and enhance the study of biomechanical behavior of the tissue structures towards better treatments (e.g. tissue-engineering applications. Methods: This paper evaluates three strategies for 3D reconstruction from sets of two dimensional (2D histological sections with different stains, by combining methods of 2D multi-stain registration and 3D volumetric reconstruction from same stain sections. Setting and Design: The different strategies have been evaluated on two liver specimens (80 sections in total stained with Hematoxylin and Eosin (H and E, Sirius Red, and Cytokeratin (CK 7. Results and Conclusion: A strategy of using multi-stain registration to align images of a second stain to a volume reconstructed by same-stain registration results in the lowest overall error, although an interlaced image registration approach may be more robust to poor section quality.

  7. Histologic diagnosis of metabolic bone diseases: bone histomorphometry

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    L. Dalle Carbonare

    2011-09-01

    Full Text Available Histomorphometry or quantitative histology is the analysis on histologic sections of bone resorption parameters, formation and structure. It is the only technique that allows a dynamic evaluation of the activity of bone modelling after labelling with tetracycline. Moreover, the new measurement procedures through the use of the computer allow an assessment of bone microarchitecture too. Histomorphometric bone biopsy is a reliable and well-tolerated procedure. Complications are reported only in 1% of the subjects (hematoma, pain, transient neuralgia. Histomorphometry is used to exclude or confirm the diagnosis of osteomalacia. It is employed in the evaluation of bone damage associated with particular treatments (for example, anticonvulsants or in case of rare bone diseases (osteogenesis imperfecta, systemic mastocytosis. It is also an essential approach when clinical, biochemical and other diagnostic data are not consistent. Finally, it is a useful method to understand the pathophysiologic mechanisms of drugs. The bone sample is taken at the level of iliac crest under local anesthesia. It is then put into methyl-metacrilate resin where the sections are prepared for the microscopic analysis of the various histomorphometric parameters.

  8. 3D prostate histology image reconstruction: Quantifying the impact of tissue deformation and histology section location

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    Eli Gibson

    2013-01-01

    Full Text Available Background: Guidelines for localizing prostate cancer on imaging are ideally informed by registered post-prostatectomy histology. 3D histology reconstruction methods can support this by reintroducing 3D spatial information lost during histology processing. The need to register small, high-grade foci drives a need for high accuracy. Accurate 3D reconstruction method design is impacted by the answers to the following central questions of this work. (1 How does prostate tissue deform during histology processing? (2 What spatial misalignment of the tissue sections is induced by microtome cutting? (3 How does the choice of reconstruction model affect histology reconstruction accuracy? Materials and Methods: Histology, paraffin block face and magnetic resonance images were acquired for 18 whole mid-gland tissue slices from six prostates. 7-15 homologous landmarks were identified on each image. Tissue deformation due to histology processing was characterized using the target registration error (TRE after landmark-based registration under four deformation models (rigid, similarity, affine and thin-plate-spline [TPS]. The misalignment of histology sections from the front faces of tissue slices was quantified using manually identified landmarks. The impact of reconstruction models on the TRE after landmark-based reconstruction was measured under eight reconstruction models comprising one of four deformation models with and without constraining histology images to the tissue slice front faces. Results: Isotropic scaling improved the mean TRE by 0.8-1.0 mm (all results reported as 95% confidence intervals, while skew or TPS deformation improved the mean TRE by <0.1 mm. The mean misalignment was 1.1-1.9΀ (angle and 0.9-1.3 mm (depth. Using isotropic scaling, the front face constraint raised the mean TRE by 0.6-0.8 mm. Conclusions: For sub-millimeter accuracy, 3D reconstruction models should not constrain histology images to the tissue slice front faces and

  9. 3D prostate histology image reconstruction: Quantifying the impact of tissue deformation and histology section location

    Science.gov (United States)

    Gibson, Eli; Gaed, Mena; Gómez, José A.; Moussa, Madeleine; Pautler, Stephen; Chin, Joseph L.; Crukley, Cathie; Bauman, Glenn S.; Fenster, Aaron; Ward, Aaron D.

    2013-01-01

    Background: Guidelines for localizing prostate cancer on imaging are ideally informed by registered post-prostatectomy histology. 3D histology reconstruction methods can support this by reintroducing 3D spatial information lost during histology processing. The need to register small, high-grade foci drives a need for high accuracy. Accurate 3D reconstruction method design is impacted by the answers to the following central questions of this work. (1) How does prostate tissue deform during histology processing? (2) What spatial misalignment of the tissue sections is induced by microtome cutting? (3) How does the choice of reconstruction model affect histology reconstruction accuracy? Materials and Methods: Histology, paraffin block face and magnetic resonance images were acquired for 18 whole mid-gland tissue slices from six prostates. 7-15 homologous landmarks were identified on each image. Tissue deformation due to histology processing was characterized using the target registration error (TRE) after landmark-based registration under four deformation models (rigid, similarity, affine and thin-plate-spline [TPS]). The misalignment of histology sections from the front faces of tissue slices was quantified using manually identified landmarks. The impact of reconstruction models on the TRE after landmark-based reconstruction was measured under eight reconstruction models comprising one of four deformation models with and without constraining histology images to the tissue slice front faces. Results: Isotropic scaling improved the mean TRE by 0.8-1.0 mm (all results reported as 95% confidence intervals), while skew or TPS deformation improved the mean TRE by <0.1 mm. The mean misalignment was 1.1-1.9° (angle) and 0.9-1.3 mm (depth). Using isotropic scaling, the front face constraint raised the mean TRE by 0.6-0.8 mm. Conclusions: For sub-millimeter accuracy, 3D reconstruction models should not constrain histology images to the tissue slice front faces and should be

  10. A Gauss-Seidel iteration scheme for reference-free 3-D histological image reconstruction.

    Science.gov (United States)

    Gaffling, Simone; Daum, Volker; Steidl, Stefan; Maier, Andreas; Kostler, Harald; Hornegger, Joachim

    2015-02-01

    Three-dimensional (3-D) reconstruction of histological slice sequences offers great benefits in the investigation of different morphologies. It features very high-resolution which is still unmatched by in vivo 3-D imaging modalities, and tissue staining further enhances visibility and contrast. One important step during reconstruction is the reversal of slice deformations introduced during histological slice preparation, a process also called image unwarping. Most methods use an external reference, or rely on conservative stopping criteria during the unwarping optimization to prevent straightening of naturally curved morphology. Our approach shows that the problem of unwarping is based on the superposition of low-frequency anatomy and high-frequency errors. We present an iterative scheme that transfers the ideas of the Gauss-Seidel method to image stacks to separate the anatomy from the deformation. In particular, the scheme is universally applicable without restriction to a specific unwarping method, and uses no external reference. The deformation artifacts are effectively reduced in the resulting histology volumes, while the natural curvature of the anatomy is preserved. The validity of our method is shown on synthetic data, simulated histology data using a CT data set and real histology data. In the case of the simulated histology where the ground truth was known, the mean Target Registration Error (TRE) between the unwarped and original volume could be reduced to less than 1 pixel on average after six iterations of our proposed method.

  11. Histology. Notes for Students of Animal Husbandry.

    Science.gov (United States)

    Price, Charles J.; Reed, Josephine E.

    This document approaches the subject of Histology by way of simple independent unicellular organisms through the lower levels of cell organization and specialization to a detailed study of the highly complex tissues of vertebrate animals. Emphasis is placed on structure, but function is explained in some detail. The relationships between tissues…

  12. Histology. Notes for Students of Animal Husbandry.

    Science.gov (United States)

    Price, Charles J.; Reed, Josephine E.

    This document approaches the subject of Histology by way of simple independent unicellular organisms through the lower levels of cell organization and specialization to a detailed study of the highly complex tissues of vertebrate animals. Emphasis is placed on structure, but function is explained in some detail. The relationships between tissues…

  13. Reptilian spermatogenesis: A histological and ultrastructural perspective.

    Science.gov (United States)

    Gribbins, Kevin M

    2011-07-01

    Until recently, the histology and ultrastructural events of spermatogenesis in reptiles were relatively unknown. Most of the available morphological information focuses on specific stages of spermatogenesis, spermiogenesis, and/or of the mature spermatozoa. No study to date has provided complete ultrastructural information on the early events of spermatogenesis, proliferation and meiosis in class Reptilia. Furthermore, no comprehensive data set exists that describes the ultrastructure of the entire ontogenic progression of germ cells through the phases of reptilian spermatogenesis (mitosis, meiosis and spermiogenesis). The purpose of this review is to provide an ultrastructural and histological atlas of spermatogenesis in reptiles. The morphological details provided here are the first of their kind and can hopefully provide histological information on spermatogenesis that can be compared to that already known for anamniotes (fish and amphibians), birds and mammals. The data supplied in this review will provide a basic model that can be utilized for the study of sperm development in other reptiles. The use of such an atlas will hopefully stimulate more interest in collecting histological and ultrastructural data sets on spermatogenesis that may play important roles in future nontraditional phylogenetic analyses and histopathological studies in reptiles.

  14. Developing the eHistology Atlas.

    Science.gov (United States)

    Richardson, Lorna; Graham, Liz; Moss, Julie; Burton, Nick; Roochun, Yogmatee; Armit, Chris; Baldock, Richard A

    2015-01-01

    The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook 'The Atlas of Mouse Development' by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php. © The Author(s) 2015. Published by Oxford University Press.

  15. Quantitative vs qualitative research methods.

    Science.gov (United States)

    Lakshman, M; Sinha, L; Biswas, M; Charles, M; Arora, N K

    2000-05-01

    Quantitative methods have been widely used because of the fact that things that can be measured or counted gain scientific credibility over the unmeasurable. But the extent of biological abnormality, severity, consequences and the impact of illness cannot be satisfactorily captured and answered by the quantitative research alone. In such situations qualitative methods take a holistic perspective preserving the complexities of human behavior by addressing the "why" and "how" questions. In this paper an attempt has been made to highlight the strengths and weaknesses of both the methods and also that a balanced mix of both qualitative as well as quantitative methods yield the most valid and reliable results.

  16. Multifeature prostate cancer diagnosis and Gleason grading of histological images.

    Science.gov (United States)

    Tabesh, Ali; Teverovskiy, Mikhail; Pang, Ho-Yuen; Kumar, Vinay P; Verbel, David; Kotsianti, Angeliki; Saidi, Olivier

    2007-10-01

    We present a study of image features for cancer diagnosis and Gleason grading of the histological images of prostate. In diagnosis, the tissue image is classified into the tumor and nontumor classes. In Gleason grading, which characterizes tumor aggressiveness, the image is classified as containing a low- or high-grade tumor. The image sets used in this paper consisted of 367 and 268 color images for the diagnosis and Gleason grading problems, respectively, and were captured from representative areas of hematoxylin and eosin-stained tissue retrieved from tissue microarray cores or whole sections. The primary contribution of this paper is to aggregate color, texture, and morphometric cues at the global and histological object levels for classification. Features representing different visual cues were combined in a supervised learning framework. We compared the performance of Gaussian, k-nearest neighbor, and support vector machine classifiers together with the sequential forward feature selection algorithm. On diagnosis, using a five-fold cross-validation estimate, an accuracy of 96.7% was obtained. On Gleason grading, the achieved accuracy of classification into low- and high-grade classes was 81.0%.

  17. Condylar hyperplasia: correlation of histological and scintigraphic features.

    Science.gov (United States)

    Gray, R J; Horner, K; Testa, H J; Lloyd, J J; Sloan, P

    1994-05-01

    Scintigaphy using 99mTc-MDP is widely advocated as a method of diagnosis and presurgical assessment of patients with condylar hyperplasia. A previous study has demonstrated that hyperplasia of the mandibular condyle is characterized histologically by the presence of an uninterrupted layer of undiffentiated germinative mesenchyme cells, a layer of hypertrophic cartilage and the presence of islands of chondrocytes in the subchondral trabecular bone. This study was undertaken to determine whether there was any association between the degree of 99mTc-MDP uptake and the histological features of condylar hyperplasia. The parameters examined were trabecular bone volume, depth of cartilage islands and the presence of forming and resorbing surfaces. The images were analyzed by three experienced observers, who ranked the images according to degree of asymmetry between sides and the degree of uptake on the affected side. There was a significant correlation between the proportions of resorbing and osteoid covered bone surfaces and scintigraphic appearances. The rank correlations were rs = 0.55 (P = 0.3) between the resorptive surfaces and degree of symmetry and rs = 0.53 (P = 0.04) between the osteoid surfaces and absolute uptake. The correlation was higher for both methods (rs = 0.64 in each case) when the osteoid surface and resorptive surface measurements were combined. The results indicate that visual examination of radioisotope bone scans by experienced observers is a valid form of assessment of bone activity in condylar hyperplasia.

  18. Semantic content analysis and annotation of histological images.

    Science.gov (United States)

    Yu, Feiyang; Ip, Horace H S

    2008-06-01

    This paper presents a novel two-dimensional (2-D) stochastic method for semantic analysis of the content of histological images Specifically, we propose a 2-D generalization of the traditional hidden Markov model (HMM). The generalization is called spatial-hidden Markov model (SHMM) that captures the contextual characteristics of complex biological features in histological images The model employs a second-order neighborhood system and assumes the conditional independence of vertical and horizontal transitions between hidden states. The notion of 'past' in SHMM is defined as what have been observed in a row-wise raster scan. This paper focuses on two fundamental problems: the best states decoding problem and the estimation of generation probability of an image by a SHMM. Based on our independence assumption of horizontal and vertical transitions, we derive computational tractable solutions to those problems. These solutions are direct extensions of their counterparts, i.e., the Viterbi algorithm and Forward-Backward algorithm, for 1-D HMM. Our experiments were carried on a medical image database with 200 images and compared with a state-of-the-art approach that was run on the same database. The annotation results demonstrated that SHMM consistently outperforms the previous approach and ameliorates many of its drawbacks. In addition, performance comparison with HMM has also validated the superiority of SHMM.

  19. Histological examination of adult Onchocerca volvulus and comparison with the collagenase technique.

    Science.gov (United States)

    Büttner, D W; Albiez, E J; von Essen, J; Erichsen, J

    1988-12-01

    The methods used for the assessment of adult Onchocerca volvulus by histology are described. Based on the results of several studies, mainly in Liberia and Burkina Faso, the morphology of the adult filariae in histological sections is represented as far as it is relevant for the evaluation. Especially are described the morphological alterations due to old age of the worms, to chronic hyperreactivity of the human host (sowda) and effects of the macrofilaricidal suramin and of microfilaricidal drugs. Quantitative results are reported on untreated adult O. volvulus from various countries, the cha