Differences between genders in colorectal morphology on CT colonography using a quantitative approach: a pilot study.

PubMed

Weber, Charles N; Poff, Jason A; Lev-Toaff, Anna S; Levine, Marc S; Zafar, Hanna M

To explore quantitative differences between genders in morphologic colonic metrics and determine metric reproducibility. Quantitative colonic metrics from 20 male and 20 female CTC datasets were evaluated twice by two readers; all exams were performed after incomplete optical colonoscopy. Intra-/inter-reader reliability was measured with intraclass correlation coefficient (ICC) and concordance correlation coefficient (CCC). Women had overall decreased colonic volume, increased tortuosity and compactness and lower sigmoid apex height on CTC compared to men (p<0.0001,all). Quantitative measurements in colonic metrics were highly reproducible (ICC=0.9989 and 0.9970; CCC=0.9945). Quantitative morphologic differences between genders can be reproducibility measured. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantitative Outline-based Shape Analysis and Classification of Planetary Craterforms using Supervised Learning Models

NASA Astrophysics Data System (ADS)

Slezak, Thomas Joseph; Radebaugh, Jani; Christiansen, Eric

2017-10-01

The shapes of craterform morphology on planetary surfaces provides rich information about their origins and evolution. While morphologic information provides rich visual clues to geologic processes and properties, the ability to quantitatively communicate this information is less easily accomplished. This study examines the morphology of craterforms using the quantitative outline-based shape methods of geometric morphometrics, commonly used in biology and paleontology. We examine and compare landforms on planetary surfaces using shape, a property of morphology that is invariant to translation, rotation, and size. We quantify the shapes of paterae on Io, martian calderas, terrestrial basaltic shield calderas, terrestrial ash-flow calderas, and lunar impact craters using elliptic Fourier analysis (EFA) and the Zahn and Roskies (Z-R) shape function, or tangent angle approach to produce multivariate shape descriptors. These shape descriptors are subjected to multivariate statistical analysis including canonical variate analysis (CVA), a multiple-comparison variant of discriminant analysis, to investigate the link between craterform shape and classification. Paterae on Io are most similar in shape to terrestrial ash-flow calderas and the shapes of terrestrial basaltic shield volcanoes are most similar to martian calderas. The shapes of lunar impact craters, including simple, transitional, and complex morphology, are classified with a 100% rate of success in all models. Multiple CVA models effectively predict and classify different craterforms using shape-based identification and demonstrate significant potential for use in the analysis of planetary surfaces.

Genetic Complexity and Quantitative Trait Loci Mapping of Yeast Morphological Traits

PubMed Central

Nogami, Satoru; Ohya, Yoshikazu; Yvert, Gaël

2007-01-01

Functional genomics relies on two essential parameters: the sensitivity of phenotypic measures and the power to detect genomic perturbations that cause phenotypic variations. In model organisms, two types of perturbations are widely used. Artificial mutations can be introduced in virtually any gene and allow the systematic analysis of gene function via mutants fitness. Alternatively, natural genetic variations can be associated to particular phenotypes via genetic mapping. However, the access to genome manipulation and breeding provided by model organisms is sometimes counterbalanced by phenotyping limitations. Here we investigated the natural genetic diversity of Saccharomyces cerevisiae cellular morphology using a very sensitive high-throughput imaging platform. We quantified 501 morphological parameters in over 50,000 yeast cells from a cross between two wild-type divergent backgrounds. Extensive morphological differences were found between these backgrounds. The genetic architecture of the traits was complex, with evidence of both epistasis and transgressive segregation. We mapped quantitative trait loci (QTL) for 67 traits and discovered 364 correlations between traits segregation and inheritance of gene expression levels. We validated one QTL by the replacement of a single base in the genome. This study illustrates the natural diversity and complexity of cellular traits among natural yeast strains and provides an ideal framework for a genetical genomics dissection of multiple traits. Our results did not overlap with results previously obtained from systematic deletion strains, showing that both approaches are necessary for the functional exploration of genomes. PMID:17319748

Quantifying Morphological Features of α-U3O8 with Image Analysis for Nuclear Forensics.

PubMed

Olsen, Adam M; Richards, Bryony; Schwerdt, Ian; Heffernan, Sean; Lusk, Robert; Smith, Braxton; Jurrus, Elizabeth; Ruggiero, Christy; McDonald, Luther W

2017-03-07

Morphological changes in U 3 O 8 based on calcination temperature have been quantified enabling a morphological feature to serve as a signature of processing history in nuclear forensics. Five separate calcination temperatures were used to synthesize α-U 3 O 8 , and each sample was characterized using powder X-ray diffraction (p-XRD) and scanning electron microscopy (SEM). The p-XRD spectra were used to evaluate the purity of the synthesized U-oxide; the morphological analysis for materials (MAMA) software was utilized to quantitatively characterize the particle shape and size as indicated by the SEM images. Analysis comparing the particle attributes, such as particle area at each of the temperatures, was completed using the Kolmogorov-Smirnov two sample test (K-S test). These results illustrate a distinct statistical difference between each calcination temperature. To provide a framework for forensic analysis of an unknown sample, the sample distributions at each temperature were compared to randomly selected distributions (100, 250, 500, and 750 particles) from each synthesized temperature to determine if they were statistically different. It was found that 750 particles were required to differentiate between all of the synthesized temperatures with a confidence interval of 99.0%. Results from this study provide the first quantitative morphological study of U-oxides, and reveals the potential strength of morphological particle analysis in nuclear forensics by providing a framework for a more rapid characterization of interdicted uranium oxide samples.

New approaches for the analysis of confluent cell layers with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Pohl, L.; Kaiser, M.; Ketelhut, S.; Pereira, S.; Goycoolea, F.; Kemper, Björn

2016-03-01

Digital holographic microscopy (DHM) enables high resolution non-destructive inspection of technical surfaces and minimally-invasive label-free live cell imaging. However, the analysis of confluent cell layers represents a challenge as quantitative DHM phase images in this case do not provide sufficient information for image segmentation, determination of the cellular dry mass or calculation of the cell thickness. We present novel strategies for the analysis of confluent cell layers with quantitative DHM phase contrast utilizing a histogram based-evaluation procedure. The applicability of our approach is illustrated by quantification of drug induced cell morphology changes and it is shown that the method is capable to quantify reliable global morphology changes of confluent cell layers.

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

PubMed

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

2016-07-22

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

Monitoring cell morphology during necrosis and apoptosis by quantitative phase imaging

NASA Astrophysics Data System (ADS)

Mugnano, Martina; Calabuig, Alejandro; Grilli, Simonetta; Miccio, Lisa; Ferraro, Pietro

2015-05-01

Cellular morphology changes and volume alterations play significant roles in many biological processes and they are mirrors of cell functions. In this paper, we propose the Digital Holographic microscope (DH) as a non-invasive imaging technique for a rapid and accurate extraction of morphological information related to cell death. In particular, we investigate the morphological variations that occur during necrosis and apoptosis. The study of necrosis is extremely important because it is often associated with unwarranted loss of cells in human pathologies such as ischemia, trauma, and some forms of neurodegeneration; therefore, a better elucidation in terms of cell morphological changes could pave the way for new treatments. Also, apoptosis is extremely important because it's involved in cancer, both in its formation and in medical treatments. Because the inability to initiate apoptosis enhances tumour formation, current cancer treatments target this pathway. Within this framework, we have developed a transmission off-axis DH apparatus integrated with a micro incubator for investigation of living cells in a temperature and CO2 controlled environment. We employ DH to analyse the necrosis cell death induced by laser light (wavelength 473 nm, light power 4 mW). We have chosen as cellular model NIH 3T3 mouse embryonic fibroblasts because their adhesive features such as morphological changes, and the time needed to adhere and spread have been well characterized in the literature. We have monitored cell volume changes and morphological alterations in real time in order to study the necrosis process accurately and quantitatively. Cell volume changes were evaluated from the measured phase changes of light transmitted through cells. Our digital holographic experiments showed that after exposure of cells to laser light for 90-120 min., they swell and then take on a balloon-like shape until the plasma membrane ruptures and finally the cell volume decreases. Furthermore, we

Quantitative analysis of surface characteristics and morphology in Death Valley, California using AIRSAR data

NASA Technical Reports Server (NTRS)

Kierein-Young, K. S.; Kruse, F. A.; Lefkoff, A. B.

1992-01-01

The Jet Propulsion Laboratory Airborne Synthetic Aperture Radar (JPL-AIRSAR) is used to collect full polarimetric measurements at P-, L-, and C-bands. These data are analyzed using the radar analysis and visualization environment (RAVEN). The AIRSAR data are calibrated using in-scene corner reflectors to allow for quantitative analysis of the radar backscatter. RAVEN is used to extract surface characteristics. Inversion models are used to calculate quantitative surface roughness values and fractal dimensions. These values are used to generate synthetic surface plots that represent the small-scale surface structure of areas in Death Valley. These procedures are applied to a playa, smooth salt-pan, and alluvial fan surfaces in Death Valley. Field measurements of surface roughness are used to verify the accuracy.

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

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

Liu, Jue; Olds, Daniel; Peng, Rui

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. It is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Quantitative morphology in canine cutaneous soft tissue sarcomas.

PubMed

Simeonov, R; Ananiev, J; Gulubova, M

2015-12-01

Stained cytological specimens from 24 dogs with spontaneous soft tissue sarcomas [fibrosarcoma (n = 8), liposarcoma (n = 8) and haemangiopericytoma (n = 8)], and 24 dogs with reactive connective tissue lesions [granulation tissue (n = 12) and dermal fibrosis (n = 12)] were analysed by computer-assisted nuclear morphometry. The studied morphometric parameters were: mean nuclear area (MNA; µm(2)), mean nuclear perimeter (MNP; µm), mean nuclear diameter (MND mean; µm), minimum nuclear diameter (Dmin; µm) and maximum nuclear diameter (Dmax; µm). The study aimed to evaluate (1) possibility for quantitative differentiation of soft tissue sarcomas from reactive connective tissue lesions and (2) by using cytomorphometry, to differentiate the various histopathological soft tissue sarcomas subtypes in dogs. The mean values of all nuclear cytomorphometric parameters (except for Dmax) were statistically significantly higher in reactive connective tissue processes than in soft tissue sarcomas. At the same time, however, there were no considerable differences among the different sarcoma subtypes. The results demonstrated that the quantitative differentiation of reactive connective tissue processes from soft tissue sarcomas in dogs is possible, but the same was not true for the different canine soft tissue sarcoma subtypes. Further investigations on this topic are necessary for thorough explication of the role of quantitative morphology in the diagnostics of mesenchymal neoplasms and tumour-like fibrous lesions in dogs. © 2014 John Wiley & Sons Ltd.

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

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

Liu, Jue; Olds, Daniel; Peng, Rui

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. As a result, it is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Quantitative Analysis of the Morphology of {101} and {001} Faceted Anatase TiO 2 Nanocrystals and Its Implication on Photocatalytic Activity

DOE PAGES

Liu, Jue; Olds, Daniel; Peng, Rui; ...

2017-06-14

The atomistic structure and morphology (shape and size) of nanomaterials have strong influences on their physical and chemical properties. However, many characterization techniques focus exclusively on one length-scale regime or another when developing quantitative morphology/structural models. In this article, we demonstrate that powder X-ray diffraction and neutron pair distribution function (PDF) can be used to obtain accurate average morphology and atomistic structure of {001} and {101} faceted anatase TiO 2 nanocrystals based on differential evolution refinements using Debye scattering equation calculations. It is also demonstrated that the morphology polydispersity of TiO 2 nanocrystals can be effectively obtained from the diffractionmore » data via a numerical refinement routine. The morphology refinement results are in good agreement with those from transmission electron microscopy and the modeling of small angle neutron scattering data. This method is successfully used to quantify the facet-specified photocatalytic hydrogen evolution activity of anatase TiO 2 nanocrystals with different {001} to {101} ratios. It is found that the sample with an intermediate amount of both {001} and {101} facets shows the best photocatalytic hydrogen evolution reaction (HER) activity. As a result, it is expected that the simultaneous structure and morphology refinement technique can be generally used to study the relationship between morphology and functionality of nanomaterials.« less

Measurements of morphology and refractive indexes on human downy hairs using three-dimensional quantitative phase imaging.

PubMed

Lee, SangYun; Kim, Kyoohyun; Lee, Yuhyun; Park, Sungjin; Shin, Heejae; Yang, Jongwon; Ko, Kwanhong; Park, HyunJoo; Park, YongKeun

2015-01-01

We present optical measurements of morphology and refractive indexes (RIs) of human downy arm hairs using three-dimensional (3-D) quantitative phase imaging techniques. 3-D RI tomograms and high-resolution two-dimensional synthetic aperture images of individual downy arm hairs were measured using a Mach–Zehnder laser interferometric microscopy equipped with a two-axis galvanometer mirror. From the measured quantitative images, the RIs and morphological parameters of downy hairs were noninvasively quantified including the mean RI, volume, cylinder, and effective radius of individual hairs. In addition, the effects of hydrogen peroxide on individual downy hairs were investigated.

Quantitative analysis of nailfold capillary morphology in patients with fibromyalgia

PubMed Central

Choi, Dug-Hyun

2015-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Image processing and machine learning in the morphological analysis of blood cells.

PubMed

Rodellar, J; Alférez, S; Acevedo, A; Molina, A; Merino, A

2018-05-01

This review focuses on how image processing and machine learning can be useful for the morphological characterization and automatic recognition of cell images captured from peripheral blood smears. The basics of the 3 core elements (segmentation, quantitative features, and classification) are outlined, and recent literature is discussed. Although red blood cells are a significant part of this context, this study focuses on malignant lymphoid cells and blast cells. There is no doubt that these technologies may help the cytologist to perform efficient, objective, and fast morphological analysis of blood cells. They may also help in the interpretation of some morphological features and may serve as learning and survey tools. Although research is still needed, it is important to define screening strategies to exploit the potential of image-based automatic recognition systems integrated in the daily routine of laboratories along with other analysis methodologies. © 2018 John Wiley & Sons Ltd.

Quantitative Morphologic Analysis of Boulder Shape and Surface Texture to Infer Environmental History: A Case Study of Rock Breakdown at the Ephrata Fan, Channeled Scabland, Washington

NASA Technical Reports Server (NTRS)

Ehlmann, Bethany L.; Viles, Heather A.; Bourke, Mary C.

2008-01-01

Boulder morphology reflects both lithology and climate and is dictated by the combined effects of erosion, transport, and weathering. At present, morphologic information at the boulder scale is underutilized as a recorder of environmental processes, partly because of the lack of a systematic quantitative parameter set for reporting and comparing data sets. We develop such a parameter set, incorporating a range of measures of boulder form and surface texture. We use standard shape metrics measured in the field and fractal and morphometric classification methods borrowed from landscape analysis and applied to laser-scanned molds. The parameter set was pilot tested on three populations of basalt boulders with distinct breakdown histories in the Channeled Scabland, Washington: (1) basalt outcrop talus; (2) flood-transported boulders recently excavated from a quarry; and (3) flood-transported boulders, extensively weathered in situ on the Ephrata Fan surface. Size and shape data were found to distinguish between flood-transported and untransported boulders. Size and edge angles (approximately 120 degrees) of flood-transported boulders suggest removal by preferential fracturing along preexisting columnar joints, and curvature data indicate rounding relative to outcrop boulders. Surface textural data show that boulders which have been exposed at the surface are significantly rougher than those buried by fan sediments. Past signatures diagnostic of flood transport still persist on surface boulders, despite ongoing overprinting by processes in the present breakdown environment through roughening and fracturing in situ. Further use of this quantitative boulder parameter set at other terrestrial and planetary sites will aid in cataloging and understanding morphologic signatures of environmental processes.

Genetic analysis of root morphological traits in wheat.

PubMed

Petrarulo, Maria; Marone, Daniela; Ferragonio, Pina; Cattivelli, Luigi; Rubiales, Diego; De Vita, Pasquale; Mastrangelo, Anna Maria

2015-06-01

Traits related to root architecture are of great importance for yield performance of crop species, although they remain poorly understood. The present study is aimed at identifying the genomic regions involved in the control of root morphological traits in durum wheat (Triticum durum Desf.). A set of 123 recombinant inbred lines derived from the durum wheat cross of cvs. 'Creso' × 'Pedroso' were grown hydroponically to two growth stages, and were phenotypically evaluated for a number of root traits. In addition, meta-(M)QTL analysis was performed that considered the results of other root traits studies in wheat, to compare with the 'Creso' × 'Pedroso' cross and to increase the QTL detection power. Eight quantitative trait loci (QTL) for traits related to root morphology were identified on chromosomes 1A, 1B, 2A, 3A, 6A and 6B in the 'Creso' × 'Pedroso' segregating population. Twenty-two MQTL that comprised from two to six individual QTL that had widely varying confidence intervals were found on 14 chromosomes. The data from the present study provide a detailed analysis of the genetic basis of morphological root traits in wheat. This study of the 'Creso' × 'Pedroso' durum-wheat population has revealed some QTL that had not been previously identified.

Patellofemoral morphology is not related to pain using three-dimensional quantitative analysis in an older population: data from the Osteoarthritis Initiative

PubMed Central

Drew, Benjamin T.; Bowes, Michael A.; Redmond, Anthony C.; Dube, Bright; Kingsbury, Sarah R.; Conaghan, Philip G.

2017-01-01

Abstract Objectives Current structural associations of patellofemoral pain (PFP) are based on 2D imaging methodology with inherent measurement uncertainty due to positioning and rotation. This study employed novel technology to create 3D measures of commonly described patellofemoral joint imaging features and compared these features in people with and without PFP in a large cohort. Methods We compared two groups from the Osteoarthritis Initiative: one with localized PFP and pain on stairs, and a control group with no knee pain; both groups had no radiographic OA. MRI bone surfaces were automatically segmented and aligned using active appearance models. We applied t-tests, logistic regression and linear discriminant analysis to compare 13 imaging features (including patella position, trochlear morphology, facet area and tilt) converted into 3D equivalents, and a measure of overall 3D shape. Results One hundred and fifteen knees with PFP (mean age 59.7, BMI 27.5 kg/m2, female 58.2%) and 438 without PFP (mean age 63.6, BMI 26.9 kg/m2, female 52.9%) were included. After correction for multiple testing, no statistically significant differences were found between groups for any of the 3D imaging features or their combinations. A statistically significant discrimination was noted for overall 3D shape between genders, confirming the validity of the 3D measures. Conclusion Challenging current perceptions, no differences in patellofemoral morphology were found between older people with and without PFP using 3D quantitative imaging analysis. Further work is needed to see if these findings are replicated in a younger PFP population. PMID:28968747

Quantitative Correlation of 7B04 Aluminum Alloys Pitting Corrosion Morphology Characteristics with Stress Concentration Factor

NASA Astrophysics Data System (ADS)

Liu, Zhiguo; Yan, Guangyao; Mu, Zhitao; Li, Xudong

2018-01-01

The accelerated pitting corrosion test of 7B04 aluminum alloy specimen was carried out according to the spectrum which simulated airport environment, and the corresponding pitting corrosion damage was obtained and was defined through three parameters A and B and C which respectively denoted the corrosion pit surface length and width and corrosion pit depth. The ratio between three parameters could determine the morphology characteristics of corrosion pits. On this basis the stress concentration factor of typical corrosion pit morphology under certain load conditions was quantitatively analyzed. The research shows that the corrosion pits gradually incline to be ellipse in surface and moderate in depth, and most value of B/A and C/A lies in 1 between 4 and few maximum exceeds 4; The stress concentration factor Kf of corrosion pits is obviously affected by the its morphology, the value of Kf increases with corrosion pits depth increasement under certain corrosion pits surface geometry. Also, the value of Kf decreases with surface width increasement under certain corrosion pits depth. The research conclusion can set theory basis for corrosion fatigue life analysis of aircraft aluminum alloy structure.

Bio-Liquid Morphological Analysis

PubMed Central

Shatokhina, S.N.; Shabalin, V.N.; Buzoverya, M.E.; Punin, V.T.

2004-01-01

Information is presented on the new scientific line in medicine and biology: bio-liquid morphology. The interdisciplinary character of the given research area is emphasized. The problems and prospects of bio-liquid morphological analysis development both in applied and fundamental aspects are discussed. PMID:15349509

Cell wall staining with Trypan blue enables quantitative analysis of morphological changes in yeast cells.

PubMed

Liesche, Johannes; Marek, Magdalena; Günther-Pomorski, Thomas

2015-01-01

Yeast cells are protected by a cell wall that plays an important role in the exchange of substances with the environment. The cell wall structure is dynamic and can adapt to different physiological states or environmental conditions. For the investigation of morphological changes, selective staining with fluorescent dyes is a valuable tool. Furthermore, cell wall staining is used to facilitate sub-cellular localization experiments with fluorescently-labeled proteins and the detection of yeast cells in non-fungal host tissues. Here, we report staining of Saccharomyces cerevisiae cell wall with Trypan Blue, which emits strong red fluorescence upon binding to chitin and yeast glucan; thereby, it facilitates cell wall analysis by confocal and super-resolution microscopy. The staining pattern of Trypan Blue was similar to that of the widely used UV-excitable, blue fluorescent cell wall stain Calcofluor White. Trypan Blue staining facilitated quantification of cell size and cell wall volume when utilizing the optical sectioning capacity of a confocal microscope. This enabled the quantification of morphological changes during growth under anaerobic conditions and in the presence of chemicals, demonstrating the potential of this approach for morphological investigations or screening assays.

Patellofemoral morphology is not related to pain using three-dimensional quantitative analysis in an older population: data from the Osteoarthritis Initiative.

PubMed

Drew, Benjamin T; Bowes, Michael A; Redmond, Anthony C; Dube, Bright; Kingsbury, Sarah R; Conaghan, Philip G

2017-12-01

Current structural associations of patellofemoral pain (PFP) are based on 2D imaging methodology with inherent measurement uncertainty due to positioning and rotation. This study employed novel technology to create 3D measures of commonly described patellofemoral joint imaging features and compared these features in people with and without PFP in a large cohort. We compared two groups from the Osteoarthritis Initiative: one with localized PFP and pain on stairs, and a control group with no knee pain; both groups had no radiographic OA. MRI bone surfaces were automatically segmented and aligned using active appearance models. We applied t-tests, logistic regression and linear discriminant analysis to compare 13 imaging features (including patella position, trochlear morphology, facet area and tilt) converted into 3D equivalents, and a measure of overall 3D shape. One hundred and fifteen knees with PFP (mean age 59.7, BMI 27.5 kg/m2, female 58.2%) and 438 without PFP (mean age 63.6, BMI 26.9 kg/m2, female 52.9%) were included. After correction for multiple testing, no statistically significant differences were found between groups for any of the 3D imaging features or their combinations. A statistically significant discrimination was noted for overall 3D shape between genders, confirming the validity of the 3D measures. Challenging current perceptions, no differences in patellofemoral morphology were found between older people with and without PFP using 3D quantitative imaging analysis. Further work is needed to see if these findings are replicated in a younger PFP population. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Rheumatology.

Quantitative Machine Learning Analysis of Brain MRI Morphology throughout Aging.

PubMed

Shamir, Lior; Long, Joe

2016-01-01

While cognition is clearly affected by aging, it is unclear whether the process of brain aging is driven solely by accumulation of environmental damage, or involves biological pathways. We applied quantitative image analysis to profile the alteration of brain tissues during aging. A dataset of 463 brain MRI images taken from a cohort of 416 subjects was analyzed using a large set of low-level numerical image content descriptors computed from the entire brain MRI images. The correlation between the numerical image content descriptors and the age was computed, and the alterations of the brain tissues during aging were quantified and profiled using machine learning. The comprehensive set of global image content descriptors provides high Pearson correlation of ~0.9822 with the chronological age, indicating that the machine learning analysis of global features is sensitive to the age of the subjects. Profiling of the predicted age shows several periods of mild changes, separated by shorter periods of more rapid alterations. The periods with the most rapid changes were around the age of 55, and around the age of 65. The results show that the process of brain aging of is not linear, and exhibit short periods of rapid aging separated by periods of milder change. These results are in agreement with patterns observed in cognitive decline, mental health status, and general human aging, suggesting that brain aging might not be driven solely by accumulation of environmental damage. Code and data used in the experiments are publicly available.

Quantitative Analysis of Rat Dorsal Root Ganglion Neurons Cultured on Microelectrode Arrays Based on Fluorescence Microscopy Image Processing.

PubMed

Mari, João Fernando; Saito, José Hiroki; Neves, Amanda Ferreira; Lotufo, Celina Monteiro da Cruz; Destro-Filho, João-Batista; Nicoletti, Maria do Carmo

2015-12-01

Microelectrode Arrays (MEA) are devices for long term electrophysiological recording of extracellular spontaneous or evocated activities on in vitro neuron culture. This work proposes and develops a framework for quantitative and morphological analysis of neuron cultures on MEAs, by processing their corresponding images, acquired by fluorescence microscopy. The neurons are segmented from the fluorescence channel images using a combination of segmentation by thresholding, watershed transform, and object classification. The positioning of microelectrodes is obtained from the transmitted light channel images using the circular Hough transform. The proposed method was applied to images of dissociated culture of rat dorsal root ganglion (DRG) neuronal cells. The morphological and topological quantitative analysis carried out produced information regarding the state of culture, such as population count, neuron-to-neuron and neuron-to-microelectrode distances, soma morphologies, neuron sizes, neuron and microelectrode spatial distributions. Most of the analysis of microscopy images taken from neuronal cultures on MEA only consider simple qualitative analysis. Also, the proposed framework aims to standardize the image processing and to compute quantitative useful measures for integrated image-signal studies and further computational simulations. As results show, the implemented microelectrode identification method is robust and so are the implemented neuron segmentation and classification one (with a correct segmentation rate up to 84%). The quantitative information retrieved by the method is highly relevant to assist the integrated signal-image study of recorded electrophysiological signals as well as the physical aspects of the neuron culture on MEA. Although the experiments deal with DRG cell images, cortical and hippocampal cell images could also be processed with small adjustments in the image processing parameter estimation.

Visualization and Quantitative Analysis of Crack-Tip Plastic Zone in Pure Nickel

NASA Astrophysics Data System (ADS)

Kelton, Randall; Sola, Jalal Fathi; Meletis, Efstathios I.; Huang, Haiying

2018-05-01

Changes in surface morphology have long been thought to be associated with crack propagation in metallic materials. We have studied areal surface texture changes around crack tips in an attempt to understand the correlations between surface texture changes and crack growth behavior. Detailed profiling of the fatigue sample surface was carried out at short fatigue intervals. An image processing algorithm was developed to calculate the surface texture changes. Quantitative analysis of the crack-tip plastic zone, crack-arrested sites near triple points, and large surface texture changes associated with crack release from arrested locations was carried out. The results indicate that surface texture imaging enables visualization of the development of plastic deformation around a crack tip. Quantitative analysis of the surface texture changes reveals the effects of local microstructures on the crack growth behavior.

Automated Morphological Analysis of Microglia After Stroke.

PubMed

Heindl, Steffanie; Gesierich, Benno; Benakis, Corinne; Llovera, Gemma; Duering, Marco; Liesz, Arthur

2018-01-01

Microglia are the resident immune cells of the brain and react quickly to changes in their environment with transcriptional regulation and morphological changes. Brain tissue injury such as ischemic stroke induces a local inflammatory response encompassing microglial activation. The change in activation status of a microglia is reflected in its gradual morphological transformation from a highly ramified into a less ramified or amoeboid cell shape. For this reason, the morphological changes of microglia are widely utilized to quantify microglial activation and studying their involvement in virtually all brain diseases. However, the currently available methods, which are mainly based on manual rating of immunofluorescent microscopic images, are often inaccurate, rater biased, and highly time consuming. To address these issues, we created a fully automated image analysis tool, which enables the analysis of microglia morphology from a confocal Z-stack and providing up to 59 morphological features. We developed the algorithm on an exploratory dataset of microglial cells from a stroke mouse model and validated the findings on an independent data set. In both datasets, we could demonstrate the ability of the algorithm to sensitively discriminate between the microglia morphology in the peri-infarct and the contralateral, unaffected cortex. Dimensionality reduction by principal component analysis allowed to generate a highly sensitive compound score for microglial shape analysis. Finally, we tested for concordance of results between the novel automated analysis tool and the conventional manual analysis and found a high degree of correlation. In conclusion, our novel method for the fully automatized analysis of microglia morphology shows excellent accuracy and time efficacy compared to traditional analysis methods. This tool, which we make openly available, could find application to study microglia morphology using fluorescence imaging in a wide range of brain disease models.

Quantitative coronary plaque analysis predicts high-risk plaque morphology on coronary computed tomography angiography: results from the ROMICAT II trial.

PubMed

Liu, Ting; Maurovich-Horvat, Pál; Mayrhofer, Thomas; Puchner, Stefan B; Lu, Michael T; Ghemigian, Khristine; Kitslaar, Pieter H; Broersen, Alexander; Pursnani, Amit; Hoffmann, Udo; Ferencik, Maros

2018-02-01

Semi-automated software can provide quantitative assessment of atherosclerotic plaques on coronary CT angiography (CTA). The relationship between established qualitative high-risk plaque features and quantitative plaque measurements has not been studied. We analyzed the association between quantitative plaque measurements and qualitative high-risk plaque features on coronary CTA. We included 260 patients with plaque who underwent coronary CTA in the Rule Out Myocardial Infarction/Ischemia Using Computer Assisted Tomography (ROMICAT) II trial. Quantitative plaque assessment and qualitative plaque characterization were performed on a per coronary segment basis. Quantitative coronary plaque measurements included plaque volume, plaque burden, remodeling index, and diameter stenosis. In qualitative analysis, high-risk plaque was present if positive remodeling, low CT attenuation plaque, napkin-ring sign or spotty calcium were detected. Univariable and multivariable logistic regression analyses were performed to assess the association between quantitative and qualitative high-risk plaque assessment. Among 888 segments with coronary plaque, high-risk plaque was present in 391 (44.0%) segments by qualitative analysis. In quantitative analysis, segments with high-risk plaque had higher total plaque volume, low CT attenuation plaque volume, plaque burden and remodeling index. Quantitatively assessed low CT attenuation plaque volume (odds ratio 1.12 per 1 mm 3 , 95% CI 1.04-1.21), positive remodeling (odds ratio 1.25 per 0.1, 95% CI 1.10-1.41) and plaque burden (odds ratio 1.53 per 0.1, 95% CI 1.08-2.16) were associated with high-risk plaque. Quantitative coronary plaque characteristics (low CT attenuation plaque volume, positive remodeling and plaque burden) measured by semi-automated software correlated with qualitative assessment of high-risk plaque features.

Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

PubMed Central

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

2016-01-01

Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

Making quantitative morphological variation from basic developmental processes: where are we? The case of the Drosophila wing

PubMed Central

Alexis, Matamoro-Vidal; Isaac, Salazar-Ciudad; David, Houle

2015-01-01

One of the aims of evolutionary developmental biology is to discover the developmental origins of morphological variation. The discipline has mainly focused on qualitative morphological differences (e.g., presence or absence of a structure) between species. Studies addressing subtle, quantitative variation are less common. The Drosophila wing is a model for the study of development and evolution, making it suitable to investigate the developmental mechanisms underlying the subtle quantitative morphological variation observed in nature. Previous reviews have focused on the processes involved in wing differentiation, patterning and growth. Here, we investigate what is known about how the wing achieves its final shape, and what variation in development is capable of generating the variation in wing shape observed in nature. Three major developmental stages need to be considered: larval development, pupariation, and pupal development. The major cellular processes involved in the determination of tissue size and shape are cell proliferation, cell death, oriented cell division and oriented cell intercalation. We review how variation in temporal and spatial distribution of growth and transcription factors affects these cellular mechanisms, which in turn affects wing shape. We then discuss which aspects of the wing morphological variation are predictable on the basis of these mechanisms. PMID:25619644

Automatic quantification of morphological features for hepatic trabeculae analysis in stained liver specimens

PubMed Central

Ishikawa, Masahiro; Murakami, Yuri; Ahi, Sercan Taha; Yamaguchi, Masahiro; Kobayashi, Naoki; Kiyuna, Tomoharu; Yamashita, Yoshiko; Saito, Akira; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie

2016-01-01

Abstract. This paper proposes a digital image analysis method to support quantitative pathology by automatically segmenting the hepatocyte structure and quantifying its morphological features. To structurally analyze histopathological hepatic images, we isolate the trabeculae by extracting the sinusoids, fat droplets, and stromata. We then measure the morphological features of the extracted trabeculae, divide the image into cords, and calculate the feature values of the local cords. We propose a method of calculating the nuclear–cytoplasmic ratio, nuclear density, and number of layers using the local cords. Furthermore, we evaluate the effectiveness of the proposed method using surgical specimens. The proposed method was found to be an effective method for the quantification of the Edmondson grade. PMID:27335894

Quantitative analysis of cardiovascular MR images.

PubMed

van der Geest, R J; de Roos, A; van der Wall, E E; Reiber, J H

1997-06-01

The diagnosis of cardiovascular disease requires the precise assessment of both morphology and function. Nearly all aspects of cardiovascular function and flow can be quantified nowadays with fast magnetic resonance (MR) imaging techniques. Conventional and breath-hold cine MR imaging allow the precise and highly reproducible assessment of global and regional left ventricular function. During the same examination, velocity encoded cine (VEC) MR imaging provides measurements of blood flow in the heart and great vessels. Quantitative image analysis often still relies on manual tracing of contours in the images. Reliable automated or semi-automated image analysis software would be very helpful to overcome the limitations associated with the manual and tedious processing of the images. Recent progress in MR imaging of the coronary arteries and myocardial perfusion imaging with contrast media, along with the further development of faster imaging sequences, suggest that MR imaging could evolve into a single technique ('one stop shop') for the evaluation of many aspects of heart disease. As a result, it is very likely that the need for automated image segmentation and analysis software algorithms will further increase. In this paper the developments directed towards the automated image analysis and semi-automated contour detection for cardiovascular MR imaging are presented.

Quantitative assessment of cancer cell morphology and movement using telecentric digital holographic microscopy

NASA Astrophysics Data System (ADS)

Nguyen, Thanh C.; Nehmetallah, George; Lam, Van; Chung, Byung Min; Raub, Christopher

2017-02-01

Digital holographic microscopy (DHM) provides label-free and real-time quantitative phase information relevant to the analysis of dynamic biological systems. A DHM based on telecentric configuration optically mitigates phase aberrations due to the microscope objective and linear high frequency fringes due to the reference beam thus minimizing digital aberration correction needed for distortion free 3D reconstruction. The purpose of this work is to quantitatively assess growth and migratory behavior of invasive cancer cells using a telecentric DHM system. Together, the height and lateral shape features of individual cells, determined from time-lapse series of phase reconstructions, should reveal aspects of cell migration, cell-matrix adhesion, and cell cycle phase transitions. To test this, MDA-MB-231 breast cancer cells were cultured on collagen-coated or un-coated glass, and 3D holograms were reconstructed over 2 hours. Cells on collagencoated glass had an average 14% larger spread area than cells on uncoated glass (n=18-22 cells/group). The spread area of cells on uncoated glass were 15-21% larger than cells seeded on collagen hydrogels (n=18-22 cells/group). Premitotic cell rounding was observed with average phase height increasing 57% over 10 minutes. Following cell division phase height decreased linearly (R2=0.94) to 58% of the original height pre-division. Phase objects consistent with lamellipodia were apparent from the reconstructions at the leading edge of migrating cells. These data demonstrate the ability to track quantitative phase parameters and relate them to cell morphology during cell migration and division on adherent substrates, using telecentric DHM. The technique enables future studies of cell-matrix interactions relevant to cancer.

Quantitative assessment of cancer cell morphology and motility using telecentric digital holographic microscopy and machine learning.

PubMed

Lam, Van K; Nguyen, Thanh C; Chung, Byung M; Nehmetallah, George; Raub, Christopher B

2018-03-01

The noninvasive, fast acquisition of quantitative phase maps using digital holographic microscopy (DHM) allows tracking of rapid cellular motility on transparent substrates. On two-dimensional surfaces in vitro, MDA-MB-231 cancer cells assume several morphologies related to the mode of migration and substrate stiffness, relevant to mechanisms of cancer invasiveness in vivo. The quantitative phase information from DHM may accurately classify adhesive cancer cell subpopulations with clinical relevance. To test this, cells from the invasive breast cancer MDA-MB-231 cell line were cultured on glass, tissue-culture treated polystyrene, and collagen hydrogels, and imaged with DHM followed by epifluorescence microscopy after staining F-actin and nuclei. Trends in cell phase parameters were tracked on the different substrates, during cell division, and during matrix adhesion, relating them to F-actin features. Support vector machine learning algorithms were trained and tested using parameters from holographic phase reconstructions and cell geometric features from conventional phase images, and used to distinguish between elongated and rounded cell morphologies. DHM was able to distinguish between elongated and rounded morphologies of MDA-MB-231 cells with 94% accuracy, compared to 83% accuracy using cell geometric features from conventional brightfield microscopy. This finding indicates the potential of DHM to detect and monitor cancer cell morphologies relevant to cell cycle phase status, substrate adhesion, and motility. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Comparative analysis of gene expression level by quantitative real-time PCR has limited application in objects with different morphology.

PubMed

Demidenko, Natalia V; Penin, Aleksey A

2012-01-01

qRT-PCR is a generally acknowledged method for gene expression analysis due to its precision and reproducibility. However, it is well known that the accuracy of qRT-PCR data varies greatly depending on the experimental design and data analysis. Recently, a set of guidelines has been proposed that aims to improve the reliability of qRT-PCR. However, there are additional factors that have not been taken into consideration in these guidelines that can seriously affect the data obtained using this method. In this study, we report the influence that object morphology can have on qRT-PCR data. We have used a number of Arabidopsis thaliana mutants with altered floral morphology as models for this study. These mutants have been well characterised (including in terms of gene expression levels and patterns) by other techniques. This allows us to compare the results from the qRT-PCR with the results inferred from other methods. We demonstrate that the comparison of gene expression levels in objects that differ greatly in their morphology can lead to erroneous results.

Collagen morphology and texture analysis: from statistics to classification

PubMed Central

Mostaço-Guidolin, Leila B.; Ko, Alex C.-T.; Wang, Fei; Xiang, Bo; Hewko, Mark; Tian, Ganghong; Major, Arkady; Shiomi, Masashi; Sowa, Michael G.

2013-01-01

In this study we present an image analysis methodology capable of quantifying morphological changes in tissue collagen fibril organization caused by pathological conditions. Texture analysis based on first-order statistics (FOS) and second-order statistics such as gray level co-occurrence matrix (GLCM) was explored to extract second-harmonic generation (SHG) image features that are associated with the structural and biochemical changes of tissue collagen networks. Based on these extracted quantitative parameters, multi-group classification of SHG images was performed. With combined FOS and GLCM texture values, we achieved reliable classification of SHG collagen images acquired from atherosclerosis arteries with >90% accuracy, sensitivity and specificity. The proposed methodology can be applied to a wide range of conditions involving collagen re-modeling, such as in skin disorders, different types of fibrosis and muscular-skeletal diseases affecting ligaments and cartilage. PMID:23846580

[Morphologic and AFLP analysis of relationships between tulip species Tulipa biebersteiniana (Liliaceae)].

PubMed

Kutlunina, N A; Polezhaeva, M A; Permiakova, M V

2013-04-01

In populations of four species of tulips, (Tulipa biebersteiniana, T. patens, T. scytica and T. riparia) from the Volgograd, Kurgansk, Orenburg, and Chelyabinsk regions and the Republic of Bashkortostan, genetic diversity was studied by means of morphological and AFLP analysis. A morphological analysis of seven quantitative and two qualitative criteria was carried out. Three selective EcoRI/MseI primer pairs allowed one to genotype 81 individuals from 13 tulip populations with 87 loci. The low level of variability by AFLP loci were revealed in all species, including T. biebersteiniana (P = 20.41%, UH(e) = 0.075), T. patens (26.97%, 0.082), T. scytica (27.53%, 0.086), and T. riparia (27.72%, 0.096). According to the AMOVA results, the variability proportion that characterizes the differences between the four Tulip species was lower (F(CT) = 0.235) than between populations within species (F(ST) = 0.439). Tulipa patens is well differentiated by means of Nei's distances, coordination, and analysis in the STRUCTURE program. An analysis in the STRUCTURE revealed four genetic groups of tulips that are not completely in accordance with the analyzed species. This acknowledges the presence of complicated genetic process in the tulip population.

Statistical analysis and data mining of digital reconstructions of dendritic morphologies.

PubMed

Polavaram, Sridevi; Gillette, Todd A; Parekh, Ruchi; Ascoli, Giorgio A

2014-01-01

Neuronal morphology is diverse among animal species, developmental stages, brain regions, and cell types. The geometry of individual neurons also varies substantially even within the same cell class. Moreover, specific histological, imaging, and reconstruction methodologies can differentially affect morphometric measures. The quantitative characterization of neuronal arbors is necessary for in-depth understanding of the structure-function relationship in nervous systems. The large collection of community-contributed digitally reconstructed neurons available at NeuroMorpho.Org constitutes a "big data" research opportunity for neuroscience discovery beyond the approaches typically pursued in single laboratories. To illustrate these potential and related challenges, we present a database-wide statistical analysis of dendritic arbors enabling the quantification of major morphological similarities and differences across broadly adopted metadata categories. Furthermore, we adopt a complementary unsupervised approach based on clustering and dimensionality reduction to identify the main morphological parameters leading to the most statistically informative structural classification. We find that specific combinations of measures related to branching density, overall size, tortuosity, bifurcation angles, arbor flatness, and topological asymmetry can capture anatomically and functionally relevant features of dendritic trees. The reported results only represent a small fraction of the relationships available for data exploration and hypothesis testing enabled by sharing of digital morphological reconstructions.

Quantitative genetic analysis of agronomic and morphological traits in sorghum, Sorghum bicolor

PubMed Central

Mohammed, Riyazaddin; Are, Ashok K.; Bhavanasi, Ramaiah; Munghate, Rajendra S.; Kavi Kishor, Polavarapu B.; Sharma, Hari C.

2015-01-01

The productivity in sorghum is low, owing to various biotic and abiotic constraints. Combining insect resistance with desirable agronomic and morphological traits is important to increase sorghum productivity. Therefore, it is important to understand the variability for various agronomic traits, their heritabilities and nature of gene action to develop appropriate strategies for crop improvement. Therefore, a full diallel set of 10 parents and their 90 crosses including reciprocals were evaluated in replicated trials during the 2013–14 rainy and postrainy seasons. The crosses between the parents with early- and late-flowering flowered early, indicating dominance of earliness for anthesis in the test material used. Association between the shoot fly resistance, morphological, and agronomic traits suggested complex interactions between shoot fly resistance and morphological traits. Significance of the mean sum of squares for GCA (general combining ability) and SCA (specific combining ability) of all the studied traits suggested the importance of both additive and non-additive components in inheritance of these traits. The GCA/SCA, and the predictability ratios indicated predominance of additive gene effects for majority of the traits studied. High broad-sense and narrow-sense heritability estimates were observed for most of the morphological and agronomic traits. The significance of reciprocal combining ability effects for days to 50% flowering, plant height and 100 seed weight, suggested maternal effects for inheritance of these traits. Plant height and grain yield across seasons, days to 50% flowering, inflorescence exsertion, and panicle shape in the postrainy season showed greater specific combining ability variance, indicating the predominance of non-additive type of gene action/epistatic interactions in controlling the expression of these traits. Additive gene action in the rainy season, and dominance in the postrainy season for days to 50% flowering and plant

A novel method for morphological pleomorphism and heterogeneity quantitative measurement: Named cell feature level co-occurrence matrix.

PubMed

Saito, Akira; Numata, Yasushi; Hamada, Takuya; Horisawa, Tomoyoshi; Cosatto, Eric; Graf, Hans-Peter; Kuroda, Masahiko; Yamamoto, Yoichiro

2016-01-01

Recent developments in molecular pathology and genetic/epigenetic analysis of cancer tissue have resulted in a marked increase in objective and measurable data. In comparison, the traditional morphological analysis approach to pathology diagnosis, which can connect these molecular data and clinical diagnosis, is still mostly subjective. Even though the advent and popularization of digital pathology has provided a boost to computer-aided diagnosis, some important pathological concepts still remain largely non-quantitative and their associated data measurements depend on the pathologist's sense and experience. Such features include pleomorphism and heterogeneity. In this paper, we propose a method for the objective measurement of pleomorphism and heterogeneity, using the cell-level co-occurrence matrix. Our method is based on the widely used Gray-level co-occurrence matrix (GLCM), where relations between neighboring pixel intensity levels are captured into a co-occurrence matrix, followed by the application of analysis functions such as Haralick features. In the pathological tissue image, through image processing techniques, each nucleus can be measured and each nucleus has its own measureable features like nucleus size, roundness, contour length, intra-nucleus texture data (GLCM is one of the methods). In GLCM each nucleus in the tissue image corresponds to one pixel. In this approach the most important point is how to define the neighborhood of each nucleus. We define three types of neighborhoods of a nucleus, then create the co-occurrence matrix and apply Haralick feature functions. In each image pleomorphism and heterogeneity are then determined quantitatively. For our method, one pixel corresponds to one nucleus feature, and we therefore named our method Cell Feature Level Co-occurrence Matrix (CFLCM). We tested this method for several nucleus features. CFLCM is showed as a useful quantitative method for pleomorphism and heterogeneity on histopathological image

Quantitative morphometric analysis of hepatocellular carcinoma: development of a programmed algorithm and preliminary application.

PubMed

Yap, Felix Y; Bui, James T; Knuttinen, M Grace; Walzer, Natasha M; Cotler, Scott J; Owens, Charles A; Berkes, Jamie L; Gaba, Ron C

2013-01-01

The quantitative relationship between tumor morphology and malignant potential has not been explored in liver tumors. We designed a computer algorithm to analyze shape features of hepatocellular carcinoma (HCC) and tested feasibility of morphologic analysis. Cross-sectional images from 118 patients diagnosed with HCC between 2007 and 2010 were extracted at the widest index tumor diameter. The tumor margins were outlined, and point coordinates were input into a MATLAB (MathWorks Inc., Natick, Massachusetts, USA) algorithm. Twelve shape descriptors were calculated per tumor: the compactness, the mean radial distance (MRD), the RD standard deviation (RDSD), the RD area ratio (RDAR), the zero crossings, entropy, the mean Feret diameter (MFD), the Feret ratio, the convex hull area (CHA) and perimeter (CHP) ratios, the elliptic compactness (EC), and the elliptic irregularity (EI). The parameters were correlated with the levels of alpha-fetoprotein (AFP) as an indicator of tumor aggressiveness. The quantitative morphometric analysis was technically successful in all cases. The mean parameters were as follows: compactness 0.88±0.086, MRD 0.83±0.056, RDSD 0.087±0.037, RDAR 0.045±0.023, zero crossings 6±2.2, entropy 1.43±0.16, MFD 4.40±3.14 cm, Feret ratio 0.78±0.089, CHA 0.98±0.027, CHP 0.98±0.030, EC 0.95±0.043, and EI 0.95±0.023. MFD and RDAR provided the widest value range for the best shape discrimination. The larger tumors were less compact, more concave, and less ellipsoid than the smaller tumors (P < 0.0001). AFP-producing tumors displayed greater morphologic irregularity based on several parameters, including compactness, MRD, RDSD, RDAR, entropy, and EI (P < 0.05 for all). Computerized HCC image analysis using shape descriptors is technically feasible. Aggressively growing tumors have wider diameters and more irregular margins. Future studies will determine further clinical applications for this morphologic analysis.

Quantitative Evaluation of Medial Temporal Lobe Morphology in Children with Febrile Status Epilepticus: Results of the FEBSTAT Study.

PubMed

McClelland, A C; Gomes, W A; Shinnar, S; Hesdorffer, D C; Bagiella, E; Lewis, D V; Bello, J A; Chan, S; MacFall, J; Chen, M; Pellock, J M; Nordli, D R; Frank, L M; Moshé, S L; Shinnar, R C; Sun, S

2016-12-01

The pathogenesis of febrile status epilepticus is poorly understood, but prior studies have suggested an association with temporal lobe abnormalities, including hippocampal malrotation. We used a quantitative morphometric method to assess the association between temporal lobe morphology and febrile status epilepticus. Brain MR imaging was performed in children presenting with febrile status epilepticus and control subjects as part of the Consequences of Prolonged Febrile Seizures in Childhood study. Medial temporal lobe morphologic parameters were measured manually, including the distance of the hippocampus from the midline, hippocampal height:width ratio, hippocampal angle, collateral sulcus angle, and width of the temporal horn. Temporal lobe morphologic parameters were correlated with the presence of visual hippocampal malrotation; the strongest association was with left temporal horn width (P < .001; adjusted OR, 10.59). Multiple morphologic parameters correlated with febrile status epilepticus, encompassing both the right and left sides. This association was statistically strongest in the right temporal lobe, whereas hippocampal malrotation was almost exclusively left-sided in this cohort. The association between temporal lobe measurements and febrile status epilepticus persisted when the analysis was restricted to cases with visually normal imaging findings without hippocampal malrotation or other visually apparent abnormalities. Several component morphologic features of hippocampal malrotation are independently associated with febrile status epilepticus, even when complete hippocampal malrotation is absent. Unexpectedly, this association predominantly involves the right temporal lobe. These findings suggest that a spectrum of bilateral temporal lobe anomalies are associated with febrile status epilepticus in children. Hippocampal malrotation may represent a visually apparent subset of this spectrum. © 2016 by American Journal of Neuroradiology.

Quantitative analysis of fetal facial morphology using 3D ultrasound and statistical shape modeling: a feasibility study.

PubMed

Dall'Asta, Andrea; Schievano, Silvia; Bruse, Jan L; Paramasivam, Gowrishankar; Kaihura, Christine Tita; Dunaway, David; Lees, Christoph C

2017-07-01

The antenatal detection of facial dysmorphism using 3-dimensional ultrasound may raise the suspicion of an underlying genetic condition but infrequently leads to a definitive antenatal diagnosis. Despite advances in array and noninvasive prenatal testing, not all genetic conditions can be ascertained from such testing. The aim of this study was to investigate the feasibility of quantitative assessment of fetal face features using prenatal 3-dimensional ultrasound volumes and statistical shape modeling. STUDY DESIGN: Thirteen normal and 7 abnormal stored 3-dimensional ultrasound fetal face volumes were analyzed, at a median gestation of 29 +4  weeks (25 +0 to 36 +1 ). The 20 3-dimensional surface meshes generated were aligned and served as input for a statistical shape model, which computed the mean 3-dimensional face shape and 3-dimensional shape variations using principal component analysis. Ten shape modes explained more than 90% of the total shape variability in the population. While the first mode accounted for overall size differences, the second highlighted shape feature changes from an overall proportionate toward a more asymmetric face shape with a wide prominent forehead and an undersized, posteriorly positioned chin. Analysis of the Mahalanobis distance in principal component analysis shape space suggested differences between normal and abnormal fetuses (median and interquartile range distance values, 7.31 ± 5.54 for the normal group vs 13.27 ± 9.82 for the abnormal group) (P = .056). This feasibility study demonstrates that objective characterization and quantification of fetal facial morphology is possible from 3-dimensional ultrasound. This technique has the potential to assist in utero diagnosis, particularly of rare conditions in which facial dysmorphology is a feature. Copyright © 2017 Elsevier Inc. All rights reserved.

Correlation and sex differences between ankle and knee cartilage morphology determined by quantitative magnetic resonance imaging

PubMed Central

Eckstein, F; Siedek, V; Glaser, C; Al-Ali, D; Englmeier, K; Reiser, M; Graichen, H

2004-01-01

Objective: To study the correlation between ankle and knee cartilage morphology to test the hypothesis that knee joint cartilage loss in gonarthritis can be estimated retrospectively using quantitative MRI analysis of the knee and ankle and established regression equations; and to test the hypothesis that sex differences in joint surface area are larger in the knee than the ankle, which may explain the greater incidence of knee osteoarthritis in elderly women than in elderly men. Methods: Sagittal MR images (3D FLASH WE) of the knee and hind foot were acquired in 29 healthy subjects (14 women, 15 men; mean (SD) age, 25 (3) years), with no signs joint disease. Cartilage volume, thickness, and joint surface area were determined in the knee, ankle, and subtalar joint. Results: Knee cartilage volumes and joint surface areas showed only moderate correlations with those of the ankle and subtalar joint (r = 0.33 to 0.81). The correlations of cartilage thickness between the two joints were weaker still (r = –0.05 to 0.53). Sex differences in cartilage morphology at the knee and the ankle were similar, with surface areas being –17.5% to –23.5% lower in women than in men. Conclusions: Only moderate correlations in cartilage morphology of healthy subjects were found between knee and ankle. It is therefore impractical to estimate knee joint cartilage loss a posteriori in cross sectional studies by measuring the hind foot and then applying a scaling factor. Sex differences in cartilage morphology do not explain differences in osteoarthritis incidence between men and women in the knee and ankle. PMID:15479900

Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

PubMed

Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

2016-11-14

A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

Automated quantitative 3D analysis of aorta size, morphology, and mural calcification distributions

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

Kurugol, Sila, E-mail: sila.kurugol@childrens.harvard.edu; Come, Carolyn E.; Diaz, Alejandro A.

Purpose: The purpose of this work is to develop a fully automated pipeline to compute aorta morphology and calcification measures in large cohorts of CT scans that can be used to investigate the potential of these measures as imaging biomarkers of cardiovascular disease. Methods: The first step of the automated pipeline is aorta segmentation. The algorithm the authors propose first detects an initial aorta boundary by exploiting cross-sectional circularity of aorta in axial slices and aortic arch in reformatted oblique slices. This boundary is then refined by a 3D level-set segmentation that evolves the boundary to the location of nearbymore » edges. The authors then detect the aortic calcifications with thresholding and filter out the false positive regions due to nearby high intensity structures based on their anatomical location. The authors extract the centerline and oblique cross sections of the segmented aortas and compute the aorta morphology and calcification measures of the first 2500 subjects from COPDGene study. These measures include volume and number of calcified plaques and measures of vessel morphology such as average cross-sectional area, tortuosity, and arch width. Results: The authors computed the agreement between the algorithm and expert segmentations on 45 CT scans and obtained a closest point mean error of 0.62 ± 0.09 mm and a Dice coefficient of 0.92 ± 0.01. The calcification detection algorithm resulted in an improved true positive detection rate of 0.96 compared to previous work. The measurements of aorta size agreed with the measurements reported in previous work. The initial results showed associations of aorta morphology with calcification and with aging. These results may indicate aorta stiffening and unwrapping with calcification and aging. Conclusions: The authors have developed an objective tool to assess aorta morphology and aortic calcium plaques on CT scans that may be used to provide information about the presence of

Automated quantitative 3D analysis of aorta size, morphology, and mural calcification distributions.

PubMed

Kurugol, Sila; Come, Carolyn E; Diaz, Alejandro A; Ross, James C; Kinney, Greg L; Black-Shinn, Jennifer L; Hokanson, John E; Budoff, Matthew J; Washko, George R; San Jose Estepar, Raul

2015-09-01

The purpose of this work is to develop a fully automated pipeline to compute aorta morphology and calcification measures in large cohorts of CT scans that can be used to investigate the potential of these measures as imaging biomarkers of cardiovascular disease. The first step of the automated pipeline is aorta segmentation. The algorithm the authors propose first detects an initial aorta boundary by exploiting cross-sectional circularity of aorta in axial slices and aortic arch in reformatted oblique slices. This boundary is then refined by a 3D level-set segmentation that evolves the boundary to the location of nearby edges. The authors then detect the aortic calcifications with thresholding and filter out the false positive regions due to nearby high intensity structures based on their anatomical location. The authors extract the centerline and oblique cross sections of the segmented aortas and compute the aorta morphology and calcification measures of the first 2500 subjects from COPDGene study. These measures include volume and number of calcified plaques and measures of vessel morphology such as average cross-sectional area, tortuosity, and arch width. The authors computed the agreement between the algorithm and expert segmentations on 45 CT scans and obtained a closest point mean error of 0.62 ± 0.09 mm and a Dice coefficient of 0.92 ± 0.01. The calcification detection algorithm resulted in an improved true positive detection rate of 0.96 compared to previous work. The measurements of aorta size agreed with the measurements reported in previous work. The initial results showed associations of aorta morphology with calcification and with aging. These results may indicate aorta stiffening and unwrapping with calcification and aging. The authors have developed an objective tool to assess aorta morphology and aortic calcium plaques on CT scans that may be used to provide information about the presence of cardiovascular disease and its clinical impact in

Automated quantitative 3D analysis of aorta size, morphology, and mural calcification distributions

PubMed Central

Kurugol, Sila; Come, Carolyn E.; Diaz, Alejandro A.; Ross, James C.; Kinney, Greg L.; Black-Shinn, Jennifer L.; Hokanson, John E.; Budoff, Matthew J.; Washko, George R.; San Jose Estepar, Raul

2015-01-01

Purpose: The purpose of this work is to develop a fully automated pipeline to compute aorta morphology and calcification measures in large cohorts of CT scans that can be used to investigate the potential of these measures as imaging biomarkers of cardiovascular disease. Methods: The first step of the automated pipeline is aorta segmentation. The algorithm the authors propose first detects an initial aorta boundary by exploiting cross-sectional circularity of aorta in axial slices and aortic arch in reformatted oblique slices. This boundary is then refined by a 3D level-set segmentation that evolves the boundary to the location of nearby edges. The authors then detect the aortic calcifications with thresholding and filter out the false positive regions due to nearby high intensity structures based on their anatomical location. The authors extract the centerline and oblique cross sections of the segmented aortas and compute the aorta morphology and calcification measures of the first 2500 subjects from COPDGene study. These measures include volume and number of calcified plaques and measures of vessel morphology such as average cross-sectional area, tortuosity, and arch width. Results: The authors computed the agreement between the algorithm and expert segmentations on 45 CT scans and obtained a closest point mean error of 0.62 ± 0.09 mm and a Dice coefficient of 0.92 ± 0.01. The calcification detection algorithm resulted in an improved true positive detection rate of 0.96 compared to previous work. The measurements of aorta size agreed with the measurements reported in previous work. The initial results showed associations of aorta morphology with calcification and with aging. These results may indicate aorta stiffening and unwrapping with calcification and aging. Conclusions: The authors have developed an objective tool to assess aorta morphology and aortic calcium plaques on CT scans that may be used to provide information about the presence of cardiovascular

The use of morphological characteristics and texture analysis in the identification of tissue composition in prostatic neoplasia.

PubMed

Diamond, James; Anderson, Neil H; Bartels, Peter H; Montironi, Rodolfo; Hamilton, Peter W

2004-09-01

Quantitative examination of prostate histology offers clues in the diagnostic classification of lesions and in the prediction of response to treatment and prognosis. To facilitate the collection of quantitative data, the development of machine vision systems is necessary. This study explored the use of imaging for identifying tissue abnormalities in prostate histology. Medium-power histological scenes were recorded from whole-mount radical prostatectomy sections at x 40 objective magnification and assessed by a pathologist as exhibiting stroma, normal tissue (nonneoplastic epithelial component), or prostatic carcinoma (PCa). A machine vision system was developed that divided the scenes into subregions of 100 x 100 pixels and subjected each to image-processing techniques. Analysis of morphological characteristics allowed the identification of normal tissue. Analysis of image texture demonstrated that Haralick feature 4 was the most suitable for discriminating stroma from PCa. Using these morphological and texture measurements, it was possible to define a classification scheme for each subregion. The machine vision system is designed to integrate these classification rules and generate digital maps of tissue composition from the classification of subregions; 79.3% of subregions were correctly classified. Established classification rates have demonstrated the validity of the methodology on small scenes; a logical extension was to apply the methodology to whole slide images via scanning technology. The machine vision system is capable of classifying these images. The machine vision system developed in this project facilitates the exploration of morphological and texture characteristics in quantifying tissue composition. It also illustrates the potential of quantitative methods to provide highly discriminatory information in the automated identification of prostatic lesions using computer vision.

Diagnostic performance of semi-quantitative and quantitative stress CMR perfusion analysis: a meta-analysis.

PubMed

van Dijk, R; van Assen, M; Vliegenthart, R; de Bock, G H; van der Harst, P; Oudkerk, M

2017-11-27

Stress cardiovascular magnetic resonance (CMR) perfusion imaging is a promising modality for the evaluation of coronary artery disease (CAD) due to high spatial resolution and absence of radiation. Semi-quantitative and quantitative analysis of CMR perfusion are based on signal-intensity curves produced during the first-pass of gadolinium contrast. Multiple semi-quantitative and quantitative parameters have been introduced. Diagnostic performance of these parameters varies extensively among studies and standardized protocols are lacking. This study aims to determine the diagnostic accuracy of semi- quantitative and quantitative CMR perfusion parameters, compared to multiple reference standards. Pubmed, WebOfScience, and Embase were systematically searched using predefined criteria (3272 articles). A check for duplicates was performed (1967 articles). Eligibility and relevance of the articles was determined by two reviewers using pre-defined criteria. The primary data extraction was performed independently by two researchers with the use of a predefined template. Differences in extracted data were resolved by discussion between the two researchers. The quality of the included studies was assessed using the 'Quality Assessment of Diagnostic Accuracy Studies Tool' (QUADAS-2). True positives, false positives, true negatives, and false negatives were subtracted/calculated from the articles. The principal summary measures used to assess diagnostic accuracy were sensitivity, specificity, andarea under the receiver operating curve (AUC). Data was pooled according to analysis territory, reference standard and perfusion parameter. Twenty-two articles were eligible based on the predefined study eligibility criteria. The pooled diagnostic accuracy for segment-, territory- and patient-based analyses showed good diagnostic performance with sensitivity of 0.88, 0.82, and 0.83, specificity of 0.72, 0.83, and 0.76 and AUC of 0.90, 0.84, and 0.87, respectively. In per territory

Comparative morphology analysis of live blood platelets using scanning ion conductance and robotic dark-field microscopy.

PubMed

Kraus, Max-Joseph; Seifert, Jan; Strasser, Erwin F; Gawaz, Meinrad; Schäffer, Tilman E; Rheinlaender, Johannes

2016-09-01

Many conventional microscopy techniques for investigating platelet morphology such as electron or fluorescence microscopy require highly invasive treatment of the platelets such as fixation, drying and metal coating or staining. Here, we present two unique but entirely different microscopy techniques for direct morphology analysis of live, unstained platelets: scanning ion conductance microscopy (SICM) and robotic dark-field microscopy (RDM). We demonstrate that both techniques allow for a quantitative evaluation of the morphological features of live adherent platelets. We show that their morphology can be quantified by both techniques using the same geometric parameters and therefore can be directly compared. By imaging the same identical platelets subsequently with SICM and RDM, we found that area, perimeter and circularity of the platelets are directly correlated between SICM and dark-field microscopy (DM), while the fractal dimension (FD) differed between the two microscopy techniques. We show that SICM and RDM are both valuable tools for the ex vivo investigation of the morphology of live platelets, which might contribute to new insights into the physiological and pathophysiological role of platelet spreading.

Morphology targets: What do seedling morphological attributes tell us?

Treesearch

Jeremiah R. Pinto

2011-01-01

Morphology is classically defined as the form and structure of individual organisms, as distinct from their anatomy or physiology. We use morphological targets in the nursery because they are easy to measure, and because we can often quantitatively link seedling morphological traits with survival and growth performance in the field. In the 20 years since the Target...

Pulmonary nodule characterization, including computer analysis and quantitative features.

PubMed

Bartholmai, Brian J; Koo, Chi Wan; Johnson, Geoffrey B; White, Darin B; Raghunath, Sushravya M; Rajagopalan, Srinivasan; Moynagh, Michael R; Lindell, Rebecca M; Hartman, Thomas E

2015-03-01

Pulmonary nodules are commonly detected in computed tomography (CT) chest screening of a high-risk population. The specific visual or quantitative features on CT or other modalities can be used to characterize the likelihood that a nodule is benign or malignant. Visual features on CT such as size, attenuation, location, morphology, edge characteristics, and other distinctive "signs" can be highly suggestive of a specific diagnosis and, in general, be used to determine the probability that a specific nodule is benign or malignant. Change in size, attenuation, and morphology on serial follow-up CT, or features on other modalities such as nuclear medicine studies or MRI, can also contribute to the characterization of lung nodules. Imaging analytics can objectively and reproducibly quantify nodule features on CT, nuclear medicine, and magnetic resonance imaging. Some quantitative techniques show great promise in helping to differentiate benign from malignant lesions or to stratify the risk of aggressive versus indolent neoplasm. In this article, we (1) summarize the visual characteristics, descriptors, and signs that may be helpful in management of nodules identified on screening CT, (2) discuss current quantitative and multimodality techniques that aid in the differentiation of nodules, and (3) highlight the power, pitfalls, and limitations of these various techniques.

Quantitative Hydrocarbon Surface Analysis

NASA Technical Reports Server (NTRS)

Douglas, Vonnie M.

2000-01-01

The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.

Multivariate Quantitative Chemical Analysis

NASA Technical Reports Server (NTRS)

Kinchen, David G.; Capezza, Mary

1995-01-01

Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

Golgi-type I and Golgi-type II neurons in the ventral anterior thalamic nucleus of the adult human: morphological features and quantitative analysis.

PubMed

Al-Hussain Bani Hani, Saleh M; El-Dwairi, Qasim A; Bataineh, Ziad M; Al-Haidari, Mohammad S; Al-Alami, Jamil

2008-05-01

The morphological and quantitative features of neurons in the adult human ventral anterior thalamic nucleus were studied in Golgi preparations. Two neuronal types were found and their quantitative features were studied. Golgi-type I neurons were medium to large cells with dense dendritic trees and dendritic protrusions and short hair-like appendages. They have somatic mean diameter of 30.8 microm (+/-9.4, n = 85). They have an average 100.3 dendritic branches, 48.97 dendritic branching points, and 58.85 dendritic tips. The mean diameters of their primary, secondary, and tertiary dendrites were 3.1 microm (+/-1, n = 80), 1.85 microm (+/-0.8, n = 145), and 1.5 microm (+/-0.4, n = 160), respectively. Golgi-type II neurons were small to medium cells with few sparsely branching dendrites and dendritic stalked appendages with or without terminal swellings. They have somatic mean diameters of 22.2 microm (+/-5.8, n = 120). They have an average 33.76 dendritic branches, 16.49 dendritic branching points, and 21.97 dendritic tips. The mean diameters of their primary, secondary, and tertiary dendrites were 1.6 microm (+/-0.86, n = 70), 1.15 microm (+/-0.55, n = 118), and 1 microm (+/-0.70, n = 95), respectively. These quantitative data may form the basis for further quantitative studies involving aging or some degenerative diseases that may affect cell bodies and/or dendritic trees of the Golgi-type I and/or Golgi-type II thalamic neurons.

Morphological analysis of dendrites and spines by hybridization of ridge detection with twin support vector machine.

PubMed

Wang, Shuihua; Chen, Mengmeng; Li, Yang; Shao, Ying; Zhang, Yudong; Du, Sidan; Wu, Jane

2016-01-01

Dendritic spines are described as neuronal protrusions. The morphology of dendritic spines and dendrites has a strong relationship to its function, as well as playing an important role in understanding brain function. Quantitative analysis of dendrites and dendritic spines is essential to an understanding of the formation and function of the nervous system. However, highly efficient tools for the quantitative analysis of dendrites and dendritic spines are currently undeveloped. In this paper we propose a novel three-step cascaded algorithm-RTSVM- which is composed of ridge detection as the curvature structure identifier for backbone extraction, boundary location based on differences in density, the Hu moment as features and Twin Support Vector Machine (TSVM) classifiers for spine classification. Our data demonstrates that this newly developed algorithm has performed better than other available techniques used to detect accuracy and false alarm rates. This algorithm will be used effectively in neuroscience research.

Quantification of mitral valve morphology with three-dimensional echocardiography--can measurement lead to better management?

PubMed

Lee, Alex Pui-Wai; Fang, Fang; Jin, Chun-Na; Kam, Kevin Ka-Ho; Tsui, Gary K W; Wong, Kenneth K Y; Looi, Jen-Li; Wong, Randolph H L; Wan, Song; Sun, Jing Ping; Underwood, Malcolm J; Yu, Cheuk-Man

2014-01-01

The mitral valve (MV) has complex 3-dimensional (3D) morphology and motion. Advance in real-time 3D echocardiography (RT3DE) has revolutionized clinical imaging of the MV by providing clinicians with realistic visualization of the valve. Thus far, RT3DE of the MV structure and dynamics has adopted an approach that depends largely on subjective and qualitative interpretation of the 3D images of the valve, rather than objective and reproducible measurement. RT3DE combined with image-processing computer techniques provides precise segmentation and reliable quantification of the complex 3D morphology and rapid motion of the MV. This new approach to imaging may provide additional quantitative descriptions that are useful in diagnostic and therapeutic decision-making. Quantitative analysis of the MV using RT3DE has increased our understanding of the pathologic mechanism of degenerative, ischemic, functional, and rheumatic MV disease. Most recently, 3D morphologic quantification has entered into clinical use to provide more accurate diagnosis of MV disease and for planning surgery and transcatheter interventions. Current limitations of this quantitative approach to MV imaging include labor-intensiveness during image segmentation and lack of a clear definition of the clinical significance of many of the morphologic parameters. This review summarizes the current development and applications of quantitative analysis of the MV morphology using RT3DE.

A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

PubMed Central

Morales-Navarrete, Hernán; Segovia-Miranda, Fabián; Klukowski, Piotr; Meyer, Kirstin; Nonaka, Hidenori; Marsico, Giovanni; Chernykh, Mikhail; Kalaidzidis, Alexander; Zerial, Marino; Kalaidzidis, Yannis

2015-01-01

A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness. DOI: http://dx.doi.org/10.7554/eLife.11214.001 PMID:26673893

3.0T MR imaging of the ankle: Axial traction for morphological cartilage evaluation, quantitative T2 mapping and cartilage diffusion imaging-A preliminary study.

PubMed

Jungmann, Pia M; Baum, Thomas; Schaeffeler, Christoph; Sauerschnig, Martin; Brucker, Peter U; Mann, Alexander; Ganter, Carl; Bieri, Oliver; Rummeny, Ernst J; Woertler, Klaus; Bauer, Jan S

2015-08-01

To determine the impact of axial traction during high resolution 3.0T MR imaging of the ankle on morphological assessment of articular cartilage and quantitative cartilage imaging parameters. MR images of n=25 asymptomatic ankles were acquired with and without axial traction (6kg). Coronal and sagittal T1-weighted (w) turbo spin echo (TSE) sequences with a driven equilibrium pulse and sagittal fat-saturated intermediate-w (IMfs) TSE sequences were acquired for morphological evaluation on a four-point scale (1=best, 4=worst). For quantitative assessment of cartilage degradation segmentation was performed on 2D multislice-multiecho (MSME) SE T2, steady-state free-precession (SSFP; n=8) T2 and SSFP diffusion-weighted imaging (DWI; n=8) images. Wilcoxon-tests and paired t-tests were used for statistical analysis. With axial traction, joint space width increased significantly and delineation of cartilage surfaces was rated superior (P<0.05). Cartilage surfaces were best visualized on coronal T1-w images (P<0.05). Differences for cartilage matrix evaluation were smaller. Subchondral bone evaluation, motion artifacts and image quality were not significantly different between the acquisition methods (P>0.05). T2 values were lower at the tibia than at the talus (P<0.001). Reproducibility was better for images with axial traction. Axial traction increased the joint space width, allowed for better visualization of cartilage surfaces and improved compartment discrimination and reproducibility of quantitative cartilage parameters. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Correlation of Rock Spectra with Quantitative Morphologic Indices: Evidence for a Single Rock Type at the Mars Pathfinder Landing Site

NASA Technical Reports Server (NTRS)

Yingst, R. A.; Biedermann, K. L.; Pierre, N. M.; Haldemann, A. F. C.; Johnson, J. R.

2005-01-01

The Mars Pathfinder (MPF) landing site was predicted to contain a broad sampling of rock types varying in mineralogical, physical, mechanical and geochemical characteristics. Although rocks have been divided into several spectral categories based on Imager for Mars Pathfinder (IMP) visible/near-infrared data, efforts in isolating and classifying spectral units among MPF rocks and soils have met with varying degrees of success, as many factors influencing spectral signatures cannot be quantified to a sufficient level to be removed. It has not been fully determined which spectral categories stem from intrinsic mineralogical differences between rocks or rock surfaces, and which result from factors such as physical or chemical weathering. This has made isolation of unique rock mineralogies difficult. Morphology, like composition, is a characteristic tied to the intrinsic properties and geologic and weathering history of rocks. Rock morphologies can be assessed quantitatively and compared with spectral data, to identify and classify rock types at the MPF landing site. They can also isolate actual rock spectra from spectral types that are surficial in origin, as compositions associated with mantling dust or chemical coatings would presumably not influence rock morphology during weathering events. We previously reported on an initial classification of rocks using the quantitative morphologic indices of size, roundness, sphericity and elongation. Here, we compare this database of rock characteristics with associated rock surface spectra to improve our ability to discriminate between spectra associated with rock types and those from other sources.

Quantitative 3D Ultrashort Time-to-Echo (UTE) MRI and Micro-CT (μCT) Evaluation of the Temporomandibular Joint (TMJ) Condylar Morphology

PubMed Central

Geiger, Daniel; Bae, Won C.; Statum, Sheronda; Du, Jiang; Chung, Christine B.

2014-01-01

Objective Temporomandibular dysfunction involves osteoarthritis of the TMJ, including degeneration and morphologic changes of the mandibular condyle. Purpose of this study was to determine accuracy of novel 3D-UTE MRI versus micro-CT (μCT) for quantitative evaluation of mandibular condyle morphology. Material & Methods Nine TMJ condyle specimens were harvested from cadavers (2M, 3F; Age 85 ± 10 yrs., mean±SD). 3D-UTE MRI (TR=50ms, TE=0.05 ms, 104 μm isotropic-voxel) was performed using a 3-T MR scanner and μCT (18 μm isotropic-voxel) was performed. MR datasets were spatially-registered with μCT dataset. Two observers segmented bony contours of the condyles. Fibrocartilage was segmented on MR dataset. Using a custom program, bone and fibrocartilage surface coordinates, Gaussian curvature, volume of segmented regions and fibrocartilage thickness were determined for quantitative evaluation of joint morphology. Agreement between techniques (MRI vs. μCT) and observers (MRI vs. MRI) for Gaussian curvature, mean curvature and segmented volume of the bone were determined using intraclass correlation correlation (ICC) analyses. Results Between MRI and μCT, the average deviation of surface coordinates was 0.19±0.15 mm, slightly higher than spatial resolution of MRI. Average deviation of the Gaussian curvature and volume of segmented regions, from MRI to μCT, was 5.7±6.5% and 6.6±6.2%, respectively. ICC coefficients (MRI vs. μCT) for Gaussian curvature, mean curvature and segmented volumes were respectively 0.892, 0.893 and 0.972. Between observers (MRI vs. MRI), the ICC coefficients were 0.998, 0.999 and 0.997 respectively. Fibrocartilage thickness was 0.55±0.11 mm, as previously described in literature for grossly normal TMJ samples. Conclusion 3D-UTE MR quantitative evaluation of TMJ condyle morphology ex-vivo, including surface, curvature and segmented volume, shows high correlation against μCT and between observers. In addition, UTE MRI allows

Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

NASA Technical Reports Server (NTRS)

Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

2002-01-01

This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

Three-dimensional Imaging Methods for Quantitative Analysis of Facial Soft Tissues and Skeletal Morphology in Patients with Orofacial Clefts: A Systematic Review

PubMed Central

Kuijpers, Mette A. R.; Chiu, Yu-Ting; Nada, Rania M.; Carels, Carine E. L.; Fudalej, Piotr S.

2014-01-01

Background Current guidelines for evaluating cleft palate treatments are mostly based on two-dimensional (2D) evaluation, but three-dimensional (3D) imaging methods to assess treatment outcome are steadily rising. Objective To identify 3D imaging methods for quantitative assessment of soft tissue and skeletal morphology in patients with cleft lip and palate. Data sources Literature was searched using PubMed (1948–2012), EMBASE (1980–2012), Scopus (2004–2012), Web of Science (1945–2012), and the Cochrane Library. The last search was performed September 30, 2012. Reference lists were hand searched for potentially eligible studies. There was no language restriction. Study selection We included publications using 3D imaging techniques to assess facial soft tissue or skeletal morphology in patients older than 5 years with a cleft lip with/or without cleft palate. We reviewed studies involving the facial region when at least 10 subjects in the sample size had at least one cleft type. Only primary publications were included. Data extraction Independent extraction of data and quality assessments were performed by two observers. Results Five hundred full text publications were retrieved, 144 met the inclusion criteria, with 63 high quality studies. There were differences in study designs, topics studied, patient characteristics, and success measurements; therefore, only a systematic review could be conducted. Main 3D-techniques that are used in cleft lip and palate patients are CT, CBCT, MRI, stereophotogrammetry, and laser surface scanning. These techniques are mainly used for soft tissue analysis, evaluation of bone grafting, and changes in the craniofacial skeleton. Digital dental casts are used to evaluate treatment and changes over time. Conclusion Available evidence implies that 3D imaging methods can be used for documentation of CLP patients. No data are available yet showing that 3D methods are more informative than conventional 2D methods. Further research

Tissue-Specific Analysis of Secondary Metabolites Creates a Reliable Morphological Criterion for Quality Grading of Polygoni Multiflori Radix.

PubMed

Liang, Li; Xu, Jun; Liang, Zhi-Tao; Dong, Xiao-Ping; Chen, Hu-Biao; Zhao, Zhong-Zhen

2018-05-08

In commercial herbal markets, Polygoni Multiflori Radix (PMR, the tuberous roots of Polygonum multiflorum Thunb.), a commonly-used Chinese medicinal material, is divided into different grades based on morphological features of size and weight. While more weight and larger size command a higher price, there is no scientific data confirming that the more expensive roots are in fact of better quality. To assess the inherent quality of various grades and of various tissues in PMR and to find reliable morphological indicators of quality, a method combining laser microdissection (LMD) and ultra-performance liquid chromatography triple-quadrupole mass spectrometry (UPLC-QqQ-MS/MS) was applied. Twelve major chemical components were quantitatively determined in both whole material and different tissues of PMR. Determination of the whole material revealed that traditional commercial grades based on size and weight of PRM did not correspond to any significant differences in chemical content. Instead, tissue-specific analysis indicated that the morphological features could be linked with quality in a new way. That is, PMR with broader cork and phloem, as seen in a transverse section, were typically of better quality as these parts are where the bioactive components accumulate. The tissue-specific analysis of secondary metabolites creates a reliable morphological criterion for quality grading of PMR.

Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D)

PubMed Central

Li, Weizhe; Germain, Ronald N.

2017-01-01

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques. PMID:28808033

Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

NASA Technical Reports Server (NTRS)

Shortle, J. F.; Allocco, M.

2005-01-01

Quantitative methods can be beneficial in many types of safety investigations. However, there are many difficulties in using quantitative m ethods. Far example, there may be little relevant data available. This paper proposes a framework for using quantitative hazard analysis to prioritize hazard scenarios most suitable for quantitative mziysis. The framework first categorizes hazard scenarios by severity and likelihood. We then propose another metric "modeling difficulty" that desc ribes the complexity in modeling a given hazard scenario quantitatively. The combined metrics of severity, likelihood, and modeling difficu lty help to prioritize hazard scenarios for which quantitative analys is should be applied. We have applied this methodology to proposed concepts of operations for reduced wake separation for airplane operatio ns at closely spaced parallel runways.

Quantitative phase imaging of platelet: assessment of cell morphology and function

NASA Astrophysics Data System (ADS)

Vasilenko, Irina; Vlasova, Elizaveta; Metelin, Vladislav; Agadzhanjan, B.; Lyfenko, R.

2017-02-01

It is well known that platelets play a central role in hemostasis and thrombosis, they also mediate tumor cell growth, dissemination and angiogenesis. The purpose of the present experiment was to evaluate living platelet size, function and morphology simultaneously in unactivated and activated states using Phase-Interference Microscope "Cytoscan" (Moscow, Russia). We enrolled 30 healthy volunteers, who had no past history of aeteriosclerosis-related disorders, such as coronary heart disease, cerebrovascular disease, hypertention, diabetes or hyperlipidemia and 30 patients with oropharynx cancer. We observed the optic-geometrical parameters of each isolated living cell and the distribution of platelets by sizes have been analysed to detect the dynamics of cell population heterogeneity. Simultaneously we identified 4 platelet forms that have different morphological features and different parameters of size distribution. We noticed that morphological platelet types correlate with morphometric platelet parameters. The data of polymorphisms of platelet reactivity in tumor progression can be used to improve patient outcomes in the cancer prevention and treatment. Moreover morphometric and functional platelet parameters can serve criteria of the efficiency of the radio- and chemotherapy carried out. In conclusion the computer phase-interference microscope provides rapid and effective analysis of living platelet morphology and function at the same time. The use of the computer phase-interference microscope could be an easy and fast method to check the state of platelets in patients with changed platelet activation and to follow a possible pharmacological therapy to reduce this phenomenon.

Quantitative Relationships Linking Rock Strength to Channel Morphology: A Case Study in Central Arizona

NASA Astrophysics Data System (ADS)

Larimer, J. E.; Yanites, B.

2016-12-01

River morphology is a consequence of the erosive forces acting on the channel boundary and the resisting forces that limit erosion. For bedrock rivers, the erosive forces are generated by the stresses exerted by impacting sediment and flowing water, while the resisting forces are controlled by the internal strength regime of the local rock. We investigate the susceptibility of different rock types to different erosional processes (i.e. abrasion and plucking) and how changes in channel morphology reflect rock strength properties across lithologic boundaries. The bedrock rivers in the Prescott National Forest, AZ flow over a number of rock types with variable strength including sedimentary, igneous, and metamorphic lithologies providing a natural experiment to quantify the influence of rock strength on channel morphology. We collected bedrock samples and channel surveys from 12 different rock types. Rock-strength and rock-mass properties include compressive strength, tensile strength, fatigue strength, decimeter scale P-wave velocity (varies by 8-fold), Schmidt rebound value, fracture spacing, fracture aperture, and slake durability (as a proxy for weathering susceptibility. Morphological measurements include channel width, channel steepness (varies by 10-fold), and grain size distribution. To distinguish between the major mechanisms of erosion we measure bedrock surface roughness factor at the centimeter scale. Preliminary results show that channel steepness (ksn) increases with P-wave velocity while normalized channel width (kwn) decreases with P-wave velocity. We use these data to quantify scaling relationships of channel geometry with rock strength properties. We consider the results in the context of the driving mechanistic process to develop new quantitative understandings of how rock strength properties influence the efficiency of erosion processes and how rock strength is reflected in river morphology. By comparing the results among different rock types in a

A methodological investigation of hominoid craniodental morphology and phylogenetics.

PubMed

Bjarnason, Alexander; Chamberlain, Andrew T; Lockwood, Charles A

2011-01-01

The evolutionary relationships of extant great apes and humans have been largely resolved by molecular studies, yet morphology-based phylogenetic analyses continue to provide conflicting results. In order to further investigate this discrepancy we present bootstrap clade support of morphological data based on two quantitative datasets, one dataset consisting of linear measurements of the whole skull from 5 hominoid genera and the second dataset consisting of 3D landmark data from the temporal bone of 5 hominoid genera, including 11 sub-species. Using similar protocols for both datasets, we were able to 1) compare distance-based phylogenetic methods to cladistic parsimony of quantitative data converted into discrete character states, 2) vary outgroup choice to observe its effect on phylogenetic inference, and 3) analyse male and female data separately to observe the effect of sexual dimorphism on phylogenies. Phylogenetic analysis was sensitive to methodological decisions, particularly outgroup selection, where designation of Pongo as an outgroup and removal of Hylobates resulted in greater congruence with the proposed molecular phylogeny. The performance of distance-based methods also justifies their use in phylogenetic analysis of morphological data. It is clear from our analyses that hominoid phylogenetics ought not to be used as an example of conflict between the morphological and molecular, but as an example of how outgroup and methodological choices can affect the outcome of phylogenetic analysis. Copyright © 2010 Elsevier Ltd. All rights reserved.

Quantitative Data Analysis--In the Graduate Curriculum

ERIC Educational Resources Information Center

Albers, Michael J.

2017-01-01

A quantitative research study collects numerical data that must be analyzed to help draw the study's conclusions. Teaching quantitative data analysis is not teaching number crunching, but teaching a way of critical thinking for how to analyze the data. The goal of data analysis is to reveal the underlying patterns, trends, and relationships of a…

Calibration-free quantitative analysis of elemental ratios in intermetallic nanoalloys and nanocomposites using Laser Induced Breakdown Spectroscopy (LIBS).

PubMed

Davari, Seyyed Ali; Hu, Sheng; Mukherjee, Dibyendu

2017-03-01

Intermetallic nanoalloys (NAs) and nanocomposites (NCs) have increasingly gained prominence as efficient catalytic materials in electrochemical energy conversion and storage systems. But their morphology and chemical compositions play critical role in tuning their catalytic activities, and precious metal contents. While advanced microscopy techniques facilitate morphological characterizations, traditional chemical characterizations are either qualitative or extremely involved. In this study, we apply Laser Induced Breakdown Spectroscopy (LIBS) for quantitative compositional analysis of NAs and NCs synthesized with varied elemental ratios by our in-house built pulsed laser ablation technique. Specifically, elemental ratios of binary PtNi, PdCo (NAs) and PtCo (NCs) of different compositions are determined from LIBS measurements employing an internal calibration scheme using the bulk matrix species as internal standards. Morphology and qualitative elemental compositions of the aforesaid NAs and NCs are confirmed from Transmission Electron Microscopy (TEM) images and Energy Dispersive X-ray Spectroscopy (EDX) measurements. LIBS experiments are carried out in ambient conditions with the NA and NC samples drop cast on silicon wafers after centrifugation to increase their concentrations. The technique does not call for cumbersome sample preparations including acid digestions and external calibration standards commonly required in Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) techniques. Yet the quantitative LIBS results are in good agreement with the results from ICP-OES measurements. Our results indicate the feasibility of using LIBS in future for rapid and in-situ quantitative chemical characterizations of wide classes of synthesized NAs and NCs. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative analysis of the right auricle with 256-slice computed tomography.

PubMed

Li, Cai-Ying; Gao, Bu-Lang; Pan, Tong; Xiang, Cheng; Zhang, Xue-Jing; Liu, Xiao-Wei; Fan, Qiong-Ying

2017-04-01

To quantitatively measure the morphology parameters of the right auricle with 256-slice multidetector computed tomography angiography (MDCTA) in healthy people. A retrospective analysis of 200 patients who had undergone coronary MDCTA with negative findings was performed. The raw imaging data were reconstructed and the right auricular volume, right atrial volume, right auricle height, base long and short axes, base perimeter and area, normal angle, and distance were quantitatively measured. Men had significantly (P < 0.05) greater values than women in the right auricular volume (13.3 ± 4.0 vs. 11.7 ± 3.7 mL) and height (33.0 ± 5.0 vs. 30.5 ± 5.2 mm), the base long axis (34.4 ± 4.1 vs. 33.2 ± 3.9 mm), area (787.6 ± 177.6 vs. 771.0 ± 143.2 mm 2 ) and perimeter (119.2 ± 17.5 vs. 115.0 ± 13.0), and the normal distance (22.4 ± 6.6 vs. 20.2 ± 6.7 mm). The normal 95 % reference range for the right auricular parameters was put forward. The right auricular parameters had a good correlation with the right atrium volume, aortic diameter, the body weight, height, and body surface area but a bad correlation with the vertebral body height. Significantly (P < 0.05) greater values were found in the normal angle and distance in subjects below than over 40 years of age. No other significant (P > 0.05) difference existed in the other right auricular parameters. Quantitative measurements of the right auricle can help us get a good understanding of the right auricular morphology and its relationship with surrounding structures and are helpful for cardiac interventions of electrophysiology and radiofrequency ablation.

A new high-resolution 3-D quantitative method for analysing small morphological features: an example using a Cambrian trilobite.

PubMed

Esteve, Jorge; Zhao, Yuan-Long; Maté-González, Miguel Ángel; Gómez-Heras, Miguel; Peng, Jin

2018-02-12

Taphonomic processes play an important role in the preservation of small morphological features such as granulation or pits. However, the assessment of these features may face the issue of the small size of the specimens and, sometimes, the destructiveness of these analyses, which makes impossible carrying them out in singular specimen, such as holotypes or lectotypes. This paper takes a new approach to analysing small-morphological features, by using an optical surface roughness (OSR) meter to create a high-resolution three-dimensional digital-elevation model (DEM). This non-destructive technique allows analysing quantitatively the DEM using geometric morphometric methods (GMM). We created a number of DEMs from three populations putatively belonging to the same species of trilobite (Oryctocephalus indicus) that present the same cranidial outline, but differ in the presence or absence of the second and third transglabellar furrows. Profile analysis of the DEMs demonstrate that all three populations show similar preservation variation in the glabellar furrows and lobes. The GMM shows that all populations exhibit the same range of variation. Differences in preservation are a consequence of different degrees of cementation and rates of dissolution. Fast cementation enhances the preservation of glabellar furrows and lobes, while fast dissolution hampers preservation of the same structures.

Morphological quantitative criteria and aesthetic evaluation of eight female Han face types.

PubMed

Zhao, Qiming; Zhou, Rongrong; Zhang, XuDong; Sun, Huafeng; Lu, Xin; Xia, Dongsheng; Song, Mingli; Liang, Yang

2013-04-01

Human facial aesthetics relies on the classification of facial features and standards of attractiveness. However, there are no widely accepted quantitative criteria for facial attractiveness, particularly for Chinese Han faces. Establishing quantitative standards of attractiveness for facial landmarks within facial types is important for planning outcomes in cosmetic plastic surgery. The aim of this study was to determine quantitatively the criteria for attractiveness of eight female Chinese Han facial types. A photographic database of young Chinese Han women's faces was created. Photographed faces (450) were classified based on eight established types and scored for attractiveness. Measurements taken at seven standard facial landmarks and their relative proportions were analyzed for correlations to attractiveness scores. Attractive faces of each type were averaged via an image-morphing algorithm to generate synthetic facial types. Results were compared with the neoclassical ideal and data for Caucasians. Morphological proportions corresponding to the highest attractiveness scores for Chinese Han women differed from the neoclassical ideal. In our population of young, normal, healthy Han women, high attractiveness ratings were given to those with greater temporal width and pogonion-gonion distance, and smaller bizygomatic and bigonial widths. As attractiveness scores increased, the ratio of the temporal to bizygomatic widths increased, and the ratio of the distance between the pogonion and gonion to the bizygomatic width also increased slightly. Among the facial types, the oval and inverted triangular were the most attractive. The neoclassical ideal of attractiveness does not apply to Han faces. However, the proportion of faces considered attractive in this population was similar to that of Caucasian populations. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please

Morphological evolution of various fungal species in the presence and absence of aluminum oxide microparticles: Comparative and quantitative insights into microparticle-enhanced cultivation (MPEC).

PubMed

Kowalska, Anna; Boruta, Tomasz; Bizukojć, Marcin

2018-03-05

The application of microparticle-enhanced cultivation (MPEC) is an attractive method to control mycelial morphology, and thus enhance the production of metabolites and enzymes in the submerged cultivations of filamentous fungi. Unfortunately, most literature data deals with the spore-agglomerating species like aspergilli. Therefore, the detailed quantitative study of the morphological evolution of four different fungal species (Aspergillus terreus, Penicillium rubens, Chaetomium globosum, and Mucor racemosus) based on the digital analysis of microscopic images was presented in this paper. In accordance with the current knowledge, these species exhibit different mechanisms of agglomerates formation. The standard submerged shake flask cultivations (as a reference) and MPEC involving 10 μm aluminum oxide microparticles (6 g·L -1 ) were performed. The morphological parameters, including mean projected area, elongation, roughness, and morphology number were determined for the mycelial objects within the first 24 hr of growth. It occurred that heretofore observed and widely discussed effect of microparticles on fungi, namely the decrease in pellet size, was not observed for the species whose pellet formation mechanism is different from spore agglomeration. In the MPEC, C. globosum developed core-shell pellets, and M. racemosus, a nonagglomerative species, formed the relatively larger, compared to standard cultures, pellets with distinct cores. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Model-Based Linkage Analysis of a Quantitative Trait.

PubMed

Song, Yeunjoo E; Song, Sunah; Schnell, Audrey H

2017-01-01

Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.

Morphologic analysis of the zebrafish digestive system.

PubMed

Trotter, Andrew J; Parslow, Adam C; Heath, Joan K

2009-01-01

The zebrafish provides an ideal model for the study of vertebrate organogenesis, including the formation of the digestive tract and its associated organs. Despite optical transparency of embryos, the internal position of the developing digestive system and its close juxtaposition with the yolk initially made morphological analysis relatively challenging, particularly during the first 3 d of development. However, methodologies have been successfully developed to address these problems and comprehensive morphologic analysis of the developing digestive system has now been achieved using a combination of light and fluorescence microscope approaches-including confocal analysis-to visualize wholemount and histological preparations of zebrafish embryos. Furthermore, the expanding number of antibodies that cross-react with zebrafish proteins and the generation of tissue-specific transgenic green fluorescent protein reporter lines that mark specific cell and tissue compartments have greatly enhanced our ability to successfully image the developing zebrafish digestive system.

[Quantitative study of the prothallial morphogenesis in Asplenium species].

PubMed

Henriet, M; Auquière, J P; Moens, P

1976-01-01

A precedent paper concerned a qualitative analysis of the gametophytic development in nine Asplenium species. By a quantitative study, we specify the parental relationships among these species. The surface of the gametophyte and the number of maginal hairs increase differently for each species. The density of the marginal hairs depends on the considered species. The relation among the morphological gametophytic parameters is constant in a group of determined species. The principal componant analysis is realized for all the parameters measured during the prothallial development. It confirms parental relationships among the diploids and tetraploids species on a morphological point of vue.

Two Algorithms for High-throughput and Multi-parametric Quantification of Drosophila Neuromuscular Junction Morphology.

PubMed

Castells-Nobau, Anna; Nijhof, Bonnie; Eidhof, Ilse; Wolf, Louis; Scheffer-de Gooyert, Jolanda M; Monedero, Ignacio; Torroja, Laura; van der Laak, Jeroen A W M; Schenck, Annette

2017-05-03

Synaptic morphology is tightly related to synaptic efficacy, and in many cases morphological synapse defects ultimately lead to synaptic malfunction. The Drosophila larval neuromuscular junction (NMJ), a well-established model for glutamatergic synapses, has been extensively studied for decades. Identification of mutations causing NMJ morphological defects revealed a repertoire of genes that regulate synapse development and function. Many of these were identified in large-scale studies that focused on qualitative approaches to detect morphological abnormalities of the Drosophila NMJ. A drawback of qualitative analyses is that many subtle players contributing to NMJ morphology likely remain unnoticed. Whereas quantitative analyses are required to detect the subtler morphological differences, such analyses are not yet commonly performed because they are laborious. This protocol describes in detail two image analysis algorithms "Drosophila NMJ Morphometrics" and "Drosophila NMJ Bouton Morphometrics", available as Fiji-compatible macros, for quantitative, accurate and objective morphometric analysis of the Drosophila NMJ. This methodology is developed to analyze NMJ terminals immunolabeled with the commonly used markers Dlg-1 and Brp. Additionally, its wider application to other markers such as Hrp, Csp and Syt is presented in this protocol. The macros are able to assess nine morphological NMJ features: NMJ area, NMJ perimeter, number of boutons, NMJ length, NMJ longest branch length, number of islands, number of branches, number of branching points and number of active zones in the NMJ terminal.

Quantitative molecular analysis in mantle cell lymphoma.

PubMed

Brízová, H; Hilská, I; Mrhalová, M; Kodet, R

2011-07-01

A molecular analysis has three major roles in modern oncopathology--as an aid in the differential diagnosis, in molecular monitoring of diseases, and in estimation of the potential prognosis. In this report we review the application of the molecular analysis in a group of patients with mantle cell lymphoma (MCL). We demonstrate that detection of the cyclin D1 mRNA level is a molecular marker in 98% of patients with MCL. Cyclin D1 quantitative monitoring is specific and sensitive for the differential diagnosis and for the molecular monitoring of the disease in the bone marrow. Moreover, the dynamics of cyclin D1 in bone marrow reflects the disease development and it predicts the clinical course. We employed the molecular analysis for a precise quantitative detection of proliferation markers, Ki-67, topoisomerase IIalpha, and TPX2, that are described as effective prognostic factors. Using the molecular approach it is possible to measure the proliferation rate in a reproducible, standard way which is an essential prerequisite for using the proliferation activity as a routine clinical tool. Comparing with immunophenotyping we may conclude that the quantitative PCR-based analysis is a useful, reliable, rapid, reproducible, sensitive and specific method broadening our diagnostic tools in hematopathology. In comparison to interphase FISH in paraffin sections quantitative PCR is less technically demanding and less time-consuming and furthermore it is more sensitive in detecting small changes in the mRNA level. Moreover, quantitative PCR is the only technology which provides precise and reproducible quantitative information about the expression level. Therefore it may be used to demonstrate the decrease or increase of a tumor-specific marker in bone marrow in comparison with a previously aspirated specimen. Thus, it has a powerful potential to monitor the course of the disease in correlation with clinical data.

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses.

PubMed

Brum, Jennifer R; Schenck, Ryan O; Sullivan, Matthew B

2013-09-01

Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.

Does skull morphology constrain bone ornamentation? A morphometric analysis in the Crocodylia.

PubMed

Clarac, F; Souter, T; Cubo, J; de Buffrénil, V; Brochu, C; Cornette, R

2016-08-01

Previous quantitative assessments of the crocodylians' dermal bone ornamentation (this ornamentation consists of pits and ridges) has shown that bone sculpture results in a gain in area that differs between anatomical regions: it tends to be higher on the skull table than on the snout. Therefore, a comparative phylogenetic analysis within 17 adult crocodylian specimens representative of the morphological diversity of the 24 extant species has been performed, in order to test if the gain in area due to ornamentation depends on the skull morphology, i.e. shape and size. Quantitative assessment of skull size and shape through geometric morphometrics, and of skull ornamentation through surface analyses, produced a dataset that was analyzed using phylogenetic least-squares regression. The analyses reveal that none of the variables that quantify ornamentation, be they on the snout or the skull table, is correlated with the size of the specimens. Conversely, there is more disparity in the relationships between skull conformations (longirostrine vs. brevirostrine) and ornamentation. Indeed, both parameters GApit (i.e. pit depth and shape) and OArelat (i.e. relative area of the pit set) are negatively correlated with snout elongation, whereas none of the values quantifying ornamentation on the skull table is correlated with skull conformation. It can be concluded that bone sculpture on the snout is influenced by different developmental constrains than on the skull table and is sensible to differences in the local growth 'context' (allometric processes) prevailing in distinct skull parts. Whatever the functional role of bone ornamentation on the skull, if any, it seems to be restricted to some anatomical regions at least for the longirostrine forms that tend to lose ornamentation on the snout. © 2016 Anatomical Society.

Accuracy of a remote quantitative image analysis in the whole slide images.

PubMed

Słodkowska, Janina; Markiewicz, Tomasz; Grala, Bartłomiej; Kozłowski, Wojciech; Papierz, Wielisław; Pleskacz, Katarzyna; Murawski, Piotr

2011-03-30

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and

Neutral model analysis of landscape patterns from mathematical morphology

Treesearch

Kurt H. Riitters; Peter Vogt; Pierre Soille; Jacek Kozak; Christine Estreguil

2007-01-01

Mathematical morphology encompasses methods for characterizing land-cover patterns in ecological research and biodiversity assessments. This paper reports a neutral model analysis of patterns in the absence of a structuring ecological process, to help set standards for comparing and interpreting patterns identified by mathematical morphology on real land-cover maps. We...

Ultrahigh resolution optical coherence tomography for quantitative topographic mapping of retinal and intraretinal architectural morphology

NASA Astrophysics Data System (ADS)

Ko, Tony H.; Hartl, Ingmar; Drexler, Wolfgang; Ghanta, Ravi K.; Fujimoto, James G.

2002-06-01

Quantitative, three-dimensional mapping of retinal architectural morphology was achieved using an ultrahigh resolution ophthalmic OCT system. This OCT system utilizes a broad bandwidth titanium-sapphire laser light source generating bandwidths of up to 300 nm near 800 nm center wavelength. The system enables real-time cross-sectional imaging of the retina with ~3 micrometers axial resolution. The macula and the papillomacular axis of a normal human subject were systematically mapped using a series of linear scans. Edge detection and segmentation algorithms were developed to quantify retinal and intraretinal thicknesses. Topographic mapping of the total retinal thickness and the total ganglion cell/inner plexiform layer thickness was achieved around the macula. A topographic mapping quantifying the progressive thickening of the nerve fiber layer (NFL) nasally approaching the optic disk was also demonstrated. The ability to create three-dimensional topographic mapping of retinal architectural morphology at ~3 micrometers axial resolution will be relevant for the diagnosis of many retinal diseases. The topographic quantification of these structures can serve as a powerful tool for developing algorithms and clinical scanning protocols for the screening and staging of ophthalmic diseases such as glaucoma.

Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

PubMed Central

Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

2013-01-01

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

Single shot white light interference microscopy with colour fringe analysis for quantitative phase imaging of biological cells

NASA Astrophysics Data System (ADS)

Srivastava, Vishal; Mehta, D. S.

2013-02-01

To quantitatively obtain the phase map of Onion and human red blood cell (RBC) from white light interferogram we used Hilbert transform color fringe analysis technique. The three Red, Blue and Green color components are decomposed from single white light interferogram and Refractive index profile for Red, Blue and Green colour were computed in a completely non-invasive manner for Onion and human RBC. The present technique might be useful for non-invasive determination of the refractive index variation within cells and tissues and morphological features of sample with ease of operation and low cost.

Segmentation and Quantitative Analysis of Apoptosis of Chinese Hamster Ovary Cells from Fluorescence Microscopy Images.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2017-06-01

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarse segmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells' images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

A three-dimensional morphometric analysis of upper forelimb morphology in the enigmatic tapir (Perissodactyla: Tapirus) hints at subtle variations in locomotor ecology.

PubMed

MacLaren, Jamie A; Nauwelaerts, Sandra

2016-11-01

Forelimb morphology is an indicator for terrestrial locomotor ecology. The limb morphology of the enigmatic tapir (Perissodactyla: Tapirus) has often been compared to that of basal perissodactyls, despite the lack of quantitative studies comparing forelimb variation in modern tapirs. Here, we present a quantitative assessment of tapir upper forelimb osteology using three-dimensional geometric morphometrics to test whether the four modern tapir species are monomorphic in their forelimb skeleton. The shape of the upper forelimb bones across four species (T. indicus; T. bairdii; T. terrestris; T. pinchaque) was investigated. Bones were laser scanned to capture surface morphology and 3D landmark analysis was used to quantify shape. Discriminant function analyses were performed to reveal features which could be used for interspecific discrimination. Overall our results show that the appendicular skeleton contains notable interspecific differences. We demonstrate that upper forelimb bones can be used to discriminate between species (>91% accuracy), with the scapula proving the most diagnostic bone (100% accuracy). Features that most successfully discriminate between the four species include the placement of the cranial angle of the scapula, depth of the humeral condyle, and the caudal deflection of the olecranon. Previous studies comparing the limbs of T. indicus and T. terrestris are corroborated by our quantitative findings. Moreover, the mountain tapir T. pinchaque consistently exhibited the greatest divergence in morphology from the other three species. Despite previous studies describing tapirs as functionally mediportal in their locomotor style, we find osteological evidence suggesting a spectrum of locomotor adaptations in the tapirs. We conclude that modern tapir forelimbs are neither monomorphic nor are tapirs as conserved in their locomotor habits as previously described. J. Morphol. 277:1469-1485, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals

[Quantitative data analysis for live imaging of bone.

PubMed

Seno, Shigeto

Bone tissue is a hard tissue, it was difficult to observe the interior of the bone tissue alive. With the progress of microscopic technology and fluorescent probe technology in recent years, it becomes possible to observe various activities of various cells forming bone society. On the other hand, the quantitative increase in data and the diversification and complexity of the images makes it difficult to perform quantitative analysis by visual inspection. It has been expected to develop a methodology for processing microscopic images and data analysis. In this article, we introduce the research field of bioimage informatics which is the boundary area of biology and information science, and then outline the basic image processing technology for quantitative analysis of live imaging data of bone.

Lateral ventricle morphology analysis via mean latitude axis.

PubMed

Paniagua, Beatriz; Lyall, Amanda; Berger, Jean-Baptiste; Vachet, Clement; Hamer, Robert M; Woolson, Sandra; Lin, Weili; Gilmore, John; Styner, Martin

2013-03-29

Statistical shape analysis has emerged as an insightful method for evaluating brain structures in neuroimaging studies, however most shape frameworks are surface based and thus directly depend on the quality of surface alignment. In contrast, medial descriptions employ thickness information as alignment-independent shape metric. We propose a joint framework that computes local medial thickness information via a mean latitude axis from the well-known spherical harmonic (SPHARM-PDM) shape framework. In this work, we applied SPHARM derived medial representations to the morphological analysis of lateral ventricles in neonates. Mild ventriculomegaly (MVM) subjects are compared to healthy controls to highlight the potential of the methodology. Lateral ventricles were obtained from MRI scans of neonates (9-144 days of age) from 30 MVM subjects as well as age- and sex-matched normal controls (60 total). SPHARM-PDM shape analysis was extended to compute a mean latitude axis directly from the spherical parameterization. Local thickness and area was straightforwardly determined. MVM and healthy controls were compared using local MANOVA and compared with the traditional SPHARM-PDM analysis. Both surface and mean latitude axis findings differentiate successfully MVM and healthy lateral ventricle morphology. Lateral ventricles in MVM neonates show enlarged shapes in tail and head. Mean latitude axis is able to find significant differences all along the lateral ventricle shape, demonstrating that local thickness analysis provides significant insight over traditional SPHARM-PDM. This study is the first to precisely quantify 3D lateral ventricle morphology in MVM neonates using shape analysis.

Morphological Properties of Siloxane-Hydrogel Contact Lens Surfaces.

PubMed

Stach, Sebastian; Ţălu, Ştefan; Trabattoni, Silvia; Tavazzi, Silvia; Głuchaczka, Alicja; Siek, Patrycja; Zając, Joanna; Giovanzana, Stefano

2017-04-01

The aim of this study was to quantitatively characterize the micromorphology of contact lens (CL) surfaces using atomic force microscopy (AFM) and multifractal analysis. AFM and multifractal analysis were used to characterize the topography of new and worn siloxane-hydrogel CLs made of Filcon V (I FDA group). CL surface roughness was studied by AFM in intermittent-contact mode, in air, on square areas of 25 and 100 μm 2 , by using a Nanoscope V MultiMode (Bruker). Detailed surface characterization of the surface topography was obtained using statistical parameters of 3-D (three-dimensional) surface roughness, in accordance with ISO 25178-2: 2012. Before wear, the surface was found to be characterized by out-of-plane and sharp structures, whilst after a wear of 8 h, two typical morphologies were observed. One morphology (sharp type) has a similar aspect as the unworn CLs and the other morphology (smooth type) is characterized by troughs and bumpy structures. The analysis of the AFM images revealed a multifractal geometry. The generalized dimension D q and the singularity spectrum f(α) provided quantitative values that characterize the local scale properties of CL surface geometry at nanometer scale. Surface statistical parameters deduced by multifractal analysis can be used to assess the CL micromorphology and can be used by manufacturers in developing CLs with improved surface characteristics. These parameters can also be used in understanding the tribological interactions of the back surface of the CL with the corneal surface and the front surface of the CL with the under-surface of the eyelid (friction, wear, and micro-elastohydrodynamic lubrication at a nanometer scale).

Quantitative trait nucleotide analysis using Bayesian model selection.

PubMed

Blangero, John; Goring, Harald H H; Kent, Jack W; Williams, Jeff T; Peterson, Charles P; Almasy, Laura; Dyer, Thomas D

2005-10-01

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

Nuclear forensics investigation of morphological signatures in the thermal decomposition of uranyl peroxide.

PubMed

Schwerdt, Ian J; Olsen, Adam; Lusk, Robert; Heffernan, Sean; Klosterman, Michael; Collins, Bryce; Martinson, Sean; Kirkham, Trenton; McDonald, Luther W

2018-01-01

The analytical techniques typically utilized in a nuclear forensic investigation often provide limited information regarding the process history and production conditions of interdicted nuclear material. In this study, scanning electron microscopy (SEM) analysis of the surface morphology of amorphous-UO 3 samples calcined at 250, 300, 350, 400, and 450°C from uranyl peroxide was performed to determine if the morphology was indicative of the synthesis route and thermal history for the samples. Thermogravimetic analysis-mass spectrometry (TGA-MS) and differential scanning calorimetry (DSC) were used to correlate transitions in the calcined material to morphological transformations. The high-resolution SEM images were processed using the Morphological Analysis for Material Attribution (MAMA) software. Morphological attributes, particle area and circularity, indicated significant trends as a result of calcination temperature. The quantitative morphological analysis was able to track the process of particle fragmentation and subsequent sintering as calcination temperature was increased. At the 90% confidence interval, with 1000 segmented particles, the use of Kolmogorov-Smirnov statistical comparisons allowed discernment between all calcination temperatures for the uranyl peroxide route. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses

PubMed Central

Brum, Jennifer R; Schenck, Ryan O; Sullivan, Matthew B

2013-01-01

Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51–92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research. PMID:23635867

Improvement of retinal blood vessel detection using morphological component analysis.

PubMed

Imani, Elaheh; Javidi, Malihe; Pourreza, Hamid-Reza

2015-03-01

Detection and quantitative measurement of variations in the retinal blood vessels can help diagnose several diseases including diabetic retinopathy. Intrinsic characteristics of abnormal retinal images make blood vessel detection difficult. The major problem with traditional vessel segmentation algorithms is producing false positive vessels in the presence of diabetic retinopathy lesions. To overcome this problem, a novel scheme for extracting retinal blood vessels based on morphological component analysis (MCA) algorithm is presented in this paper. MCA was developed based on sparse representation of signals. This algorithm assumes that each signal is a linear combination of several morphologically distinct components. In the proposed method, the MCA algorithm with appropriate transforms is adopted to separate vessels and lesions from each other. Afterwards, the Morlet Wavelet Transform is applied to enhance the retinal vessels. The final vessel map is obtained by adaptive thresholding. The performance of the proposed method is measured on the publicly available DRIVE and STARE datasets and compared with several state-of-the-art methods. An accuracy of 0.9523 and 0.9590 has been respectively achieved on the DRIVE and STARE datasets, which are not only greater than most methods, but are also superior to the second human observer's performance. The results show that the proposed method can achieve improved detection in abnormal retinal images and decrease false positive vessels in pathological regions compared to other methods. Also, the robustness of the method in the presence of noise is shown via experimental result. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Channel morphology investigations using Geographic Information Systems and field research

Treesearch

Scott N. Miller; Ann Youberg; D. Phillip Guertin; David C. Goodrich

2000-01-01

Stream channels are integral to watershed function and are affected by watershed management decisions. Given an understanding of the relationships among channel and watershed variables, they may serve as indicators of upland condition or used in distributed rainfall-runoff models. This paper presents a quantitative analysis of fluvial morphology as related to watershed...

Digital pathology and image analysis for robust high-throughput quantitative assessment of Alzheimer disease neuropathologic changes.

PubMed

Neltner, Janna Hackett; Abner, Erin Lynn; Schmitt, Frederick A; Denison, Stephanie Kay; Anderson, Sonya; Patel, Ela; Nelson, Peter T

2012-12-01

Quantitative neuropathologic methods provide information that is important for both research and clinical applications. The technologic advancement of digital pathology and image analysis offers new solutions to enable valid quantification of pathologic severity that is reproducible between raters regardless of experience. Using an Aperio ScanScope XT and its accompanying image analysis software, we designed algorithms for quantitation of amyloid and tau pathologies on 65 β-amyloid (6F/3D antibody) and 48 phospho-tau (PHF-1)-immunostained sections of human temporal neocortex. Quantitative digital pathologic data were compared with manual pathology counts. There were excellent correlations between manually counted and digitally analyzed neuropathologic parameters (R² = 0.56-0.72). Data were highly reproducible among 3 participants with varying degrees of expertise in neuropathology (intraclass correlation coefficient values, >0.910). Digital quantification also provided additional parameters, including average plaque area, which shows statistically significant differences when samples are stratified according to apolipoprotein E allele status (average plaque area, 380.9 μm² in apolipoprotein E [Latin Small Letter Open E]4 carriers vs 274.4 μm² for noncarriers; p < 0.001). Thus, digital pathology offers a rigorous and reproducible method for quantifying Alzheimer disease neuropathologic changes and may provide additional insights into morphologic characteristics that were previously more challenging to assess because of technical limitations.

Regional Morphology Analysis Package (RMAP): Empirical Orthogonal Function Analysis, Background and Examples

DTIC Science & Technology

2007-10-01

1984. Complex principal component analysis : Theory and examples. Journal of Climate and Applied Meteorology 23: 1660-1673. Hotelling, H. 1933...Sediments 99. ASCE: 2,566-2,581. Von Storch, H., and A. Navarra. 1995. Analysis of climate variability. Applications of statistical techniques. Berlin...ERDC TN-SWWRP-07-9 October 2007 Regional Morphology Empirical Analysis Package (RMAP): Orthogonal Function Analysis , Background and Examples by

A functional-structural model of rice linking quantitative genetic information with morphological development and physiological processes.

PubMed

Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

2011-04-01

Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype-phenotype model, we present here a three-dimensional functional-structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed.

A functional–structural model of rice linking quantitative genetic information with morphological development and physiological processes

PubMed Central

Xu, Lifeng; Henke, Michael; Zhu, Jun; Kurth, Winfried; Buck-Sorlin, Gerhard

2011-01-01

Background and Aims Although quantitative trait loci (QTL) analysis of yield-related traits for rice has developed rapidly, crop models using genotype information have been proposed only relatively recently. As a first step towards a generic genotype–phenotype model, we present here a three-dimensional functional–structural plant model (FSPM) of rice, in which some model parameters are controlled by functions describing the effect of main-effect and epistatic QTLs. Methods The model simulates the growth and development of rice based on selected ecophysiological processes, such as photosynthesis (source process) and organ formation, growth and extension (sink processes). It was devised using GroIMP, an interactive modelling platform based on the Relational Growth Grammar formalism (RGG). RGG rules describe the course of organ initiation and extension resulting in final morphology. The link between the phenotype (as represented by the simulated rice plant) and the QTL genotype was implemented via a data interface between the rice FSPM and the QTLNetwork software, which computes predictions of QTLs from map data and measured trait data. Key Results Using plant height and grain yield, it is shown how QTL information for a given trait can be used in an FSPM, computing and visualizing the phenotypes of different lines of a mapping population. Furthermore, we demonstrate how modification of a particular trait feeds back on the entire plant phenotype via the physiological processes considered. Conclusions We linked a rice FSPM to a quantitative genetic model, thereby employing QTL information to refine model parameters and visualizing the dynamics of development of the entire phenotype as a result of ecophysiological processes, including the trait(s) for which genetic information is available. Possibilities for further extension of the model, for example for the purposes of ideotype breeding, are discussed. PMID:21247905

Differentiation between diverticulitis and colorectal cancer: quantitative CT perfusion measurements versus morphologic criteria--initial experience.

PubMed

Goh, Vicky; Halligan, Steve; Taylor, Stuart A; Burling, David; Bassett, Paul; Bartram, Clive I

2007-02-01

To determine whether computed tomographic (CT) perfusion measurements in prospectively recruited patients can be used to differentiate between diverticulitis and colorectal cancer and to compare this discrimination with that of standard morphologic criteria. After institutional review board approval and written informed consent were obtained, 60 patients (24 men, 36 women; mean age, 69 years; range, 33.5-90.4 years; 20 patients with cancer, 20 with diverticulitis, and 20 with inactive diverticular disease) underwent CT perfusion imaging at the level of the colonic abnormality, and perfusion parameters were calculated. Analysis of variance was used to investigate any differences in perfusion between the patient groups. Two independent observers also analyzed an abdominopelvic CT study obtained immediately after the CT perfusion study and noted standard morphologic criteria for differential diagnosis. The sensitivity and specificity of CT perfusion measurements for determining the diagnostic category were compared with morphologic criteria by means of multivariate analysis to identify the most discriminatory criteria. Mean blood volume, blood flow, transit time, and permeability were significantly different between patients with cancer and those with diverticulitis (P < .0001); patients with cancer had the highest blood volume, blood flow, and permeability and the shortest transit time. The most discriminatory criteria for determining diagnostic category were blood volume, transit time, permeability, and presence of pericolonic nodes (P = .05, .02, .04, and .02, respectively). Blood volume and blood flow each had a sensitivity of 80% and had specificity of 70% and 75%, respectively, for cancer in comparison with standard morphologic criteria: less than 5 cm of bowel involvement (45% sensitivity, 95% specificity), presence of a mass (85% sensitivity, 90% specificity), pericolonic inflammation (75% sensitivity, 5% specificity), and pericolonic nodes (90% sensitivity

Linear morphological stability analysis of the solid-liquid interface in rapidsolidification of a binary system

NASA Astrophysics Data System (ADS)

Galenko, P. K.; Danilov, D. A.

2004-05-01

The interface stability against small perturbations of the planar solid-liquid interface is considered analytically in linear approximation. Following the analytical procedure of Trivedi and Kurz [

Design and analysis issues in quantitative proteomics studies.

PubMed

Karp, Natasha A; Lilley, Kathryn S

2007-09-01

Quantitative proteomics is the comparison of distinct proteomes which enables the identification of protein species which exhibit changes in expression or post-translational state in response to a given stimulus. Many different quantitative techniques are being utilized and generate large datasets. Independent of the technique used, these large datasets need robust data analysis to ensure valid conclusions are drawn from such studies. Approaches to address the problems that arise with large datasets are discussed to give insight into the types of statistical analyses of data appropriate for the various experimental strategies that can be employed by quantitative proteomic studies. This review also highlights the importance of employing a robust experimental design and highlights various issues surrounding the design of experiments. The concepts and examples discussed within will show how robust design and analysis will lead to confident results that will ensure quantitative proteomics delivers.

Analysis of the English morphology by semantic networks

NASA Astrophysics Data System (ADS)

Žáček, Martin; Homola, Dan

2017-11-01

The article is devoted to study the morphology of natural language, in this case English language. The research is of the language is from the perspective of knowledge representation, when we look at the word as a concept in the Concept languages. The research is in the relationship of the individual words and their classification in the sentence. For the analysis there are used several methods (syntax, lexical categories, morphology). This article focuses mainly on the word, as the foundation of every natural language (English).

Quantitative analysis on PUVA-induced skin photodamages using optical coherence tomography

NASA Astrophysics Data System (ADS)

Zhai, Juan; Guo, Zhouyi; Liu, Zhiming; Xiong, Honglian; Zeng, Changchun; Jin, Ying

2009-08-01

Psoralen plus ultraviolet A radiation (PUVA) therapy is a very important clinical treatment of skin diseases such as vitiligo and psoriasis, but associated with an increased risk of skin photodamages especially photoaging. Since skin biopsy alters the original skin morphology and always requires an iatrogenic trauma, optical coherence tomography (OCT) appears to be a promising technique to study skin damage in vivo. In this study, the Balb/c mice had 8-methoxypsralen (8-MOP) treatment prior to UVA radiation was used as PUVA-induced photo-damaged modal. The OCT imaging of photo-damaged group (modal) and normal group (control) in vivo was obtained of mice dorsal skin at 0, 24, 48, 72 hours after irradiation respectively. And then the results were quantitatively analyzed combined with histological information. The experimental results showed that, PUVA-induced photo-damaged skin had an increase in epidermal thickness (ET), a reduction of attenuation coefficient in OCT images signal, and an increase in brightness of the epidermis layer compared with the control group. In conclusion, noninvasive high-resolution imaging techniques such as OCT may be a promising tool for photobiological studies aimed at assessing photo-damage and repair processes in vivo. It can be used to quantitative analysis of changes in photo-damaged skin, such as the ET and collagen in dermis, provides a theoretical basis for treatment and prevention of skin photodamages.

Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery.

PubMed

Xiao, Hua; Langerman, Alexander; Zhang, Yan; Khalid, Omar; Hu, Shen; Cao, Cheng-Xi; Lingen, Mark W; Wong, David T W

2015-11-01

Specific biomarkers are urgently needed for the detection and progression of oral cancer. The objective of this study was to discover cancer biomarkers from oral epithelium through utilizing high throughput quantitative proteomics approaches. Morphologically malignant, epithelial dysplasia, and adjacent normal epithelial tissues were laser capture microdissected (LCM) from 19 patients and used for proteomics analysis. Total proteins from each group were extracted, digested and then labelled with corresponding isobaric tags for relative and absolute quantitation (iTRAQ). Labelled peptides from each sample were combined and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS) for protein identification and quantification. In total, 500 proteins were identified and 425 of them were quantified. When compared with adjacent normal oral epithelium, 17 and 15 proteins were consistently up-regulated or down-regulated in malignant and epithelial dysplasia, respectively. Half of these candidate biomarkers were discovered for oral cancer for the first time. Cornulin was initially confirmed in tissue protein extracts and was further validated in tissue microarray. Its presence in the saliva of oral cancer patients was also explored. Myoglobin and S100A8 were pre-validated by tissue microarray. These data demonstrated that the proteomic biomarkers discovered through this strategy are potential targets for oral cancer detection and salivary diagnostics. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

An Image Analysis Method for the Precise Selection and Quantitation of Fluorescently Labeled Cellular Constituents

PubMed Central

Agley, Chibeza C.; Velloso, Cristiana P.; Lazarus, Norman R.

2012-01-01

The accurate measurement of the morphological characteristics of cells with nonuniform conformations presents difficulties. We report here a straightforward method using immunofluorescent staining and the commercially available imaging program Adobe Photoshop, which allows objective and precise information to be gathered on irregularly shaped cells. We have applied this measurement technique to the analysis of human muscle cells and their immunologically marked intracellular constituents, as these cells are prone to adopting a highly branched phenotype in culture. Use of this method can be used to overcome many of the long-standing limitations of conventional approaches for quantifying muscle cell size in vitro. In addition, wider applications of Photoshop as a quantitative and semiquantitative tool in immunocytochemistry are explored. PMID:22511600

Analysis of the microvascular morphology and hemodynamics of breast cancer in mice using SPring-8 synchrotron radiation microangiography

PubMed Central

Torii, Masae; Fukui, Toshifumi; Inoue, Masashi; Umetani, Keiji; Shirai, Mikiyasu; Inagaki, Tadakatsu; Tsuchimochi, Hirotsugu; Toi, Masakazu

2017-01-01

Tumor vasculature is characterized by morphological and functional abnormalities. However, analysis of the dynamics in blood flow is still challenging because of limited spatial and temporal resolution. Synchrotron radiation (SR) microangiography above the K-edge of the iodine contrast agent can provide high-contrast imaging of microvessels in time orders of milliseconds. In this study, mice bearing the human breast cancer cell lines MDAMB231 and NOTCH4 overexpression in MDAMB231 (MDAMB231NOTCH4+) and normal mice were assessed using SR microangiography. NOTCH is transmembrane protein that has crucial roles for vasculogenesis, angiogenesis and tumorigenesis, and NOTCH4 is considered to be a cause of high-flow arteriovenous shunting. A subgroup of mice received intravenous eribulin treatment, which is known to improve intratumor core circulation (MDAMB231_eribulin). Microvessel branches from approximately 200 µm to less than 20 µm in diameter were observed within the same visual field. The mean transition time (MTT) was measured as a dynamic parameter and quantitative analysis was performed. MTT in MDAMB231 was longer than that in normal tissue, and MDAMB231NOTCH4+ showed shorter MTT [5.0 ± 1.4 s, 3.6 ± 1.0 s and 3.6 ± 1.1 s (mean ± standard deviation), respectively]. After treatment, average MTT was correlated to tumor volume (r = 0.999) in MDAMB231_eribulin, while in contrast there was no correlation in MDAMB231 (r = −0.026). These changes in MTT profile are considered to be driven by the modulation of intratumoral circulation dynamics. These results demonstrate that a SR microangiography approach enables quantitative analysis of morphological and dynamic characteristics of tumor vasculature in vivo. Further studies will reveal new findings concerning vessel function in tumors. PMID:28862627

Preliminary Discussion On The Three Dimensional Space Quantitative Analysis Of Erythrocytes By SEMP And Some Applications On The Clinic And Research Of Blood Disease.

NASA Astrophysics Data System (ADS)

Lian-Huang, Lu; Wen-Meng, Tong; Zhi-Jun, Zhang; Gui-Huan, He; Su-Hui, Huan

1989-04-01

The abnormity of the quality and quantity for erythrocytes is one of the important changes of blood disease. It shows the abnormal blood-making function of human body. Therefore, the study of the change of shape of erythrocytes is the indispensible and important basis of reference in the clinic, diagnose and research of blood disease. In this paper, a preliminary discussion is made on the acquisition of scanning stereographs for erythrocytes, the application of the theory of photographic measurement on the three dimensional space quantitative analysis of erythrocytes, drawings of isoline map and section map of various erythrocytes for normal persons, paroxysmal nocturanal hemoglobinuria (PNH) patients and aplastic anemia patients, study of the shape characteristics of normal erythrocytes and various abnormal erytnrocytes and the applications in clinic, diagnose and research. This research is a combination of microphotogrammetry and erythrocyte morphology. It is polssible to push fotward the study of erythrocyte morphology from LM, SEM to a higher stage of scanning electron micrographic photogrammetry(SEMP) for stereograpic observationand three diamensional quantitative analysis to explore a new path for the further study of the shape of erthrocytes.

Quantitative Analysis of Intracellular Motility Based on Optical Flow Model

PubMed Central

Li, Heng

2017-01-01

Analysis of cell mobility is a key issue for abnormality identification and classification in cell biology research. However, since cell deformation induced by various biological processes is random and cell protrusion is irregular, it is difficult to measure cell morphology and motility in microscopic images. To address this dilemma, we propose an improved variation optical flow model for quantitative analysis of intracellular motility, which not only extracts intracellular motion fields effectively but also deals with optical flow computation problem at the border by taking advantages of the formulation based on L1 and L2 norm, respectively. In the energy functional of our proposed optical flow model, the data term is in the form of L2 norm; the smoothness of the data changes with regional features through an adaptive parameter, using L1 norm near the edge of the cell and L2 norm away from the edge. We further extract histograms of oriented optical flow (HOOF) after optical flow field of intracellular motion is computed. Then distances of different HOOFs are calculated as the intracellular motion features to grade the intracellular motion. Experimental results show that the features extracted from HOOFs provide new insights into the relationship between the cell motility and the special pathological conditions. PMID:29065574

An Quantitative Analysis Method Of Trabecular Pattern In A Bone

NASA Astrophysics Data System (ADS)

Idesawa, Masanor; Yatagai, Toyohiko

1982-11-01

Orientation and density of trabecular pattern observed in a bone is closely related to its mechanical properties and deseases of a bone are appeared as changes of orientation and/or density distrbution of its trabecular patterns. They have been treated from a qualitative point of view so far because quantitative analysis method has not be established. In this paper, the authors proposed and investigated some quantitative analysis methods of density and orientation of trabecular patterns observed in a bone. These methods can give an index for evaluating orientation of trabecular pattern quantitatively and have been applied to analyze trabecular pattern observed in a head of femur and their availabilities are confirmed. Key Words: Index of pattern orientation, Trabecular pattern, Pattern density, Quantitative analysis

Quantitative imaging of aggregated emulsions.

PubMed

Penfold, Robert; Watson, Andrew D; Mackie, Alan R; Hibberd, David J

2006-02-28

Noise reduction, restoration, and segmentation methods are developed for the quantitative structural analysis in three dimensions of aggregated oil-in-water emulsion systems imaged by fluorescence confocal laser scanning microscopy. Mindful of typical industrial formulations, the methods are demonstrated for concentrated (30% volume fraction) and polydisperse emulsions. Following a regularized deconvolution step using an analytic optical transfer function and appropriate binary thresholding, novel application of the Euclidean distance map provides effective discrimination of closely clustered emulsion droplets with size variation over at least 1 order of magnitude. The a priori assumption of spherical nonintersecting objects provides crucial information to combat the ill-posed inverse problem presented by locating individual particles. Position coordinates and size estimates are recovered with sufficient precision to permit quantitative study of static geometrical features. In particular, aggregate morphology is characterized by a novel void distribution measure based on the generalized Apollonius problem. This is also compared with conventional Voronoi/Delauney analysis.

Morphological image analysis for classification of gastrointestinal tissues using optical coherence tomography

NASA Astrophysics Data System (ADS)

Garcia-Allende, P. Beatriz; Amygdalos, Iakovos; Dhanapala, Hiruni; Goldin, Robert D.; Hanna, George B.; Elson, Daniel S.

2012-01-01

Computer-aided diagnosis of ophthalmic diseases using optical coherence tomography (OCT) relies on the extraction of thickness and size measures from the OCT images, but such defined layers are usually not observed in emerging OCT applications aimed at "optical biopsy" such as pulmonology or gastroenterology. Mathematical methods such as Principal Component Analysis (PCA) or textural analyses including both spatial textural analysis derived from the two-dimensional discrete Fourier transform (DFT) and statistical texture analysis obtained independently from center-symmetric auto-correlation (CSAC) and spatial grey-level dependency matrices (SGLDM), as well as, quantitative measurements of the attenuation coefficient have been previously proposed to overcome this problem. We recently proposed an alternative approach consisting of a region segmentation according to the intensity variation along the vertical axis and a pure statistical technology for feature quantification. OCT images were first segmented in the axial direction in an automated manner according to intensity. Afterwards, a morphological analysis of the segmented OCT images was employed for quantifying the features that served for tissue classification. In this study, a PCA processing of the extracted features is accomplished to combine their discriminative power in a lower number of dimensions. Ready discrimination of gastrointestinal surgical specimens is attained demonstrating that the approach further surpasses the algorithms previously reported and is feasible for tissue classification in the clinical setting.

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

The Hebrew CHILDES corpus: transcription and morphological analysis

PubMed Central

Albert, Aviad; MacWhinney, Brian; Nir, Bracha

2014-01-01

We present a corpus of transcribed spoken Hebrew that reflects spoken interactions between children and adults. The corpus is an integral part of the CHILDES database, which distributes similar corpora for over 25 languages. We introduce a dedicated transcription scheme for the spoken Hebrew data that is sensitive to both the phonology and the standard orthography of the language. We also introduce a morphological analyzer that was specifically developed for this corpus. The analyzer adequately covers the entire corpus, producing detailed correct analyses for all tokens. Evaluation on a new corpus reveals high coverage as well. Finally, we describe a morphological disambiguation module that selects the correct analysis of each token in context. The result is a high-quality morphologically-annotated CHILDES corpus of Hebrew, along with a set of tools that can be applied to new corpora. PMID:25419199

Multi-Parametric Analysis and Modeling of Relationships between Mitochondrial Morphology and Apoptosis

PubMed Central

Reis, Yara; Wolf, Thomas; Brors, Benedikt; Hamacher-Brady, Anne; Eils, Roland; Brady, Nathan R.

2012-01-01

Mitochondria exist as a network of interconnected organelles undergoing constant fission and fusion. Current approaches to study mitochondrial morphology are limited by low data sampling coupled with manual identification and classification of complex morphological phenotypes. Here we propose an integrated mechanistic and data-driven modeling approach to analyze heterogeneous, quantified datasets and infer relations between mitochondrial morphology and apoptotic events. We initially performed high-content, multi-parametric measurements of mitochondrial morphological, apoptotic, and energetic states by high-resolution imaging of human breast carcinoma MCF-7 cells. Subsequently, decision tree-based analysis was used to automatically classify networked, fragmented, and swollen mitochondrial subpopulations, at the single-cell level and within cell populations. Our results revealed subtle but significant differences in morphology class distributions in response to various apoptotic stimuli. Furthermore, key mitochondrial functional parameters including mitochondrial membrane potential and Bax activation, were measured under matched conditions. Data-driven fuzzy logic modeling was used to explore the non-linear relationships between mitochondrial morphology and apoptotic signaling, combining morphological and functional data as a single model. Modeling results are in accordance with previous studies, where Bax regulates mitochondrial fragmentation, and mitochondrial morphology influences mitochondrial membrane potential. In summary, we established and validated a platform for mitochondrial morphological and functional analysis that can be readily extended with additional datasets. We further discuss the benefits of a flexible systematic approach for elucidating specific and general relationships between mitochondrial morphology and apoptosis. PMID:22272225

Quantitative T2 evaluation at 3.0T compared to morphological grading of the lumbar intervertebral disc: a standardized evaluation approach in patients with low back pain.

PubMed

Stelzeneder, David; Welsch, Goetz Hannes; Kovács, Balázs Krisztián; Goed, Sabine; Paternostro-Sluga, Tatjana; Vlychou, Marianna; Friedrich, Klaus; Mamisch, Tallal Charles; Trattnig, Siegfried

2012-02-01

The purpose of our investigation was to compare quantitative T2 relaxation time measurement evaluation of lumbar intervertebral discs with morphological grading in young to middle-aged patients with low back pain, using a standardized region-of-interest evaluation approach. Three hundred thirty lumbar discs from 66 patients (mean age, 39 years) with low back pain were examined on a 3.0T MR unit. Sagittal T1-FSE, sagittal, coronal, and axial T2-weighted FSE for morphological MRI, as well as a multi-echo spin-echo sequence for T2 mapping, were performed. Morphologically, all discs were classified according to Pfirrmann et al. Equally sized rectangular regions of interest (ROIs) for the annulus fibrosus were selected anteriorly and posteriorly in the outermost 20% of the disc. The space between was defined as the nucleus pulposus. To assess the reproducibility of this evaluation, inter- and intraobserver statistics were performed. The Pfirrmann scoring of 330 discs showed the following results: grade I: six discs (1.8%); grade II: 189 (57.3%); grade III: 96 (29.1%); grade IV: 38 (11.5%); and grade V: one (0.3%). The mean T2 values (in milliseconds) for the anterior and the posterior annulus, and the nucleus pulposus for the respective Pfirrmann groups were: I: 57/30/239; II: 44/67/129; III: 42/51/82; and IV: 42/44/56. The nucleus pulposus T2 values showed a stepwise decrease from Pfirrmann grade I to IV. The posterior annulus showed the highest T2 values in Pfirrmann group II, while the anterior annulus showed relatively constant T2 values in all Pfirrmann groups. The inter- and intraobserver analysis yielded intraclass correlation coefficients (ICC) for average measures in a range from 0.82 (anterior annulus) to 0.99 (nucleus). Our standardized method of region-specific quantitative T2 relaxation time evaluation seems to be able to characterize different degrees of disc degeneration quantitatively. The reproducibility of our ROI measurements is sufficient to

Good practices for quantitative bias analysis.

PubMed

Lash, Timothy L; Fox, Matthew P; MacLehose, Richard F; Maldonado, George; McCandless, Lawrence C; Greenland, Sander

2014-12-01

Quantitative bias analysis serves several objectives in epidemiological research. First, it provides a quantitative estimate of the direction, magnitude and uncertainty arising from systematic errors. Second, the acts of identifying sources of systematic error, writing down models to quantify them, assigning values to the bias parameters and interpreting the results combat the human tendency towards overconfidence in research results, syntheses and critiques and the inferences that rest upon them. Finally, by suggesting aspects that dominate uncertainty in a particular research result or topic area, bias analysis can guide efficient allocation of sparse research resources. The fundamental methods of bias analyses have been known for decades, and there have been calls for more widespread use for nearly as long. There was a time when some believed that bias analyses were rarely undertaken because the methods were not widely known and because automated computing tools were not readily available to implement the methods. These shortcomings have been largely resolved. We must, therefore, contemplate other barriers to implementation. One possibility is that practitioners avoid the analyses because they lack confidence in the practice of bias analysis. The purpose of this paper is therefore to describe what we view as good practices for applying quantitative bias analysis to epidemiological data, directed towards those familiar with the methods. We focus on answering questions often posed to those of us who advocate incorporation of bias analysis methods into teaching and research. These include the following. When is bias analysis practical and productive? How does one select the biases that ought to be addressed? How does one select a method to model biases? How does one assign values to the parameters of a bias model? How does one present and interpret a bias analysis?. We hope that our guide to good practices for conducting and presenting bias analyses will encourage

Combining Multiobjective Optimization and Cluster Analysis to Study Vocal Fold Functional Morphology

PubMed Central

Palaparthi, Anil; Riede, Tobias

2017-01-01

Morphological design and the relationship between form and function have great influence on the functionality of a biological organ. However, the simultaneous investigation of morphological diversity and function is difficult in complex natural systems. We have developed a multiobjective optimization (MOO) approach in association with cluster analysis to study the form-function relation in vocal folds. An evolutionary algorithm (NSGA-II) was used to integrate MOO with an existing finite element model of the laryngeal sound source. Vocal fold morphology parameters served as decision variables and acoustic requirements (fundamental frequency, sound pressure level) as objective functions. A two-layer and a three-layer vocal fold configuration were explored to produce the targeted acoustic requirements. The mutation and crossover parameters of the NSGA-II algorithm were chosen to maximize a hypervolume indicator. The results were expressed using cluster analysis and were validated against a brute force method. Results from the MOO and the brute force approaches were comparable. The MOO approach demonstrated greater resolution in the exploration of the morphological space. In association with cluster analysis, MOO can efficiently explore vocal fold functional morphology. PMID:24771563

Nanoscale Structure of Type I Collagen Fibrils: Quantitative Measurement of D-spacing

PubMed Central

Erickson, Blake; Fang, Ming; Wallace, Joseph M.; Orr, Bradford G.; Les, Clifford M.; Holl, Mark M. Banaszak

2012-01-01

This paper details a quantitative method to measure the D-periodic spacing of Type I collagen fibrils using Atomic Force Microscopy coupled with analysis using a 2D Fast Fourier Transform approach. Instrument calibration, data sampling and data analysis are all discussed and comparisons of the data to the complementary methods of electron microscopy and X-ray scattering are made. Examples of the application of this new approach to the analysis of Type I collagen morphology in disease models of estrogen depletion and Osteogenesis Imperfecta are provided. We demonstrate that it is the D-spacing distribution, not the D-spacing mean, that showed statistically significant differences in estrogen depletion associated with early stage Osteoporosis and Osteogenesis Imperfecta. The ability to quantitatively characterize nanoscale morphological features of Type I collagen fibrils will provide important structural information regarding Type I collagen in many research areas, including tissue aging and disease, tissue engineering, and gene knock out studies. Furthermore, we also envision potential clinical applications including evaluation of tissue collagen integrity under the impact of diseases or drug treatments. PMID:23027700

Quantitative biology of single neurons

PubMed Central

Eberwine, James; Lovatt, Ditte; Buckley, Peter; Dueck, Hannah; Francis, Chantal; Kim, Tae Kyung; Lee, Jaehee; Lee, Miler; Miyashiro, Kevin; Morris, Jacqueline; Peritz, Tiina; Schochet, Terri; Spaethling, Jennifer; Sul, Jai-Yoon; Kim, Junhyong

2012-01-01

The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible. PMID:22915636

Quantitative mass spectrometry methods for pharmaceutical analysis

PubMed Central

Loos, Glenn; Van Schepdael, Ann

2016-01-01

Quantitative pharmaceutical analysis is nowadays frequently executed using mass spectrometry. Electrospray ionization coupled to a (hybrid) triple quadrupole mass spectrometer is generally used in combination with solid-phase extraction and liquid chromatography. Furthermore, isotopically labelled standards are often used to correct for ion suppression. The challenges in producing sensitive but reliable quantitative data depend on the instrumentation, sample preparation and hyphenated techniques. In this contribution, different approaches to enhance the ionization efficiencies using modified source geometries and improved ion guidance are provided. Furthermore, possibilities to minimize, assess and correct for matrix interferences caused by co-eluting substances are described. With the focus on pharmaceuticals in the environment and bioanalysis, different separation techniques, trends in liquid chromatography and sample preparation methods to minimize matrix effects and increase sensitivity are discussed. Although highly sensitive methods are generally aimed for to provide automated multi-residue analysis, (less sensitive) miniaturized set-ups have a great potential due to their ability for in-field usage. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644982

Label-free cell-cycle analysis by high-throughput quantitative phase time-stretch imaging flow cytometry

NASA Astrophysics Data System (ADS)

Mok, Aaron T. Y.; Lee, Kelvin C. M.; Wong, Kenneth K. Y.; Tsia, Kevin K.

2018-02-01

Biophysical properties of cells could complement and correlate biochemical markers to characterize a multitude of cellular states. Changes in cell size, dry mass and subcellular morphology, for instance, are relevant to cell-cycle progression which is prevalently evaluated by DNA-targeted fluorescence measurements. Quantitative-phase microscopy (QPM) is among the effective biophysical phenotyping tools that can quantify cell sizes and sub-cellular dry mass density distribution of single cells at high spatial resolution. However, limited camera frame rate and thus imaging throughput makes QPM incompatible with high-throughput flow cytometry - a gold standard in multiparametric cell-based assay. Here we present a high-throughput approach for label-free analysis of cell cycle based on quantitative-phase time-stretch imaging flow cytometry at a throughput of > 10,000 cells/s. Our time-stretch QPM system enables sub-cellular resolution even at high speed, allowing us to extract a multitude (at least 24) of single-cell biophysical phenotypes (from both amplitude and phase images). Those phenotypes can be combined to track cell-cycle progression based on a t-distributed stochastic neighbor embedding (t-SNE) algorithm. Using multivariate analysis of variance (MANOVA) discriminant analysis, cell-cycle phases can also be predicted label-free with high accuracy at >90% in G1 and G2 phase, and >80% in S phase. We anticipate that high throughput label-free cell cycle characterization could open new approaches for large-scale single-cell analysis, bringing new mechanistic insights into complex biological processes including diseases pathogenesis.

Changes in cell morphology due to plasma membrane wounding by acoustic cavitation

PubMed Central

Schlicher, Robyn K.; Hutcheson, Joshua D.; Radhakrishna, Harish; Apkarian, Robert P.; Prausnitz, Mark R.

2010-01-01

Acoustic cavitation-mediated wounding (i.e., sonoporation) has great potential to improve medical and laboratory applications requiring intracellular uptake of exogenous molecules; however, the field lacks detailed understanding of cavitation-induced morphological changes in cells and their relative importance. Here, we present an in-depth study of the effects of acoustic cavitation on cells using electron and confocal microscopy coupled with quantitative flow cytometry. High resolution images of treated cells show that morphologically different types of blebs can occur after wounding conditions caused by ultrasound exposure as well as by mechanical shear and strong laser ablation. In addition, these treatments caused wound-induced non-lytic necrotic death resulting in cell bodies we call wound-derived perikarya (WD-P). However, only cells exposed to acoustic cavitation experienced ejection of intact nuclei and nearly instant lytic necrosis. Quantitative analysis by flow cytometry indicates that wound-derived perikarya are the dominant morphology of nonviable cells, except at the strongest wounding conditions, where nuclear ejection accounts for a significant portion of cell death after ultrasound exposure. PMID:20350691

Quantitative analysis of single-molecule superresolution images

PubMed Central

Coltharp, Carla; Yang, Xinxing; Xiao, Jie

2014-01-01

This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

[Quantitative morphological characteristics of the changes in the effector component of the immune system in dyshormonal hyperplasias and breast cancer].

PubMed

Abrakova, E L

1982-01-01

The effector component of immune system was studied in 39 cases of fibroadenomatosis by morphometric and histochemical methods. Signs of immunosuppression (decreased fraction of free cells of stroma and disturbances in their cooperation) were identified in cases of precancerous changes and cancer. A considerable difference in nucleic acid level in fibroadenomatosis and cancer was established. It is suggested that quantitative morphological study of the effector component of immune system may provide more diagnostic criteria for identification of prognostically unfavorable forms of fibroadenomatosis and cancer.

Human Lymphatic Mesenteric Vessels: Morphology and Possible Function of Aminergic and NPY-ergic Nerve Fibers.

PubMed

D'Andrea, Vito; Panarese, Alessandra; Taurone, Samanta; Coppola, Luigi; Cavallotti, Carlo; Artico, Marco

2015-09-01

The lymphatic vessels have been studied in different organs from a morphological to a clinical point of view. Nevertheless, the knowledge of the catecholaminergic control of the lymphatic circulation is still incomplete. The aim of this work is to study the presence and distribution of the catecholaminergic and NPY-ergic nerve fibers in the whole wall of the human mesenteric lymphatic vessels in order to obtain knowledge about their morphology and functional significance. The following experimental procedures were performed: 1) drawing of tissue containing lymphatic vessels; 2) cutting of tissue; 3) staining of tissue; 4) staining of nerve fibers; 5) histofluorescence microscopy for the staining of catecholaminergic nerve fibers; 6) staining of neuropeptide Y like-immune reactivity; 7) biochemical assay of proteins; 8) measurement of noradrenaline; 9) quantitative analysis of images; 10) statistical analysis of data. Numerous nerve fibers run in the wall of lymphatic vessels. Many of them are catecholaminergic in nature. Some nerve fibers are NPY-positive. The biochemical results on noradrenaline amounts are in agreement with morphological results on catecholaminergic nerve fibers. Moreover, the morphometric results, obtained by the quantitative analysis of images and the subsequent statistical analysis of data, confirm all our morphological and biochemical data. The knowledge of the physiological or pathological mechanism regulating the functions of the lymphatic system is incomplete. Nevertheless the catecholaminergic nerve fibers of the human mesenteric lymphatic vessels come from the adrenergic periarterial plexuses of the mesenterial arterial bed. NPY-ergic nerve fibers may modulate the microcirculatory mesenterial bed in different pathological conditions.

Classification and phylogenetic analysis of Chinese hawthorn assessed by plant and pollen morphology.

PubMed

Ma, S L Y; Lu, Y M

2016-09-19

The Chinese hawthorn (Crataegus pinnatifida Bge. var. major N.E.Br.) is uniquely originated in northern China. The ecological and horticultural importance of Chinese hawthorn is considerable and some varieties are valued for their fruit or medicine extracts. Its taxonomy and phylogeny remain poorly understood. Apart from general plant morphological traits, pollen is an important trait for the classification of plants and their evolutionary origin. However, few studies have investigated the pollen of Chinese hawthorn. Here, an analysis of plant and pollen morphological characteristics was conducted in 57 cultivars from the Shenyang region. Thirty plant morphological characters and nine pollen grain characters were investigated. The plant morphological analysis revealed that the coefficient of variation for 13 traits was >20%, which indicates a high degree of variability. We also found that the pollen grains varied greatly in size, shape (from prolate to perprolate), and exine pattern (striate-perforate predominantly). The number of apertures was typically three. Based on these findings, we suggest that pollen morphology associated with plant morphological traits can be used for classification and phylogenetic analysis of Chinese hawthorn cultivars. In sum, our results provide new insights and constitute a scientific basis for future studies on the classification and evolution of Chinese hawthorn.

Quantitative analysis of histopathological findings using image processing software.

PubMed

Horai, Yasushi; Kakimoto, Tetsuhiro; Takemoto, Kana; Tanaka, Masaharu

2017-10-01

In evaluating pathological changes in drug efficacy and toxicity studies, morphometric analysis can be quite robust. In this experiment, we examined whether morphometric changes of major pathological findings in various tissue specimens stained with hematoxylin and eosin could be recognized and quantified using image processing software. Using Tissue Studio, hypertrophy of hepatocytes and adrenocortical cells could be quantified based on the method of a previous report, but the regions of red pulp, white pulp, and marginal zones in the spleen could not be recognized when using one setting condition. Using Image-Pro Plus, lipid-derived vacuoles in the liver and mucin-derived vacuoles in the intestinal mucosa could be quantified using two criteria (area and/or roundness). Vacuoles derived from phospholipid could not be quantified when small lipid deposition coexisted in the liver and adrenal cortex. Mononuclear inflammatory cell infiltration in the liver could be quantified to some extent, except for specimens with many clustered infiltrating cells. Adipocyte size and the mean linear intercept could be quantified easily and efficiently using morphological processing and the macro tool equipped in Image-Pro Plus. These methodologies are expected to form a base system that can recognize morphometric features and analyze quantitatively pathological findings through the use of information technology.

Nonlinear optical microscopy: use of second harmonic generation and two-photon microscopy for automated quantitative liver fibrosis studies.

PubMed

Sun, Wanxin; Chang, Shi; Tai, Dean C S; Tan, Nancy; Xiao, Guangfa; Tang, Huihuan; Yu, Hanry

2008-01-01

Liver fibrosis is associated with an abnormal increase in an extracellular matrix in chronic liver diseases. Quantitative characterization of fibrillar collagen in intact tissue is essential for both fibrosis studies and clinical applications. Commonly used methods, histological staining followed by either semiquantitative or computerized image analysis, have limited sensitivity, accuracy, and operator-dependent variations. The fibrillar collagen in sinusoids of normal livers could be observed through second-harmonic generation (SHG) microscopy. The two-photon excited fluorescence (TPEF) images, recorded simultaneously with SHG, clearly revealed the hepatocyte morphology. We have systematically optimized the parameters for the quantitative SHG/TPEF imaging of liver tissue and developed fully automated image analysis algorithms to extract the information of collagen changes and cell necrosis. Subtle changes in the distribution and amount of collagen and cell morphology are quantitatively characterized in SHG/TPEF images. By comparing to traditional staining, such as Masson's trichrome and Sirius red, SHG/TPEF is a sensitive quantitative tool for automated collagen characterization in liver tissue. Our system allows for enhanced detection and quantification of sinusoidal collagen fibers in fibrosis research and clinical diagnostics.

Phylogeny of kemenyan (Styrax sp.) from North Sumatra based on morphological characters

NASA Astrophysics Data System (ADS)

Susilowati, A.; Kholibrina, C. R.; Rachmat, H. H.; Munthe, M. A.

2018-02-01

Kemenyan is the most famous local tree species from North Sumatra. Kemenyan is known as rosin producer that very valuable for pharmacheutical, cosmetic, food preservatives and vernis. Based on its history, there were only two species of kemenyan those were kemenyan durame and toba, but in its the natural distribution we also found others species showing different characteristics with previously known ones. The objectives of this research were:The objectives of this research were: (1). To determine the morphological diversity of kemenyan in North Sumatra and (2). To determine phylogeny clustering based on the morphological characters. Data was collected from direct observation and morphological characterization, based on purposive sampling technique to those samples trees atPakpak Bharat, North Sumatra. Morphological characters were examined using descriptive analysis, phenotypic variability using standard deviation, and cluster analysis. The result showed that there was a difference between 4 species kemenyen (batak, minyak, durame and toba) according to 75 observed characters including flower, fruits, leaf, stem, bark, crown type, wood and the resin. Analysis and both quantitative and qualitative characters kemenyan clustered into two groups. In which, kemenyan toba separated with other clusters.

Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

ERIC Educational Resources Information Center

Anderson, James L.; And Others

1980-01-01

Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

Quantitative analysis of arm movement smoothness

NASA Astrophysics Data System (ADS)

Szczesna, Agnieszka; Błaszczyszyn, Monika

2017-07-01

The paper deals with the problem of motion data quantitative smoothness analysis. We investigated values of movement unit, fluidity and jerk for healthy and paralyzed arm of patients with hemiparesis after stroke. Patients were performing drinking task. To validate the approach, movement of 24 patients were captured using optical motion capture system.

Lipophilic organic pollutants induce changes in phospholipid and membrane protein composition leading to Vero cell morphological change.

PubMed

Liao, Ting T; Wang, Lei; Jia, Ru W; Fu, Xiao H; Chua, Hong

2014-01-01

Membrane damage related to morphological change in Vero cells is a sensitive index of the composite biotoxicity of trace lipophilic chemicals. However, judging whether the morphological change in Vero cells happens and its ratio are difficult because it is not a quantitative characteristic. To find biomarkers of cell morphological change for quantitatively representing the ratio of morphological changed cell, the mechanism of cell membrane damage driven by typical lipophilic chemicals, such as trichlorophenol (TCP) and perfluorooctanesulphonate (PFOS), was explored. The ratio of morphologically changed cells generally increased with increased TCP or PFOS concentrations, and the level of four major components of phospholipids varied with concentrations of TCP or PFOS, but only the ratio of phosphatidylcholine (PC)/phosphatidylethanolamine (PE) decreased regularly as TCP or PFOS concentrations increased. Analysis of membrane proteins showed that the level of vimentin in normal cell membranes is high, while it decreases or vanishes after TCP exposure. These variations in phospholipid and membrane protein components may result in membrane leakage and variation in rigid structure, which leads to changes in cell morphology. Therefore, the ratio of PC/PE and amount of vimentin may be potential biomarkers for representing the ratio of morphological changed Vero cell introduced by trace lipophilic compounds, thus their composite bio-toxicity.

Revision of the Malagasy Camponotus edmondi species group (Hymenoptera, Formicidae, Formicinae): integrating qualitative morphology and multivariate morphometric analysis.

PubMed

Rakotonirina, Jean Claude; Csősz, Sándor; Fisher, Brian L

2016-01-01

The Malagasy Camponotus edmondi species group is revised based on both qualitative morphological traits and multivariate analysis of continuous morphometric data. To minimize the effect of the scaling properties of diverse traits due to worker caste polymorphism, and to achieve the desired near-linearity of data, morphometric analyses were done only on minor workers. The majority of traits exhibit broken scaling on head size, dividing Camponotus workers into two discrete subcastes, minors and majors. This broken scaling prevents the application of algorithms that uses linear combination of data to the entire dataset, hence only minor workers were analyzed statistically. The elimination of major workers resulted in linearity and the data meet required assumptions. However, morphometric ratios for the subsets of minor and major workers were used in species descriptions and redefinitions. Prior species hypotheses and the goodness of clusters were tested on raw data by confirmatory linear discriminant analysis. Due to the small sample size available for some species, a factor known to reduce statistical reliability, hypotheses generated by exploratory analyses were tested with extreme care and species delimitations were inferred via the combined evidence of both qualitative (morphology and biology) and quantitative data. Altogether, fifteen species are recognized, of which 11 are new to science: Camponotus alamaina sp. n. , Camponotus androy sp. n. , Camponotus bevohitra sp. n. , Camponotus galoko sp. n. , Camponotus matsilo sp. n. , Camponotus mifaka sp. n. , Camponotus orombe sp. n. , Camponotus tafo sp. n. , Camponotus tratra sp. n. , Camponotus varatra sp. n. , and Camponotus zavo sp. n. Four species are redescribed: Camponotus echinoploides Forel, Camponotus edmondi André, Camponotus ethicus Forel, and Camponotus robustus Roger. Camponotus edmondi ernesti Forel, syn. n. is synonymized under Camponotus edmondi . This revision also includes an identification key to

Quantitative assessment of the relationships among ecological, morphological and aesthetic values in a river rehabilitation initiative.

PubMed

McCormick, Ashlee; Fisher, Karen; Brierley, Gary

2015-04-15

Promoting community support in rehabilitation efforts through incorporation of aesthetic considerations is an important component of environmental management. This research utilised a small-scale survey methodology to explore relationships among the ecological and morphological goals of scientists and the aesthetic goals of the public using the Twin Streams Catchment, Auckland, New Zealand, as a case study. Analyses using a linear model and a generalised linear mixed model showed statistically significant relationships between perceived naturalness of landscapes and their aesthetic ratings, and among ratings of perceived naturalness and ecological integrity and morphological condition. Expert measures of health and the aesthetic evaluations of the public were well aligned, indicating public preferences for landscapes of high ecological integrity with good morphological condition. Further analysis revealed participants used 'cues to care' to rate naturalness. This suggests that environmental education endeavours could further align values with these cues in efforts to enhance approaches to landscape sustainability. Copyright © 2014 Elsevier Ltd. All rights reserved.

Quantitative morphology of the vascularisation of organs: A stereological approach illustrated using the cardiac circulation.

PubMed

Mühlfeld, Christian

2014-01-01

The vasculature of the heart is able to adapt to various physiological and pathological stimuli and its failure to do so is well-reflected by the great impact of ischaemic heart disease on personal morbidity and mortality and on the health care systems of industrial countries. Studies on physiological or genetic interventions as well as therapeutic angiogenesis rely on quantitative data to characterize the effects in a statistically robust way. The gold standard for obtaining quantitative morphological data is design-based stereology which allows the estimation of volume, surface area, length and number of blood vessels as well as their thickness, diameter or wall composition. Unfortunately, the use of stereological methods for this purpose is still rare. One of the reasons for this is the fact that the transfer of the theoretical foundations into laboratory practice requires a remarkable amount of considerations before touching the first piece of tissue. These considerations, however, are often based on already acquired experience and are usually not dealt with in stereological review articles. The present article therefore delineates the procedures for estimating the most important characteristics of the cardiac vasculature and highlights potential problems and their practical solutions. Worked examples are used to illustrate the methods and provide examples of the calculations. Hopefully, the considerations and examples contained herein will provide researchers in this field with the necessary equipment to add stereological methods to their study designs. Copyright © 2012 Elsevier GmbH. All rights reserved.

Rock surface roughness measurement using CSI technique and analysis of surface characterization by qualitative and quantitative results

NASA Astrophysics Data System (ADS)

Mukhtar, Husneni; Montgomery, Paul; Gianto; Susanto, K.

2016-01-01

In order to develop image processing that is widely used in geo-processing and analysis, we introduce an alternative technique for the characterization of rock samples. The technique that we have used for characterizing inhomogeneous surfaces is based on Coherence Scanning Interferometry (CSI). An optical probe is first used to scan over the depth of the surface roughness of the sample. Then, to analyse the measured fringe data, we use the Five Sample Adaptive method to obtain quantitative results of the surface shape. To analyse the surface roughness parameters, Hmm and Rq, a new window resizing analysis technique is employed. The results of the morphology and surface roughness analysis show micron and nano-scale information which is characteristic of each rock type and its history. These could be used for mineral identification and studies in rock movement on different surfaces. Image processing is thus used to define the physical parameters of the rock surface.

Quantitative investigation of red blood cell three-dimensional geometric and chemical changes in the storage lesion using digital holographic microscopy.

PubMed

Jaferzadeh, Keyvan; Moon, Inkyu

2015-11-01

Quantitative phase information obtained by digital holographic microscopy (DHM) can provide new insight into the functions and morphology of single red blood cells (RBCs). Since the functionality of a RBC is related to its three-dimensional (3-D) shape, quantitative 3-D geometric changes induced by storage time can help hematologists realize its optimal functionality period. We quantitatively investigate RBC 3-D geometric changes in the storage lesion using DHM. Our experimental results show that the substantial geometric transformation of the biconcave-shaped RBCs to the spherocyte occurs due to RBC storage lesion. This transformation leads to progressive loss of cell surface area, surface-to-volume ratio, and functionality of RBCs. Furthermore, our quantitative analysis shows that there are significant correlations between chemical and morphological properties of RBCs.

Morphology Analysis and Optimization: Crucial Factor Determining the Performance of Perovskite Solar Cells.

PubMed

Zeng, Wenjin; Liu, Xingming; Guo, Xiangru; Niu, Qiaoli; Yi, Jianpeng; Xia, Ruidong; Min, Yong

2017-03-24

This review presents an overall discussion on the morphology analysis and optimization for perovskite (PVSK) solar cells. Surface morphology and energy alignment have been proven to play a dominant role in determining the device performance. The effect of the key parameters such as solution condition and preparation atmosphere on the crystallization of PVSK, the characterization of surface morphology and interface distribution in the perovskite layer is discussed in detail. Furthermore, the analysis of interface energy level alignment by using X-ray photoelectron spectroscopy and ultraviolet photoelectron spectroscopy is presented to reveals the correlation between morphology and charge generation and collection within the perovskite layer, and its influence on the device performance. The techniques including architecture modification, solvent annealing, etc. were reviewed as an efficient approach to improve the morphology of PVSK. It is expected that further progress will be achieved with more efforts devoted to the insight of the mechanism of surface engineering in the field of PVSK solar cells.

MRI quantitative morphologic analysis of patellofemoral region: lack of correlation with chondromalacia patellae at surgery.

PubMed

Endo, Yoshimi; Schweitzer, Mark E; Bordalo-Rodrigues, Marcelo; Rokito, Andrew S; Babb, James S

2007-11-01

In numerous studies, the morphologic features of the patellofemoral joint have been analyzed on radiographs. The objective of this study was to assess patellofemoral measurements on MR images and to correlate the measurements with the presence or absence of chondromalacia patellae confirmed at surgery. Axial and sagittal MR images of 98 knees (97 patients) were evaluated. Lateral and medial patellar facet lengths, lateral-to-medial facet length ratio, and interfacet angle were measured at three levels through the patella. Trochlear depth was measured on an axial slice. Patella and patellar tendon lengths, patellar tendon-to-patella ratio, and overlap of the patellar and trochlear articular cartilages were measured on sagittal slices. These measurements in knees with chondromalacia patellae were compared with those in knees without chondromalacia patellae. For assessment of reproducibility, axial measurements were repeated by a second observer. There was no statistically significant difference in any of the axial and sagittal slice measurements between knees with and those without chondromalacia patellae. Interobserver reliability was excellent for measurements of trochlear depth and measurements in the superior and middle aspects of the patella. Measurements through the inferior patella were slightly less reproducible. The results of our study with MRI confirmed many previous radiographic findings. Although we did not find correlation between the presence of chondromalacia patellae and the patellofemoral indexes we analyzed, it is possible that the results of further investigations incorporating different grades of chondromalacia and different locations along the patellar articular surface may lead to further insight regarding the morphologic risk factors for chondromalacia patellae.

Quantitative diagnosis of bladder cancer by morphometric analysis of HE images

NASA Astrophysics Data System (ADS)

Wu, Binlin; Nebylitsa, Samantha V.; Mukherjee, Sushmita; Jain, Manu

2015-02-01

In clinical practice, histopathological analysis of biopsied tissue is the main method for bladder cancer diagnosis and prognosis. The diagnosis is performed by a pathologist based on the morphological features in the image of a hematoxylin and eosin (HE) stained tissue sample. This manuscript proposes algorithms to perform morphometric analysis on the HE images, quantify the features in the images, and discriminate bladder cancers with different grades, i.e. high grade and low grade. The nuclei are separated from the background and other types of cells such as red blood cells (RBCs) and immune cells using manual outlining, color deconvolution and image segmentation. A mask of nuclei is generated for each image for quantitative morphometric analysis. The features of the nuclei in the mask image including size, shape, orientation, and their spatial distributions are measured. To quantify local clustering and alignment of nuclei, we propose a 1-nearest-neighbor (1-NN) algorithm which measures nearest neighbor distance and nearest neighbor parallelism. The global distributions of the features are measured using statistics of the proposed parameters. A linear support vector machine (SVM) algorithm is used to classify the high grade and low grade bladder cancers. The results show using a particular group of nuclei such as large ones, and combining multiple parameters can achieve better discrimination. This study shows the proposed approach can potentially help expedite pathological diagnosis by triaging potentially suspicious biopsies.

Quantitative Classification of Rice (Oryza sativa L.) Root Length and Diameter Using Image Analysis.

PubMed

Gu, Dongxiang; Zhen, Fengxian; Hannaway, David B; Zhu, Yan; Liu, Leilei; Cao, Weixing; Tang, Liang

2017-01-01

Quantitative study of root morphological characteristics of plants is helpful for understanding the relationships between their morphology and function. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). The aims of this study were to quantitatively classify fine lateral roots (FLRs), thick lateral roots (TLRs), and nodal roots (NRs) and analyze their dynamics of mean diameter (MD), lengths and surface area percentage with growth stages in rice plant. Pot experiments were carried out during three years with three rice cultivars, three nitrogen (N) rates and three water regimes. In cultivar experiment, among the three cultivars, root length of 'Yangdao 6' was longest, while the MD of its FLR was the smallest, and the mean diameters for TLR and NR were the largest, the surface area percentage (SAP) of TLRs (SAPT) was the highest, indicating that Yangdao 6 has better nitrogen and water uptake ability. High N rate increased the length of different types of roots and increased the MD of lateral roots, decreased the SAP of FLRs (SAPF) and TLRs, but increased the SAP of NRs (SAPN). Moderate decrease of water supply increased root length and diameter, water stress increased the SAPF and SAPT, but decreased SAPN. The quantitative results indicate that rice plant tends to increase lateral roots to get more surface area for nitrogen and water uptake when available assimilates are limiting under nitrogen and water stress environments.

The APOSTEL recommendations for reporting quantitative optical coherence tomography studies.

PubMed

Cruz-Herranz, Andrés; Balk, Lisanne J; Oberwahrenbrock, Timm; Saidha, Shiv; Martinez-Lapiscina, Elena H; Lagreze, Wolf A; Schuman, Joel S; Villoslada, Pablo; Calabresi, Peter; Balcer, Laura; Petzold, Axel; Green, Ari J; Paul, Friedemann; Brandt, Alexander U; Albrecht, Philipp

2016-06-14

To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. A panel of experienced OCT researchers (including 11 neurologists, 2 ophthalmologists, and 2 neuroscientists) discussed requirements for performing and reporting quantitative analyses of retinal morphology and developed a list of initial recommendations based on experience and previous studies. The list of recommendations was subsequently revised during several meetings of the coordinating group. We provide a 9-point checklist encompassing aspects deemed relevant when reporting quantitative OCT studies. The areas covered are study protocol, acquisition device, acquisition settings, scanning protocol, funduscopic imaging, postacquisition data selection, postacquisition data analysis, recommended nomenclature, and statistical analysis. The Advised Protocol for OCT Study Terminology and Elements recommendations include core items to standardize and improve quality of reporting in quantitative OCT studies. The recommendations will make reporting of quantitative OCT studies more consistent and in line with existing standards for reporting research in other biomedical areas. The recommendations originated from expert consensus and thus represent Class IV evidence. They will need to be regularly adjusted according to new insights and practices. © 2016 American Academy of Neurology.

Control of separation and quantitative analysis by GC-FTIR

NASA Astrophysics Data System (ADS)

Semmoud, A.; Huvenne, Jean P.; Legrand, P.

1992-03-01

Software for 3-D representations of the 'Absorbance-Wavenumber-Retention time' is used to control the quality of the GC separation. Spectral information given by the FTIR detection allows the user to be sure that a chromatographic peak is 'pure.' The analysis of peppermint essential oil is presented as an example. This assurance is absolutely required for quantitative applications. In these conditions, we have worked out a quantitative analysis of caffeine. Correlation coefficients between integrated absorbance measurements and concentration of caffeine are discussed at two steps of the data treatment.

Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

ERIC Educational Resources Information Center

Franklin, Wilfred A.

2010-01-01

In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

Quantitative Analysis of the Efficiency of OLEDs.

PubMed

Sim, Bomi; Moon, Chang-Ki; Kim, Kwon-Hyeon; Kim, Jang-Joo

2016-12-07

We present a comprehensive model for the quantitative analysis of factors influencing the efficiency of organic light-emitting diodes (OLEDs) as a function of the current density. The model takes into account the contribution made by the charge carrier imbalance, quenching processes, and optical design loss of the device arising from various optical effects including the cavity structure, location and profile of the excitons, effective radiative quantum efficiency, and out-coupling efficiency. Quantitative analysis of the efficiency can be performed with an optical simulation using material parameters and experimental measurements of the exciton profile in the emission layer and the lifetime of the exciton as a function of the current density. This method was applied to three phosphorescent OLEDs based on a single host, mixed host, and exciplex-forming cohost. The three factors (charge carrier imbalance, quenching processes, and optical design loss) were influential in different ways, depending on the device. The proposed model can potentially be used to optimize OLED configurations on the basis of an analysis of the underlying physical processes.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method.

PubMed

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-02-01

To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method

PubMed Central

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-01-01

Objective To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. Methods TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Results Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. Conclusions The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil. PMID:25182282

Fabrication of type I collagen microcarrier using a microfluidic 3D T-junction device and its application for the quantitative analysis of cell-ECM interactions.

PubMed

Yoon, Junghyo; Kim, Jaehoon; Jeong, Hyo Eun; Sudo, Ryo; Park, Myung-Jin; Chung, Seok

2016-08-26

We presented a new quantitative analysis for cell and extracellular matrix (ECM) interactions, using cell-coated ECM hydrogel microbeads (hydrobeads) made of type I collagen. The hydrobeads can carry cells as three-dimensional spheroidal forms with an ECM inside, facilitating a direct interaction between the cells and ECM. The cells on hydrobeads do not have a hypoxic core, which opens the possibility for using as a cell microcarrier for bottom-up tissue reconstitution. This technique can utilize various types of cells, even MDA-MB-231 cells, which have weak cell-cell interactions and do not form spheroids in conventional spheroid culture methods. Morphological indices of the cell-coated hydrobead visually present cell-ECM interactions in a quantitative manner.

[Neotropical plant morphology].

PubMed

Pérez-García, Blanca; Mendoza, Aniceto

2002-01-01

An analysis on plant morphology and the sources that are important to the morphologic interpretations is done. An additional analysis is presented on all published papers in this subject by the Revista de Biología Tropical since its foundation, as well as its contribution to the plant morphology development in the neotropics.

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

NASA Technical Reports Server (NTRS)

Shortle, John F.; Allocco, Michael

2005-01-01

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

Quantitative phase imaging of human red blood cells using phase-shifting white light interference microscopy with colour fringe analysis

NASA Astrophysics Data System (ADS)

Singh Mehta, Dalip; Srivastava, Vishal

2012-11-01

We report quantitative phase imaging of human red blood cells (RBCs) using phase-shifting interference microscopy. Five phase-shifted white light interferograms are recorded using colour charge coupled device camera. White light interferograms were decomposed into red, green, and blue colour components. The phase-shifted interferograms of each colour were then processed by phase-shifting analysis and phase maps for red, green, and blue colours were reconstructed. Wavelength dependent refractive index profiles of RBCs were computed from the single set of white light interferogram. The present technique has great potential for non-invasive determination of refractive index variation and morphological features of cells and tissues.

Quantitative evaluation method of the bubble structure of sponge cake by using morphology image processing

NASA Astrophysics Data System (ADS)

Tatebe, Hironobu; Kato, Kunihito; Yamamoto, Kazuhiko; Katsuta, Yukio; Nonaka, Masahiko

2005-12-01

Now a day, many evaluation methods for the food industry by using image processing are proposed. These methods are becoming new evaluation method besides the sensory test and the solid-state measurement that are using for the quality evaluation. An advantage of the image processing is to be able to evaluate objectively. The goal of our research is structure evaluation of sponge cake by using image processing. In this paper, we propose a feature extraction method of the bobble structure in the sponge cake. Analysis of the bubble structure is one of the important properties to understand characteristics of the cake from the image. In order to take the cake image, first we cut cakes and measured that's surface by using the CIS scanner. Because the depth of field of this type scanner is very shallow, the bubble region of the surface has low gray scale values, and it has a feature that is blur. We extracted bubble regions from the surface images based on these features. First, input image is binarized, and the feature of bubble is extracted by the morphology analysis. In order to evaluate the result of feature extraction, we compared correlation with "Size of the bubble" of the sensory test result. From a result, the bubble extraction by using morphology analysis gives good correlation. It is shown that our method is as well as the subjectivity evaluation.

A quantitative analysis of the F18 flight control system

NASA Technical Reports Server (NTRS)

Doyle, Stacy A.; Dugan, Joanne B.; Patterson-Hine, Ann

1993-01-01

This paper presents an informal quantitative analysis of the F18 flight control system (FCS). The analysis technique combines a coverage model with a fault tree model. To demonstrate the method's extensive capabilities, we replace the fault tree with a digraph model of the F18 FCS, the only model available to us. The substitution shows that while digraphs have primarily been used for qualitative analysis, they can also be used for quantitative analysis. Based on our assumptions and the particular failure rates assigned to the F18 FCS components, we show that coverage does have a significant effect on the system's reliability and thus it is important to include coverage in the reliability analysis.

Multiscale morphological filtering for analysis of noisy and complex images

NASA Astrophysics Data System (ADS)

Kher, A.; Mitra, S.

Images acquired with passive sensing techniques suffer from illumination variations and poor local contrasts that create major difficulties in interpretation and identification tasks. On the other hand, images acquired with active sensing techniques based on monochromatic illumination are degraded with speckle noise. Mathematical morphology offers elegant techniques to handle a wide range of image degradation problems. Unlike linear filters, morphological filters do not blur the edges and hence maintain higher image resolution. Their rich mathematical framework facilitates the design and analysis of these filters as well as their hardware implementation. Morphological filters are easier to implement and are more cost effective and efficient than several conventional linear filters. Morphological filters to remove speckle noise while maintaining high resolution and preserving thin image regions that are particularly vulnerable to speckle noise were developed and applied to SAR imagery. These filters used combination of linear (one-dimensional) structuring elements in different (typically four) orientations. Although this approach preserves more details than the simple morphological filters using two-dimensional structuring elements, the limited orientations of one-dimensional elements approximate the fine details of the region boundaries. A more robust filter designed recently overcomes the limitation of the fixed orientations. This filter uses a combination of concave and convex structuring elements. Morphological operators are also useful in extracting features from visible and infrared imagery. A multiresolution image pyramid obtained with successive filtering and a subsampling process aids in the removal of the illumination variations and enhances local contrasts. A morphology-based interpolation scheme was also introduced to reduce intensity discontinuities created in any morphological filtering task. The generality of morphological filtering techniques in

Multiscale Morphological Filtering for Analysis of Noisy and Complex Images

NASA Technical Reports Server (NTRS)

Kher, A.; Mitra, S.

1993-01-01

Images acquired with passive sensing techniques suffer from illumination variations and poor local contrasts that create major difficulties in interpretation and identification tasks. On the other hand, images acquired with active sensing techniques based on monochromatic illumination are degraded with speckle noise. Mathematical morphology offers elegant techniques to handle a wide range of image degradation problems. Unlike linear filters, morphological filters do not blur the edges and hence maintain higher image resolution. Their rich mathematical framework facilitates the design and analysis of these filters as well as their hardware implementation. Morphological filters are easier to implement and are more cost effective and efficient than several conventional linear filters. Morphological filters to remove speckle noise while maintaining high resolution and preserving thin image regions that are particularly vulnerable to speckle noise were developed and applied to SAR imagery. These filters used combination of linear (one-dimensional) structuring elements in different (typically four) orientations. Although this approach preserves more details than the simple morphological filters using two-dimensional structuring elements, the limited orientations of one-dimensional elements approximate the fine details of the region boundaries. A more robust filter designed recently overcomes the limitation of the fixed orientations. This filter uses a combination of concave and convex structuring elements. Morphological operators are also useful in extracting features from visible and infrared imagery. A multiresolution image pyramid obtained with successive filtering and a subsampling process aids in the removal of the illumination variations and enhances local contrasts. A morphology-based interpolation scheme was also introduced to reduce intensity discontinuities created in any morphological filtering task. The generality of morphological filtering techniques in

Correlation Study of PVDF Membrane Morphology with Protein Adsorption: Quantitative Analysis by FTIR/ATR Technique

NASA Astrophysics Data System (ADS)

Ideris, N.; Ahmad, A. L.; Ooi, B. S.; Low, S. C.

2018-05-01

Microporous PVDF membranes were used as protein capture matrices in immunoassays. Because the most common labels in immunoassays were detected based on the colour change, an understanding of how protein concentration varies on different PVDF surfaces was needed. Herein, the correlation between the membrane pore size and protein adsorption was systematically investigated. Five different PVDF membrane morphologies were prepared and FTIR/ATR was employed to accurately quantify the surface protein concentration on membranes with small pore sizes. SigmaPlot® was used to find a suitable curve fit for protein adsorption and membrane pore size, with a high correlation coefficient, R2, of 0.9971.

A strategy to apply quantitative epistasis analysis on developmental traits.

PubMed

Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

2017-05-15

Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

Quantitative analysis of thyroid tumors vascularity: A comparison between 3-D contrast-enhanced ultrasound and 3-D Power Doppler on benign and malignant thyroid nodules.

PubMed

Caresio, Cristina; Caballo, Marco; Deandrea, Maurilio; Garberoglio, Roberto; Mormile, Alberto; Rossetto, Ruth; Limone, Paolo; Molinari, Filippo

2018-05-15

To perform a comparative quantitative analysis of Power Doppler ultrasound (PDUS) and Contrast-Enhancement ultrasound (CEUS) for the quantification of thyroid nodules vascularity patterns, with the goal of identifying biomarkers correlated with the malignancy of the nodule with both imaging techniques. We propose a novel method to reconstruct the vascular architecture from 3-D PDUS and CEUS images of thyroid nodules, and to automatically extract seven quantitative features related to the morphology and distribution of vascular network. Features include three tortuosity metrics, the number of vascular trees and branches, the vascular volume density, and the main spatial vascularity pattern. Feature extraction was performed on 20 thyroid lesions (ten benign and ten malignant), of which we acquired both PDUS and CEUS. MANOVA (multivariate analysis of variance) was used to differentiate benign and malignant lesions based on the most significant features. The analysis of the extracted features showed a significant difference between the benign and malignant nodules for both PDUS and CEUS techniques for all the features. Furthermore, by using a linear classifier on the significant features identified by the MANOVA, benign nodules could be entirely separated from the malignant ones. Our early results confirm the correlation between the morphology and distribution of blood vessels and the malignancy of the lesion, and also show (at least for the dataset used in this study) a considerable similarity in terms of findings of PDUS and CEUS imaging for thyroid nodules diagnosis and classification. © 2018 American Association of Physicists in Medicine.

Spectral interferometry for morphological imaging in in vitro fertilization (IVF) (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhu, Yizheng; Li, Chengshuai

2016-03-01

Morphological assessment of spermatozoa is of critical importance for in vitro fertilization (IVF), especially intracytoplasmic sperm injection (ICSI)-based IVF. In ICSI, a single sperm cell is selected and injected into an egg to achieve fertilization. The quality of the sperm cell is found to be highly correlated to IVF success. Sperm morphology, such as shape, head birefringence and motility, among others, are typically evaluated under a microscope. Current observation relies on conventional techniques such as differential interference contrast microscopy and polarized light microscopy. Their qualitative nature, however, limits the ability to provide accurate quantitative analysis. Here, we demonstrate quantitative morphological measurement of sperm cells using two types of spectral interferometric techniques, namely spectral modulation interferometry and spectral multiplexing interferometry. Both are based on spectral-domain low coherence interferometry, which is known for its exquisite phase determination ability. While spectral modulation interferometry encodes sample phase in a single spectrum, spectral multiplexing interferometry does so for sample birefringence. Therefore they are capable of highly sensitive phase and birefringence imaging. These features suit well in the imaging of live sperm cells, which are small, dynamic objects with only low to moderate levels of phase and birefringence contrast. We will introduce the operation of both techniques and demonstrate their application to measuring the phase and birefringence morphology of sperm cells.

FlowerMorphology: fully automatic flower morphometry software.

PubMed

Rozov, Sergey M; Deineko, Elena V; Deyneko, Igor V

2018-05-01

The software FlowerMorphology is designed for automatic morphometry of actinomorphic flowers. The novel complex parameters of flowers calculated by FlowerMorphology allowed us to quantitatively characterize a polyploid series of tobacco. Morphological differences of plants representing closely related lineages or mutants are mostly quantitative. Very often, there are only very fine variations in plant morphology. Therefore, accurate and high-throughput methods are needed for their quantification. In addition, new characteristics are necessary for reliable detection of subtle changes in morphology. FlowerMorphology is an all-in-one software package to automatically image and analyze five-petal actinomorphic flowers of the dicotyledonous plants. Sixteen directly measured parameters and ten calculated complex parameters of a flower allow us to characterize variations with high accuracy. The program was developed for the needs of automatic characterization of Nicotiana tabacum flowers, but is applicable to many other plants with five-petal actinomorphic flowers and can be adopted for flowers of other merosity. A genetically similar polyploid series of N. tabacum plants was used to investigate differences in flower morphology. For the first time, we could quantify the dependence between ploidy and size and form of the tobacco flowers. We found that the radius of inner petal incisions shows a persistent positive correlation with the chromosome number. In contrast, a commonly used parameter-radius of outer corolla-does not discriminate 2n and 4n plants. Other parameters show that polyploidy leads to significant aberrations in flower symmetry and are also positively correlated with chromosome number. Executables of FlowerMorphology, source code, documentation, and examples are available at the program website: https://github.com/Deyneko/FlowerMorphology .

Quantiprot - a Python package for quantitative analysis of protein sequences.

PubMed

Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

2017-07-17

The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

FLIPPER, a combinatorial probe for correlated live imaging and electron microscopy, allows identification and quantitative analysis of various cells and organelles.

PubMed

Kuipers, Jeroen; van Ham, Tjakko J; Kalicharan, Ruby D; Veenstra-Algra, Anneke; Sjollema, Klaas A; Dijk, Freark; Schnell, Ulrike; Giepmans, Ben N G

2015-04-01

Ultrastructural examination of cells and tissues by electron microscopy (EM) yields detailed information on subcellular structures. However, EM is typically restricted to small fields of view at high magnification; this makes quantifying events in multiple large-area sample sections extremely difficult. Even when combining light microscopy (LM) with EM (correlated LM and EM: CLEM) to find areas of interest, the labeling of molecules is still a challenge. We present a new genetically encoded probe for CLEM, named "FLIPPER", which facilitates quantitative analysis of ultrastructural features in cells. FLIPPER consists of a fluorescent protein (cyan, green, orange, or red) for LM visualization, fused to a peroxidase allowing visualization of targets at the EM level. The use of FLIPPER is straightforward and because the module is completely genetically encoded, cells can be optimally prepared for EM examination. We use FLIPPER to quantify cellular morphology at the EM level in cells expressing a normal and disease-causing point-mutant cell-surface protein called EpCAM (epithelial cell adhesion molecule). The mutant protein is retained in the endoplasmic reticulum (ER) and could therefore alter ER function and morphology. To reveal possible ER alterations, cells were co-transfected with color-coded full-length or mutant EpCAM and a FLIPPER targeted to the ER. CLEM examination of the mixed cell population allowed color-based cell identification, followed by an unbiased quantitative analysis of the ER ultrastructure by EM. Thus, FLIPPER combines bright fluorescent proteins optimized for live imaging with high sensitivity for EM labeling, thereby representing a promising tool for CLEM.

What Really Happens in Quantitative Group Research? Results of a Content Analysis of Recent Quantitative Research in "JSGW"

ERIC Educational Resources Information Center

Boyle, Lauren H.; Whittaker, Tiffany A.; Eyal, Maytal; McCarthy, Christopher J.

2017-01-01

The authors conducted a content analysis on quantitative studies published in "The Journal for Specialists in Group Work" ("JSGW") between 2012 and 2015. This brief report provides a general overview of the current practices of quantitative group research in counseling. The following study characteristics are reported and…

Method and apparatus for chromatographic quantitative analysis

DOEpatents

Fritz, James S.; Gjerde, Douglas T.; Schmuckler, Gabriella

1981-06-09

An improved apparatus and method for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single eluent and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

Discrimination of Mediterranean mussel (Mytilus galloprovincialis) feces in deposited materials by fecal morphology.

PubMed

Akiyama, Yoshihiro B; Iseri, Erina; Kataoka, Tomoya; Tanaka, Makiko; Katsukoshi, Kiyonori; Moki, Hirotada; Naito, Ryoji; Hem, Ramrav; Okada, Tomonari

2017-02-15

In the present study, we determined the common morphological characteristics of the feces of Mytilus galloprovincialis to develop a method for visually discriminating the feces of this mussel in deposited materials. This method can be used to assess the effect of mussel feces on benthic environments. The accuracy of visual morphology-based discrimination of mussel feces in deposited materials was confirmed by DNA analysis. Eighty-nine percent of mussel feces shared five common morphological characteristics. Of the 372 animal species investigated, only four species shared all five of these characteristics. More than 96% of the samples were visually identified as M. galloprovincialis feces on the basis of morphology of the particles containing the appropriate mitochondrial DNA. These results suggest that mussel feces can be discriminated with high accuracy on the basis of their morphological characteristics. Thus, our method can be used to quantitatively assess the effect of mussel feces on local benthic environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantitative analysis of three-dimensional biological cells using interferometric microscopy

NASA Astrophysics Data System (ADS)

Shaked, Natan T.; Wax, Adam

2011-06-01

Live biological cells are three-dimensional microscopic objects that constantly adjust their sizes, shapes and other biophysical features. Wide-field digital interferometry (WFDI) is a holographic technique that is able to record the complex wavefront of the light which has interacted with in-vitro cells in a single camera exposure, where no exogenous contrast agents are required. However, simple quasi-three-dimensional holographic visualization of the cell phase profiles need not be the end of the process. Quantitative analysis should permit extraction of numerical parameters which are useful for cytology or medical diagnosis. Using a transmission-mode setup, the phase profile represents the multiplication between the integral refractive index and the thickness of the sample. These coupled variables may not be distinct when acquiring the phase profiles of dynamic cells. Many morphological parameters which are useful for cell biologists are based on the cell thickness profile rather than on its phase profile. We first overview methods to decouple the cell thickness and its refractive index using the WFDI-based phase profile. Then, we present a whole-cell-imaging approach which is able to extract useful numerical parameters on the cells even in cases where decoupling of cell thickness and refractive index is not possible or desired.

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata

PubMed Central

Diniz, Daniel G.; Silva, Geane O.; Naves, Thaís B.; Fernandes, Taiany N.; Araújo, Sanderson C.; Diniz, José A. P.; de Farias, Luis H. S.; Sosthenes, Marcia C. K.; Diniz, Cristovam G.; Anthony, Daniel C.; da Costa Vasconcelos, Pedro F.; Picanço Diniz, Cristovam W.

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous. PMID:27047345

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata.

PubMed

Diniz, Daniel G; Silva, Geane O; Naves, Thaís B; Fernandes, Taiany N; Araújo, Sanderson C; Diniz, José A P; de Farias, Luis H S; Sosthenes, Marcia C K; Diniz, Cristovam G; Anthony, Daniel C; da Costa Vasconcelos, Pedro F; Picanço Diniz, Cristovam W

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous.

Quantitative dispersion microscopy

PubMed Central

Fu, Dan; Choi, Wonshik; Sung, Yongjin; Yaqoob, Zahid; Dasari, Ramachandra R.; Feld, Michael

2010-01-01

Refractive index dispersion is an intrinsic optical property and a useful source of contrast in biological imaging studies. In this report, we present the first dispersion phase imaging of living eukaryotic cells. We have developed quantitative dispersion microscopy based on the principle of quantitative phase microscopy. The dual-wavelength quantitative phase microscope makes phase measurements at 310 nm and 400 nm wavelengths to quantify dispersion (refractive index increment ratio) of live cells. The measured dispersion of living HeLa cells is found to be around 1.088, which agrees well with that measured directly for protein solutions using total internal reflection. This technique, together with the dry mass and morphology measurements provided by quantitative phase microscopy, could prove to be a useful tool for distinguishing different types of biomaterials and studying spatial inhomogeneities of biological samples. PMID:21113234

First morphological and molecular analysis of Eucoleus boehmi like eggs in dogs from Argentina.

PubMed

Lavallén, Carla Mariela; Petrigh, Romina Sandra; Fugassa, Martín Horacio; Denegri, Guillermo María; Dopchiz, Marcela Cecilia

2018-07-01

The canid parasites Eucoleus aerophilus (syn. Capillaria aerophila) and Eucoleus boehmi (syn. Capillaria boehmi) parasitize the lower and the upper respiratory tract, respectively. Reports and descriptions of these nematodes are scarce in Argentina, possibly due to misdiagnosis of morphologically similar trichuroids eggs, and the lack of knowledge about the species of Eucoleus in this geographical area. Scanning electron microscopy is a useful tool for identification of E. boehmi eggs based on the characteristics of the shell structure which differentiate between species. Molecular analysis complements morphological identification. Until now, there are no studies based on the analysis of E. boehmi eggs in Argentina. The aim of the present work was to study by morphological, morphometric, and molecular analysis, eggs attributable to E. boehmi isolated from dogs naturally infected in Mar del Plata city, Argentina. Eggs isolated from two dog fecal samples were analyzed by light and scanning electron microscopy. A fragment of mitochondrial DNA (mtDNA) of the cytochrome c oxidase subunit I gene (cox1) from eggs was sequenced, and phylogenetic analysis was performed in this study. According to morphological results based on the wall surface ultrastructure, the eggs studied were assigned to E. boehmi. Molecular analysis supported the morphological identification. The divergence of 9-12% with the European isolated could suggest a new geographical genetic variation of E. boehmi, but also question the possible existence of cryptic species. This is the first characterization of E. boehmi eggs in dogs from Argentina.

Quantitative Analysis of High-Quality Officer Selection by Commandants Career-Level Education Board

DTIC Science & Technology

2017-03-01

due to Marines being evaluated before the end of their initial service commitment. Our research utilizes quantitative variables to analyze the...not provide detailed information why. B. LIMITATIONS The photograph analysis in this research is strictly limited to a quantitative analysis in...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. QUANTITATIVE

Data from quantitative label free proteomics analysis of rat spleen.

PubMed

Dudekula, Khadar; Le Bihan, Thierry

2016-09-01

The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

Quantitative Classification of Rice (Oryza sativa L.) Root Length and Diameter Using Image Analysis

PubMed Central

Gu, Dongxiang; Zhen, Fengxian; Hannaway, David B.; Zhu, Yan; Liu, Leilei; Cao, Weixing; Tang, Liang

2017-01-01

Quantitative study of root morphological characteristics of plants is helpful for understanding the relationships between their morphology and function. However, few studies and little detailed and accurate information of root characteristics were reported in fine-rooted plants like rice (Oryza sativa L.). The aims of this study were to quantitatively classify fine lateral roots (FLRs), thick lateral roots (TLRs), and nodal roots (NRs) and analyze their dynamics of mean diameter (MD), lengths and surface area percentage with growth stages in rice plant. Pot experiments were carried out during three years with three rice cultivars, three nitrogen (N) rates and three water regimes. In cultivar experiment, among the three cultivars, root length of ‘Yangdao 6’ was longest, while the MD of its FLR was the smallest, and the mean diameters for TLR and NR were the largest, the surface area percentage (SAP) of TLRs (SAPT) was the highest, indicating that Yangdao 6 has better nitrogen and water uptake ability. High N rate increased the length of different types of roots and increased the MD of lateral roots, decreased the SAP of FLRs (SAPF) and TLRs, but increased the SAP of NRs (SAPN). Moderate decrease of water supply increased root length and diameter, water stress increased the SAPF and SAPT, but decreased SAPN. The quantitative results indicate that rice plant tends to increase lateral roots to get more surface area for nitrogen and water uptake when available assimilates are limiting under nitrogen and water stress environments. PMID:28103264

Morphological analysis of pore size and connectivity in a thick mixed-culture biofilm.

PubMed

Rosenthal, Alex F; Griffin, James S; Wagner, Michael; Packman, Aaron I; Balogun, Oluwaseyi; Wells, George F

2018-05-19

Morphological parameters are commonly used to predict transport and metabolic kinetics in biofilms. Yet, quantification of biofilm morphology remains challenging due to imaging technology limitations and lack of robust analytical approaches. We present a novel set of imaging and image analysis techniques to estimate internal porosity, pore size distributions, and pore network connectivity to a depth of 1 mm at a resolution of 10 µm in a biofilm exhibiting both heterotrophic and nitrifying activity. Optical coherence tomography (OCT) scans revealed an extensive pore network with diameters as large as 110 µm directly connected to the biofilm surface and surrounding fluid. Thin section fluorescence in situ hybridization microscopy revealed ammonia oxidizing bacteria (AOB) distributed through the entire thickness of the biofilm. AOB were particularly concentrated in the biofilm around internal pores. Areal porosity values estimated from OCT scans were consistently lower than those estimated from multiphoton laser scanning microscopy, though the two imaging modalities showed a statistically significant correlation (r = 0.49, p<0.0001). Estimates of areal porosity were moderately sensitive to grey level threshold selection, though several automated thresholding algorithms yielded similar values to those obtained by manually thresholding performed by a panel of environmental engineering researchers (±25% relative error). These findings advance our ability to quantitatively describe the geometry of biofilm internal pore networks at length scales relevant to engineered biofilm reactors and suggest that internal pore structures provide crucial habitat for nitrifier growth. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Global scaling for semi-quantitative analysis in FP-CIT SPECT.

PubMed

Kupitz, D; Apostolova, I; Lange, C; Ulrich, G; Amthauer, H; Brenner, W; Buchert, R

2014-01-01

Semi-quantitative characterization of dopamine transporter availability from single photon emission computed tomography (SPECT) with 123I-ioflupane (FP-CIT) is based on uptake ratios relative to a reference region. The aim of this study was to evaluate the whole brain as reference region for semi-quantitative analysis of FP-CIT SPECT. The rationale was that this might reduce statistical noise associated with the estimation of non-displaceable FP-CIT uptake. 150 FP-CIT SPECTs were categorized as neurodegenerative or non-neurodegenerative by an expert. Semi-quantitative analysis of specific binding ratios (SBR) was performed with a custom-made tool based on the Statistical Parametric Mapping software package using predefined regions of interest (ROIs) in the anatomical space of the Montreal Neurological Institute. The following reference regions were compared: predefined ROIs for frontal and occipital lobe and whole brain (without striata, thalamus and brainstem). Tracer uptake in the reference region was characterized by the mean, median or 75th percentile of its voxel intensities. The area (AUC) under the receiver operating characteristic curve was used as performance measure. The highest AUC of 0.973 was achieved by the SBR of the putamen with the 75th percentile in the whole brain as reference. The lowest AUC for the putamen SBR of 0.937 was obtained with the mean in the frontal lobe as reference. We recommend the 75th percentile in the whole brain as reference for semi-quantitative analysis in FP-CIT SPECT. This combination provided the best agreement of the semi-quantitative analysis with visual evaluation of the SPECT images by an expert and, therefore, is appropriate to support less experienced physicians.

Looking into the puparium: Micro-CT visualization of the internal morphological changes during metamorphosis of the blow fly, Calliphora vicina, with the first quantitative analysis of organ development in cyclorrhaphous dipterans.

PubMed

Martín-Vega, Daniel; Simonsen, Thomas J; Hall, Martin J R

2017-05-01

Metamorphosis of cyclorrhaphous flies takes place inside a barrel-like puparium, formed by the shrinking, hardening and darkening of the third-instar larval cuticle. The opacity of this structure hampers the visualization of the morphological changes occurring inside and therefore a full understanding of the metamorphosis process. Here, we use micro-computed tomography (micro-CT) to describe the internal morphological changes that occur during metamorphosis of the blow fly, Calliphora vicina Robineau-Desvoidy 1830 (Diptera: Calliphoridae) at a greater temporal resolution than anything hitherto published. The morphological changes were documented at 10% intervals of the total intra-puparial period, and down to 2.5% intervals during the first 20% interval, when the most dramatic morphological changes occur. Moreover, the development of an internal gas bubble, which plays an essential role during early metamorphosis, was further investigated with X-ray images and micro-CT virtual sections. The origin of this gas bubble has been largely unknown, but micro-CT virtual sections show that it is connected to one of the main tracheal trunks. Micro-CT virtual sections also provided enough resolution for determining the completion of the larval-pupal and pupal-adult apolyses, thus enabling an accurate timing of the different intra-puparial life stages. The prepupal, pupal, and pharate adult stages last for 7.5%, 22.5%, and 70% of the total intra-puparial development, respectively. Furthermore, we provide for the first time quantitative data on the development of two organ systems of the blow fly: the alimentary canal and the indirect flight muscles. There is a significant and negative correlation between the volume of the indirect flight muscles and the pre-helicoidal region of the midgut during metamorphosis. The latter occupies a large portion of the thorax during the pupal stage but narrows progressively as the indirect flight muscles increase in volume during the

A Statistical Analysis of Brain Morphology Using Wild Bootstrapping

PubMed Central

Ibrahim, Joseph G.; Tang, Niansheng; Rowe, Daniel B.; Hao, Xuejun; Bansal, Ravi; Peterson, Bradley S.

2008-01-01

Methods for the analysis of brain morphology, including voxel-based morphology and surface-based morphometries, have been used to detect associations between brain structure and covariates of interest, such as diagnosis, severity of disease, age, IQ, and genotype. The statistical analysis of morphometric measures usually involves two statistical procedures: 1) invoking a statistical model at each voxel (or point) on the surface of the brain or brain subregion, followed by mapping test statistics (e.g., t test) or their associated p values at each of those voxels; 2) correction for the multiple statistical tests conducted across all voxels on the surface of the brain region under investigation. We propose the use of new statistical methods for each of these procedures. We first use a heteroscedastic linear model to test the associations between the morphological measures at each voxel on the surface of the specified subregion (e.g., cortical or subcortical surfaces) and the covariates of interest. Moreover, we develop a robust test procedure that is based on a resampling method, called wild bootstrapping. This procedure assesses the statistical significance of the associations between a measure of given brain structure and the covariates of interest. The value of this robust test procedure lies in its computationally simplicity and in its applicability to a wide range of imaging data, including data from both anatomical and functional magnetic resonance imaging (fMRI). Simulation studies demonstrate that this robust test procedure can accurately control the family-wise error rate. We demonstrate the application of this robust test procedure to the detection of statistically significant differences in the morphology of the hippocampus over time across gender groups in a large sample of healthy subjects. PMID:17649909

Quantitative T2 Magnetic Resonance Imaging Compared to Morphological Grading of the Early Cervical Intervertebral Disc Degeneration: An Evaluation Approach in Asymptomatic Young Adults

PubMed Central

Han, Zhihua; Shao, Lixin; Xie, Yan; Wu, Jianhong; Zhang, Yan; Xin, Hongkui; Ren, Aijun; Guo, Yong; Wang, Deli; He, Qing; Ruan, Dike

2014-01-01

Objective The objective of this study was to evaluate the efficacy of quantitative T2 magnetic resonance imaging (MRI) for quantifying early cervical intervertebral disc (IVD) degeneration in asymptomatic young adults by correlating the T2 value with Pfirrmann grade, sex, and anatomic level. Methods Seventy asymptomatic young subjects (34 men and 36 women; mean age, 22.80±2.11 yr; range, 18–25 years) underwent 3.0-T MRI to obtain morphological data (one T1-fast spin echo (FSE) and three-plane T2-FSE, used to assign a Pfirrmann grade (I–V)) and for T2 mapping (multi-echo spin echo). T2 values in the nucleus pulposus (NP, n = 350) and anulus fibrosus (AF, n = 700) were obtained. Differences in T2 values between sexes and anatomic level were evaluated, and linear correlation analysis of T2 values versus degenerative grade was conducted. Findings Cervical IVDs of healthy young adults were commonly determined to be at Pfirrmann grades I and II. T2 values of NPs were significantly higher than those of AF at all anatomic levels (P<0.000). The NP, anterior AF and posterior AF values did not differ significantly between genders at the same anatomic level (P>0.05). T2 values decreased linearly with degenerative grade. Linear correlation analysis revealed a strong negative association between the Pfirrmann grade and the T2 values of the NP (P = 0.000) but not the T2 values of the AF (P = 0.854). However, non-degenerated discs (Pfirrmann grades I and II) showed a wide range of T2 relaxation time. T2 values according to disc degeneration level classification were as follows: grade I (>62.03 ms), grade II (54.60–62.03 ms), grade III (<54.60 ms). Conclusions T2 quantitation provides a more sensitive and robust approach for detecting and characterizing the early stage of cervical IVD degeneration and to create a reliable quantitative in healthy young adults. PMID:24498384

Quantitative T2 magnetic resonance imaging compared to morphological grading of the early cervical intervertebral disc degeneration: an evaluation approach in asymptomatic young adults.

PubMed

Chen, Chun; Huang, Minghua; Han, Zhihua; Shao, Lixin; Xie, Yan; Wu, Jianhong; Zhang, Yan; Xin, Hongkui; Ren, Aijun; Guo, Yong; Wang, Deli; He, Qing; Ruan, Dike

2014-01-01

The objective of this study was to evaluate the efficacy of quantitative T2 magnetic resonance imaging (MRI) for quantifying early cervical intervertebral disc (IVD) degeneration in asymptomatic young adults by correlating the T2 value with Pfirrmann grade, sex, and anatomic level. Seventy asymptomatic young subjects (34 men and 36 women; mean age, 22.80±2.11 yr; range, 18-25 years) underwent 3.0-T MRI to obtain morphological data (one T1-fast spin echo (FSE) and three-plane T2-FSE, used to assign a Pfirrmann grade (I-V)) and for T2 mapping (multi-echo spin echo). T2 values in the nucleus pulposus (NP, n = 350) and anulus fibrosus (AF, n = 700) were obtained. Differences in T2 values between sexes and anatomic level were evaluated, and linear correlation analysis of T2 values versus degenerative grade was conducted. Cervical IVDs of healthy young adults were commonly determined to be at Pfirrmann grades I and II. T2 values of NPs were significantly higher than those of AF at all anatomic levels (P<0.000). The NP, anterior AF and posterior AF values did not differ significantly between genders at the same anatomic level (P>0.05). T2 values decreased linearly with degenerative grade. Linear correlation analysis revealed a strong negative association between the Pfirrmann grade and the T2 values of the NP (P = 0.000) but not the T2 values of the AF (P = 0.854). However, non-degenerated discs (Pfirrmann grades I and II) showed a wide range of T2 relaxation time. T2 values according to disc degeneration level classification were as follows: grade I (>62.03 ms), grade II (54.60-62.03 ms), grade III (<54.60 ms). T2 quantitation provides a more sensitive and robust approach for detecting and characterizing the early stage of cervical IVD degeneration and to create a reliable quantitative in healthy young adults.

Seniors' Online Communities: A Quantitative Content Analysis

ERIC Educational Resources Information Center

Nimrod, Galit

2010-01-01

Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

The Relationship of Morphological Analysis and Morphological Decoding to Reading Comprehension

ERIC Educational Resources Information Center

Deacon, S. Hélène; Tong, Xiuli; Francis, Kathryn

2017-01-01

The ultimate goal of children's reading development is the full and fluid understanding of texts. Morphological structure awareness, or children's awareness of the minimal units of meaning in language, has been identified as a key skill influencing reading comprehension. Here, we evaluate the roles of morphological structure awareness and two…

Targeted methods for quantitative analysis of protein glycosylation

PubMed Central

Goldman, Radoslav; Sanda, Miloslav

2018-01-01

Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated. PMID:25522218

Morphological leaf variability in natural populations of Pistacia atlantica Desf. subsp. atlantica along climatic gradient: new features to update Pistacia atlantica subsp. atlantica key.

PubMed

El Zerey-Belaskri, Asma; Benhassaini, Hachemi

2016-04-01

The effect of bioclimate range on the variation in Pistacia atlantica Desf. subsp. atlantica leaf morphology was studied on 16 sites in Northwest Algeria. The study examined biometrically mature leaves totaling 3520 compound leaves. Fifteen characters (10 quantitative and 5 qualitative) were assessed on each leaf. For each quantitative character, the nested analysis of variance (ANOVA) was used to examine relative magnitude of variation at each level of the nested hierarchy. The correlation between the climatic parameters and the leaf morphology was examined. The statistical analysis applied on the quantitative leaf characters showed highly significant variation at the within-site level and between-site variation. The correlation coefficient (r) showed also an important correlation between climatic parameters and leaf morphology. The results of this study exhibited several values reported for the first time on the species, such as the length and the width of the leaf (reaching up to 24.5 cm/21.9 cm), the number of leaflets (up to 18 leaflets/leaf), and the petiole length of the terminal leaflet (reaching up to 3.4 cm). The original findings of this study are used to update the P. atlantica subsp. atlantica identification key.

Preparation, quantitative surface analysis, intercalation characteristics and industrial implications of low temperature expandable graphite

NASA Astrophysics Data System (ADS)

Peng, Tiefeng; Liu, Bin; Gao, Xuechao; Luo, Liqun; Sun, Hongjuan

2018-06-01

Expandable graphite is widely used as a new functional carbon material, especially as fire-retardant; however, its practical application is limited due to the high expansion temperature. In this work, preparation process of low temperature and highly expandable graphite was studied, using natural flake graphite as raw material and KMnO4/HClO4/NH4NO3 as oxidative intercalations. The structure, morphology, functional groups and thermal properties were characterized during expanding process by Fourier transform infrared spectroscopy (FTIR), Raman spectra, thermo-gravimetry differential scanning calorimetry (TG-DSC), X-ray diffraction (XRD), and scanning electron microscope (SEM). The analysis showed that by oxidation intercalation, some oxygen-containing groups were grafted on the edge and within the graphite layer. The intercalation reagent entered the graphite layer to increase the interlayer spacing. After expansion, the original flaky expandable graphite was completely transformed into worm-like expanded graphite. The order of graphite intercalation compounds (GICs) was proposed and determined to be 3 for the prepared expandable graphite, based on quantitative XRD peak analysis. Meanwhile, the detailed intercalation mechanisms were also proposed. The comprehensive investigation paved a benchmark for the industrial application of such sulfur-free expanded graphite.

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

PubMed

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

2013-06-01

Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Facial Phenotyping by Quantitative Photography Reflects Craniofacial Morphology Measured on Magnetic Resonance Imaging in Icelandic Sleep Apnea Patients

PubMed Central

Sutherland, Kate; Schwab, Richard J.; Maislin, Greg; Lee, Richard W.W.; Benedikstdsottir, Bryndis; Pack, Allan I.; Gislason, Thorarinn; Juliusson, Sigurdur; Cistulli, Peter A.

2014-01-01

Study Objectives: (1) To determine whether facial phenotype, measured by quantitative photography, relates to underlying craniofacial obstructive sleep apnea (OSA) risk factors, measured with magnetic resonance imaging (MRI); (2) To assess whether these associations are independent of body size and obesity. Design: Cross-sectional cohort. Setting: Landspitali, The National University Hospital, Iceland. Participants: One hundred forty patients (87.1% male) from the Icelandic Sleep Apnea Cohort who had both calibrated frontal and profile craniofacial photographs and upper airway MRI. Mean ± standard deviation age 56.1 ± 10.4 y, body mass index 33.5 ± 5.05 kg/m2, with on-average severe OSA (apnea-hypopnea index 45.4 ± 19.7 h-1). Interventions: N/A. Measurements and Results: Relationships between surface facial dimensions (photos) and facial bony dimensions and upper airway soft-tissue volumes (MRI) was assessed using canonical correlation analysis. Photo and MRI craniofacial datasets related in four significant canonical correlations, primarily driven by measurements of (1) maxillary-mandibular relationship (r = 0.8, P < 0.0001), (2) lower face height (r = 0.76, P < 0.0001), (3) mandibular length (r = 0.67, P < 0.0001), and (4) tongue volume (r = 0.52, P = 0.01). Correlations 1, 2, and 3 were unchanged when controlled for weight and neck and waist circumference. However, tongue volume was no longer significant, suggesting facial dimensions relate to tongue volume as a result of obesity. Conclusions: Significant associations were found between craniofacial variable sets from facial photography and MRI. This study confirms that facial photographic phenotype reflects underlying aspects of craniofacial skeletal abnormalities associated with OSA. Therefore, facial photographic phenotyping may be a useful tool to assess intermediate phenotypes for OSA, particularly in large-scale studies. Citation: Sutherland K, Schwab RJ, Maislin G, Lee RW, Benedikstdsottir B, Pack AI

Revision of the Malagasy Camponotus edmondi species group (Hymenoptera, Formicidae, Formicinae): integrating qualitative morphology and multivariate morphometric analysis

PubMed Central

Rakotonirina, Jean Claude; Csősz, Sándor; Fisher, Brian L.

2016-01-01

Abstract The Malagasy Camponotus edmondi species group is revised based on both qualitative morphological traits and multivariate analysis of continuous morphometric data. To minimize the effect of the scaling properties of diverse traits due to worker caste polymorphism, and to achieve the desired near-linearity of data, morphometric analyses were done only on minor workers. The majority of traits exhibit broken scaling on head size, dividing Camponotus workers into two discrete subcastes, minors and majors. This broken scaling prevents the application of algorithms that uses linear combination of data to the entire dataset, hence only minor workers were analyzed statistically. The elimination of major workers resulted in linearity and the data meet required assumptions. However, morphometric ratios for the subsets of minor and major workers were used in species descriptions and redefinitions. Prior species hypotheses and the goodness of clusters were tested on raw data by confirmatory linear discriminant analysis. Due to the small sample size available for some species, a factor known to reduce statistical reliability, hypotheses generated by exploratory analyses were tested with extreme care and species delimitations were inferred via the combined evidence of both qualitative (morphology and biology) and quantitative data. Altogether, fifteen species are recognized, of which 11 are new to science: Camponotus alamaina sp. n., Camponotus androy sp. n., Camponotus bevohitra sp. n., Camponotus galoko sp. n., Camponotus matsilo sp. n., Camponotus mifaka sp. n., Camponotus orombe sp. n., Camponotus tafo sp. n., Camponotus tratra sp. n., Camponotus varatra sp. n., and Camponotus zavo sp. n. Four species are redescribed: Camponotus echinoploides Forel, Camponotus edmondi André, Camponotus ethicus Forel, and Camponotus robustus Roger. Camponotus edmondi ernesti Forel, syn. n. is synonymized under Camponotus edmondi. This revision also includes an identification key to

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

PubMed

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

Quantification of Dynamic Morphological Drug Responses in 3D Organotypic Cell Cultures by Automated Image Analysis

PubMed Central

Härmä, Ville; Schukov, Hannu-Pekka; Happonen, Antti; Ahonen, Ilmari; Virtanen, Johannes; Siitari, Harri; Åkerfelt, Malin; Lötjönen, Jyrki; Nees, Matthias

2014-01-01

Glandular epithelial cells differentiate into complex multicellular or acinar structures, when embedded in three-dimensional (3D) extracellular matrix. The spectrum of different multicellular morphologies formed in 3D is a sensitive indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. In addition, single cells or cell aggregates may actively invade the matrix, utilizing epithelial, mesenchymal or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are sensitive to specific small-molecule inhibitors that target the actin cytoskeleton. We have used a panel of inhibitors to demonstrate the power of automated image analysis as a phenotypic or morphometric readout in cell-based assays. We introduce a streamlined stand-alone software solution that supports large-scale high-content screens, based on complex and organotypic cultures. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of large numbers of images and structures, with a multitude of different spheroid shapes, sizes, and textures. AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. We have used a representative panel of 12 prostate and breast cancer lines that display a broad spectrum of different spheroid morphologies and modes of invasion, challenged by a library of 19 direct or indirect modulators of the actin cytoskeleton which induce systematic changes in spheroid morphology and differentiation versus invasion. These results were independently validated by 2D proliferation, apoptosis and cell motility assays. We identified three drugs that primarily attenuated the invasion and formation of invasive processes in 3D, without affecting proliferation or apoptosis. Two of these compounds block Rac signalling, one affects cellular cAMP/cGMP accumulation. Our approach supports

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

NASA Astrophysics Data System (ADS)

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

2011-08-01

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

A review of state-of-the-art stereology for better quantitative 3D morphology in cardiac research.

PubMed

Mühlfeld, Christian; Nyengaard, Jens Randel; Mayhew, Terry M

2010-01-01

The aim of stereological methods in biomedical research is to obtain quantitative information about three-dimensional (3D) features of tissues, cells, or organelles from two-dimensional physical or optical sections. With immunogold labeling, stereology can even be used for the quantitative analysis of the distribution of molecules within tissues and cells. Nowadays, a large number of design-based stereological methods offer an efficient quantitative approach to intriguing questions in cardiac research, such as "Is there a significant loss of cardiomyocytes during progression from ventricular hypertrophy to heart failure?" or "Does a specific treatment reduce the degree of fibrosis in the heart?" Nevertheless, the use of stereological methods in cardiac research is rare. The present review article demonstrates how some of the potential pitfalls in quantitative microscopy may be avoided. To this end, we outline the concepts of design-based stereology and illustrate their practical applications to a wide range of biological questions in cardiac research. We hope that the present article will stimulate researchers in cardiac research to incorporate design-based stereology into their study designs, thus promoting an unbiased quantitative 3D microscopy.

Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

PubMed

Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

2015-05-22

Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection.

3D quantitative analysis of early decomposition changes of the human face.

PubMed

Caplova, Zuzana; Gibelli, Daniele Maria; Poppa, Pasquale; Cummaudo, Marco; Obertova, Zuzana; Sforza, Chiarella; Cattaneo, Cristina

2018-03-01

Decomposition of the human body and human face is influenced, among other things, by environmental conditions. The early decomposition changes that modify the appearance of the face may hamper the recognition and identification of the deceased. Quantitative assessment of those changes may provide important information for forensic identification. This report presents a pilot 3D quantitative approach of tracking early decomposition changes of a single cadaver in controlled environmental conditions by summarizing the change with weekly morphological descriptions. The root mean square (RMS) value was used to evaluate the changes of the face after death. The results showed a high correlation (r = 0.863) between the measured RMS and the time since death. RMS values of each scan are presented, as well as the average weekly RMS values. The quantification of decomposition changes could improve the accuracy of antemortem facial approximation and potentially could allow the direct comparisons of antemortem and postmortem 3D scans.

Quantitation of fixative-induced morphologic and antigenic variation in mouse and human breast cancers

PubMed Central

Cardiff, Robert D; Hubbard, Neil E; Engelberg, Jesse A; Munn, Robert J; Miller, Claramae H; Walls, Judith E; Chen, Jane Q; Velásquez-García, Héctor A; Galvez, Jose J; Bell, Katie J; Beckett, Laurel A; Li, Yue-Ju; Borowsky, Alexander D

2013-01-01

Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor models of human breast cancer. The relative preservation of structure and immunogenicity of the three mouse models and three human breast cancers was also compared when fixed with representatives of four distinct classes of fixatives. The three mouse mammary tumor cell models were an ER + /PR + model (SSM2), a Her2 + model (NDL), and a triple negative model (MET1). The four breast cancer antigens were ER, PR, Her2, and Ki67. The fixatives included examples of (1) strong cross-linkers, (2) weak cross-linkers, (3) coagulants, and (4) combination fixatives. Each parameter was quantitatively analyzed using modified Aperio Technologies ImageScope algorithms. Careful pre-analytical adjustments to the algorithms were required to provide accurate results. The QIA permitted rigorous statistical analysis of results and grading by rank order. The analyses suggested excellent technical reproducibility and confirmed biological heterogeneity within each tumor. The strong cross-linker fixatives, such as formalin, consistently ranked higher than weak cross-linker, coagulant and combination fixatives in both the morphometric and immunohistochemical parameters. PMID:23399853

Three-dimensional morphological imaging of human induced pluripotent stem cells by using low-coherence quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Kakuno, Yumi; Goto, Kentaro; Fukami, Tadashi; Sugiyama, Norikazu; Iwai, Hidenao; Mizuguchi, Yoshinori; Yamashita, Yutaka

2014-03-01

There is an increasing need for non-invasive imaging techniques in the field of stem cell research. Label-free techniques are the best choice for assessment of stem cells because the cells remain intact after imaging and can be used for further studies such as differentiation induction. To develop a high-resolution label-free imaging system, we have been working on a low-coherence quantitative phase microscope (LC-QPM). LC-QPM is a Linnik-type interference microscope equipped with nanometer-resolution optical-path-length control and capable of obtaining three-dimensional volumetric images. The lateral and vertical resolutions of our system are respectively 0.5 and 0.93 μm and this performance allows capturing sub-cellular morphological features of live cells without labeling. Utilizing LC-QPM, we reported on three-dimensional imaging of membrane fluctuations, dynamics of filopodia, and motions of intracellular organelles. In this presentation, we report three-dimensional morphological imaging of human induced pluripotent stem cells (hiPS cells). Two groups of monolayer hiPS cell cultures were prepared so that one group was cultured in a suitable culture medium that kept the cells undifferentiated, and the other group was cultured in a medium supplemented with retinoic acid, which forces the stem cells to differentiate. The volumetric images of the 2 groups show distinctive differences, especially in surface roughness. We believe that our LC-QPM system will prove useful in assessing many other stem cell conditions.

Scaling laws for coastal overwash morphology

NASA Astrophysics Data System (ADS)

Lazarus, Eli D.

2016-12-01

Overwash is a physical process of coastal sediment transport driven by storm events and is essential to landscape resilience in low-lying barrier environments. This work establishes a comprehensive set of scaling laws for overwash morphology: unifying quantitative descriptions with which to compare overwash features by their morphological attributes across case examples. Such scaling laws also help relate overwash features to other morphodynamic phenomena. Here morphometric data from a physical experiment are compared with data from natural examples of overwash features. The resulting scaling relationships indicate scale invariance spanning several orders of magnitude. Furthermore, these new relationships for overwash morphology align with classic scaling laws for fluvial drainages and alluvial fans.

The relationship of quantitative nuclear morphology to molecular genetic alterations in the adenoma-carcinoma sequence of the large bowel.

PubMed Central

Mulder, J. W.; Offerhaus, G. J.; de Feyter, E. P.; Floyd, J. J.; Kern, S. E.; Vogelstein, B.; Hamilton, S. R.

1992-01-01

The relationship of abnormal nuclear morphology to molecular genetic alterations that are important in colorectal tumorigenesis is unknown. Therefore, Feulgen-stained isolated nuclei from 22 adenomas and 42 carcinomas that had been analyzed for ras gene mutations and allelic deletions on chromosomes 5q, 18q, and 17p were characterized by computerized image analysis. Both nuclear area and the nuclear shape factor representing irregularity correlated with adenoma-carcinoma progression (r = 0.57 and r = 0.52, P < 0.0001), whereas standard nuclear texture, a parameter of chromatin homogeneity, was inversely correlated with progression (r = -0.80, P < 0.0001). The nuclear parameters were strongly interrelated (P < 0.0005). In multivariate analysis, the nuclear parameters were predominantly associated with adenoma-carcinoma progression (P < or = 0.0001) and were not influenced significantly by the individual molecular genetic alterations. Nuclear texture, however, was inversely correlated with fractional allelic loss, a global measure of genetic changes, in carcinomas (r = -0.39, P = 0.011). The findings indicate that nuclear morphology in colorectal neoplasms is strongly related to tumor progression. Nuclear morphology and biologic behavior appear to be influenced by accumulated alterations in cancer-associated genes. Images Figure 1 PMID:1357973

Anniversary Paper: History and status of CAD and quantitative image analysis: The role of Medical Physics and AAPM

PubMed Central

Giger, Maryellen L.; Chan, Heang-Ping; Boone, John

2008-01-01

algorithms using appropriate cases to measure performance and robustness; conducting observer studies with which to evaluate radiologists in the diagnostic task without and with the use of the computer aid; and ultimately assessing performance with a clinical trial. Medical physicists also have an important role in quantitative imaging, by validating the quantitative integrity of scanners and developing imaging techniques, and image analysis tools that extract quantitative data in a more accurate and automated fashion. As imaging systems become more complex and the need for better quantitative information from images grows, the future includes the combined research efforts from physicists working in CAD with those working on quantitative imaging systems to readily yield information on morphology, function, molecular structure, and more—from animal imaging research to clinical patient care. A historical review of CAD and a discussion of challenges for the future are presented here, along with the extension to quantitative image analysis. PMID:19175137

Anniversary Paper: History and status of CAD and quantitative image analysis: The role of Medical Physics and AAPM

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

Giger, Maryellen L.; Chan, Heang-Ping; Boone, John

2008-12-15

algorithms using appropriate cases to measure performance and robustness; conducting observer studies with which to evaluate radiologists in the diagnostic task without and with the use of the computer aid; and ultimately assessing performance with a clinical trial. Medical physicists also have an important role in quantitative imaging, by validating the quantitative integrity of scanners and developing imaging techniques, and image analysis tools that extract quantitative data in a more accurate and automated fashion. As imaging systems become more complex and the need for better quantitative information from images grows, the future includes the combined research efforts from physicists working in CAD with those working on quantitative imaging systems to readily yield information on morphology, function, molecular structure, and more--from animal imaging research to clinical patient care. A historical review of CAD and a discussion of challenges for the future are presented here, along with the extension to quantitative image analysis.« less

Quantitative subsurface analysis using frequency modulated thermal wave imaging

NASA Astrophysics Data System (ADS)

Subhani, S. K.; Suresh, B.; Ghali, V. S.

2018-01-01

Quantitative depth analysis of the anomaly with an enhanced depth resolution is a challenging task towards the estimation of depth of the subsurface anomaly using thermography. Frequency modulated thermal wave imaging introduced earlier provides a complete depth scanning of the object by stimulating it with a suitable band of frequencies and further analyzing the subsequent thermal response using a suitable post processing approach to resolve subsurface details. But conventional Fourier transform based methods used for post processing unscramble the frequencies with a limited frequency resolution and contribute for a finite depth resolution. Spectral zooming provided by chirp z transform facilitates enhanced frequency resolution which can further improves the depth resolution to axially explore finest subsurface features. Quantitative depth analysis with this augmented depth resolution is proposed to provide a closest estimate to the actual depth of subsurface anomaly. This manuscript experimentally validates this enhanced depth resolution using non stationary thermal wave imaging and offers an ever first and unique solution for quantitative depth estimation in frequency modulated thermal wave imaging.

Automated classification of cell morphology by coherence-controlled holographic microscopy

NASA Astrophysics Data System (ADS)

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity.

Quantitative analysis of pork and chicken products by droplet digital PCR.

PubMed

Cai, Yicun; Li, Xiang; Lv, Rong; Yang, Jielin; Li, Jian; He, Yuping; Pan, Liangwen

2014-01-01

In this project, a highly precise quantitative method based on the digital polymerase chain reaction (dPCR) technique was developed to determine the weight of pork and chicken in meat products. Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of species-specific DNAs in meat products. However, it is limited in amplification efficiency and relies on standard curves based Ct values, detecting and quantifying low copy number target DNA, as in some complex mixture meat products. By using the dPCR method, we find the relationships between the raw meat weight and DNA weight and between the DNA weight and DNA copy number were both close to linear. This enabled us to establish formulae to calculate the raw meat weight based on the DNA copy number. The accuracy and applicability of this method were tested and verified using samples of pork and chicken powder mixed in known proportions. Quantitative analysis indicated that dPCR is highly precise in quantifying pork and chicken in meat products and therefore has the potential to be used in routine analysis by government regulators and quality control departments of commercial food and feed enterprises.

Computerized image analysis for quantitative neuronal phenotyping in zebrafish.

PubMed

Liu, Tianming; Lu, Jianfeng; Wang, Ye; Campbell, William A; Huang, Ling; Zhu, Jinmin; Xia, Weiming; Wong, Stephen T C

2006-06-15

An integrated microscope image analysis pipeline is developed for automatic analysis and quantification of phenotypes in zebrafish with altered expression of Alzheimer's disease (AD)-linked genes. We hypothesize that a slight impairment of neuronal integrity in a large number of zebrafish carrying the mutant genotype can be detected through the computerized image analysis method. Key functionalities of our zebrafish image processing pipeline include quantification of neuron loss in zebrafish embryos due to knockdown of AD-linked genes, automatic detection of defective somites, and quantitative measurement of gene expression levels in zebrafish with altered expression of AD-linked genes or treatment with a chemical compound. These quantitative measurements enable the archival of analyzed results and relevant meta-data. The structured database is organized for statistical analysis and data modeling to better understand neuronal integrity and phenotypic changes of zebrafish under different perturbations. Our results show that the computerized analysis is comparable to manual counting with equivalent accuracy and improved efficacy and consistency. Development of such an automated data analysis pipeline represents a significant step forward to achieve accurate and reproducible quantification of neuronal phenotypes in large scale or high-throughput zebrafish imaging studies.

Physical reconstruction of packed beds and their morphological analysis: core-shell packings as an example.

PubMed

Bruns, Stefan; Tallarek, Ulrich

2011-04-08

We report a fast, nondestructive, and quantitative approach to characterize the morphology of packed beds of fine particles by their three-dimensional reconstruction from confocal laser scanning microscopy images, exemplarily shown for a 100μm i.d. fused-silica capillary packed with 2.6μm-sized core-shell particles. The presented method is generally applicable to silica-based capillary columns, monolithic or particulate, and comprises column pretreatment, image acquisition, image processing, and statistical analysis of the image data. It defines a unique platform for fundamental comparisons of particulate and monolithic supports using the statistical measures derived from their reconstructions. Received morphological data are column cross-sectional porosity profiles and chord length distributions from the interparticle macropore space, which are a descriptor of local density and can be characterized by a simplified k-gamma distribution. This distribution function provides a parameter of location and a parameter of dispersion which can be correlated to individual chromatographic band broadening processes (i.e., to transchannel and short-range interchannel contributions to eddy dispersion, respectively). Together with the transcolumn porosity profile the presented approach allows to analyze and quantify the packing microstructure from pore to column scale and therefore holds great promise in a comparative study of packing conditions and particle properties, particularly for characterizing and minimizing the packing process-specific heterogeneities in the final bed structure. Copyright © 2011 Elsevier B.V. All rights reserved.

Magnetic fingerprints of rolling cells for quantitative flow cytometry in whole blood

NASA Astrophysics Data System (ADS)

Reisbeck, Mathias; Helou, Michael Johannes; Richter, Lukas; Kappes, Barbara; Friedrich, Oliver; Hayden, Oliver

2016-09-01

Over the past 50 years, flow cytometry has had a profound impact on preclinical and clinical applications requiring single cell function information for counting, sub-typing and quantification of epitope expression. At the same time, the workflow complexity and high costs of such optical systems still limit flow cytometry applications to specialized laboratories. Here, we present a quantitative magnetic flow cytometer that incorporates in situ magnetophoretic cell focusing for highly accurate and reproducible rolling of the cellular targets over giant magnetoresistance sensing elements. Time-of-flight analysis is used to unveil quantitative single cell information contained in its magnetic fingerprint. Furthermore, we used erythrocytes as a biological model to validate our methodology with respect to precise analysis of the hydrodynamic cell diameter, quantification of binding capacity of immunomagnetic labels, and discrimination of cell morphology. The extracted time-of-flight information should enable point-of-care quantitative flow cytometry in whole blood for clinical applications, such as immunology and primary hemostasis.

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

PubMed

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

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. Copyright © 2011 Elsevier Inc. All rights reserved.

Morphological Analysis of Human Induced Pluripotent Stem Cells During Induced Differentiation and Reverse Programming

PubMed Central

Magniez, Aurélie; Oudrhiri, Noufissa; Féraud, Olivier; Bacci, Josette; Gobbo, Emilie; Proust, Stéphanie; Turhan, Ali G.

2014-01-01

Abstract The fine analysis of cell components during the generation of pluripotent cells and their comparison to bone fide human embryonic stem cells (hESCs) are valuable tools to understand their biological behavior. In this report, human mesenchymal cells (hMSCs) generated from the human ES cell line H9, were reprogrammed back to induced pluripotent state using Oct-4, Sox2, Nanog, and Lin28 transgenes. Human induced pluripotent stem cells (hIPSCs) were analyzed using electron microscopy and compared with regard to the original hESCs and the hMSCs from which they were derived. This analysis shows that hIPSCs and the original hESCs are morphologically undistinguishable but differ from the hMSCs with respect to the presence of several morphological features of undifferentiated cells at both the cytoplasmic (ribosomes, lipid droplets, glycogen, scarce reticulum) and nuclear levels (features of nuclear plasticity, presence of euchromatin, reticulated nucleoli). We show that hIPSC colonies generated this way presented epithelial aspects with specialized junctions highlighting morphological criteria of the mesenchymal–epithelial transition in cells engaged in a successful reprogramming process. Electron microscopic analysis revealed also specific morphological aspects of partially reprogrammed cells. These results highlight the valuable use of electron microscopy for a better knowledge of the morphological aspects of IPSC and cellular reprogramming. PMID:25371857

Correlation of quantitative histopathological morphology and quantitative radiological analysis during aseptic loosening of hip endoprostheses.

PubMed

Bertz, S; Kriegsmann, J; Eckardt, A; Delank, K-S; Drees, P; Hansen, T; Otto, M

2006-01-01

Aseptic hip prosthesis loosening is the most important long-term complication in total hip arthroplasty. Polyethylene (PE) wear is the dominant etiologic factor in aseptic loosening, which together with other factors induces mechanisms resulting in bone loss, and finally in implant loosening. The single-shot radiograph analysis (EBRA, abbreviation for the German term "Einzel-Bild-Röntgenanalyse") is a computerized method for early radiological prediction of aseptic loosening. In this study, EBRA parameters were correlated with histomorphological parameters of the periprosthetic membrane. Periprosthetic membranes obtained from 19 patients during revision surgery of loosened ABG I-type total hip pros-theses were analyzed histologically and morphometrically. The pre-existing EBRA parameters, the thickness of the PE debris lay-er and the dimension of inclination and anteversion, were compared with the density of macrophages and giant cells. Addi-tionally, the semiquantitatively determined density of lymphocytes, plasma cells, giant cells and the size of the necrotic areas were correlated with the EBRA results. All periprosthetic membranes were classified as debris-induced type membranes. We found a positive correlation between the number of giant cells and the thickness of the PE debris layer. There was no significant correlation between the number of macrophages or all semiquantitative parameters and EBRA parameters. The number of giant cells decreased with implant duration. The morphometrically measured number of foreign body giant cells more closely reflects the results of the EBRA. The semiquantitative estimation of giant cell density could not substitute for the morphometrical analysis. The density of macrophages, lymphocytes, plasma cells and the size of necrotic areas did not correlate with the EBRA parameters, indicating that there is no correlation with aseptic loosening.

Stable Isotope Quantitative N-Glycan Analysis by Liquid Separation Techniques and Mass Spectrometry.

PubMed

Mittermayr, Stefan; Albrecht, Simone; Váradi, Csaba; Millán-Martín, Silvia; Bones, Jonathan

2017-01-01

Liquid phase separation analysis and subsequent quantitation remains a challenging task for protein-derived oligosaccharides due to their inherent structural complexity and diversity. Incomplete resolution or co-detection of multiple glycan species complicates peak area-based quantitation and associated statistical analysis when optical detection methods are used. The approach outlined herein describes the utilization of stable isotope variants of commonly used fluorescent tags that allow for mass-based glycan identification and relative quantitation following separation by liquid chromatography (LC) or capillary electrophoresis (CE). Comparability assessment of glycoprotein-derived oligosaccharides is performed by derivatization with commercially available isotope variants of 2-aminobenzoic acid or aniline and analysis by LC- and CE-mass spectrometry. Quantitative information is attained from the extracted ion chromatogram/electropherogram ratios generated from the light and heavy isotope clusters.

[Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

PubMed

Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

2013-11-01

In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

Quantitatively in Situ Imaging Silver Nanowire Hollowing Kinetics

DOE PAGES

Yu, Le; Yan, Zhongying; Cai, Zhonghou; ...

2016-09-28

We report the in-situ investigation of the morphological evolution of silver nanowires to hollow silver oxide nanotubes using transmission x-ray microscopy (TXM). Complex silver diffusion kinetics and hollowing process via the Kirkendall effect have been captured in real time. Further quantitative x-ray absorption analysis reveals the difference between the longitudinal and radial diffusions. In conclusion, the diffusion coefficient of silver in its oxide nanoshell is, for the first time, calculated to be 1.2 × 10 -13 cm 2/s from the geometrical parameters extracted from the TXM images.

Gold-standard for computer-assisted morphological sperm analysis.

PubMed

Chang, Violeta; Garcia, Alejandra; Hitschfeld, Nancy; Härtel, Steffen

2017-04-01

Published algorithms for classification of human sperm heads are based on relatively small image databases that are not open to the public, and thus no direct comparison is available for competing methods. We describe a gold-standard for morphological sperm analysis (SCIAN-MorphoSpermGS), a dataset of sperm head images with expert-classification labels in one of the following classes: normal, tapered, pyriform, small or amorphous. This gold-standard is for evaluating and comparing known techniques and future improvements to present approaches for classification of human sperm heads for semen analysis. Although this paper does not provide a computational tool for morphological sperm analysis, we present a set of experiments for comparing sperm head description and classification common techniques. This classification base-line is aimed to be used as a reference for future improvements to present approaches for human sperm head classification. The gold-standard provides a label for each sperm head, which is achieved by majority voting among experts. The classification base-line compares four supervised learning methods (1- Nearest Neighbor, naive Bayes, decision trees and Support Vector Machine (SVM)) and three shape-based descriptors (Hu moments, Zernike moments and Fourier descriptors), reporting the accuracy and the true positive rate for each experiment. We used Fleiss' Kappa Coefficient to evaluate the inter-expert agreement and Fisher's exact test for inter-expert variability and statistical significant differences between descriptors and learning techniques. Our results confirm the high degree of inter-expert variability in the morphological sperm analysis. Regarding the classification base line, we show that none of the standard descriptors or classification approaches is best suitable for tackling the problem of sperm head classification. We discovered that the correct classification rate was highly variable when trying to discriminate among non-normal sperm

Chevron-type medial malleolar osteotomy: a functional, radiographic and quantitative T2-mapping MRI analysis.

PubMed

Lamb, Joshua; Murawski, Christopher D; Deyer, Timothy W; Kennedy, John G

2013-06-01

The purpose of this study was to retrospectively evaluate a large series of patients for functional, radiographic and MRI outcomes after a Chevron-type medial malleolar osteotomy. Sixty-two patients underwent a Chevron-type medial malleolar osteotomy with a median follow-up of 34.5 months. Standard digital radiographs were used to determine bony union and the angle of the osteotomy relative to the longitudinal axis of the tibia. Morphologic and quantitative T2-mapping MRI was also analysed in 32 patients. Fifty-eight patients (94 %) reported being asymptomatic at the site of the medial malleolar osteotomy. The median time to healing on standard radiograph was 6 weeks (range, 4-6 weeks) with an angle of 31.7° ± 6.9°. Quantitative T2-mapping MRI analysis demonstrated that the deep half of interface repair tissue had relaxation times that were not significantly different from normal tibial cartilage. In contrast, interface repair tissue in the superficial half demonstrated significant prolongation from normal relaxation time values, indicating a more fibrocartilaginous repair. Four patients (6 %) reported pain post-operatively. A Chevron-type medial malleolar osteotomy demonstrates satisfactory healing and fixation, with fibrocartilaginous tissue evident superficially at the osteotomy interface. Further investigation is warranted in the form of longitudinal study to assess the long-term outcomes of medial malleolar osteotomy.

Improved method and apparatus for chromatographic quantitative analysis

DOEpatents

Fritz, J.S.; Gjerde, D.T.; Schmuckler, G.

An improved apparatus and method are described for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single element and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

Development of a quantitative morphological assessment of toxicant-treated zebrafish larvae using brightfield imaging and high-content analysis.

PubMed

Deal, Samantha; Wambaugh, John; Judson, Richard; Mosher, Shad; Radio, Nick; Houck, Keith; Padilla, Stephanie

2016-09-01

One of the rate-limiting procedures in a developmental zebrafish screen is the morphological assessment of each larva. Most researchers opt for a time-consuming, structured visual assessment by trained human observer(s). The present studies were designed to develop a more objective, accurate and rapid method for screening zebrafish for dysmorphology. Instead of the very detailed human assessment, we have developed the computational malformation index, which combines the use of high-content imaging with a very brief human visual assessment. Each larva was quickly assessed by a human observer (basic visual assessment), killed, fixed and assessed for dysmorphology with the Zebratox V4 BioApplication using the Cellomics® ArrayScan® V(TI) high-content image analysis platform. The basic visual assessment adds in-life parameters, and the high-content analysis assesses each individual larva for various features (total area, width, spine length, head-tail length, length-width ratio, perimeter-area ratio). In developing the computational malformation index, a training set of hundreds of embryos treated with hundreds of chemicals were visually assessed using the basic or detailed method. In the second phase, we assessed both the stability of these high-content measurements and its performance using a test set of zebrafish treated with a dose range of two reference chemicals (trans-retinoic acid or cadmium). We found the measures were stable for at least 1 week and comparison of these automated measures to detailed visual inspection of the larvae showed excellent congruence. Our computational malformation index provides an objective manner for rapid phenotypic brightfield assessment of individual larva in a developmental zebrafish assay. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Evidence from neglect dyslexia for morphological decomposition at the early stages of orthographic-visual analysis

PubMed Central

Reznick, Julia; Friedmann, Naama

2015-01-01

This study examined whether and how the morphological structure of written words affects reading in word-based neglect dyslexia (neglexia), and what can be learned about morphological decomposition in reading from the effect of morphology on neglexia. The oral reading of 7 Hebrew-speaking participants with acquired neglexia at the word level—6 with left neglexia and 1 with right neglexia—was evaluated. The main finding was that the morphological role of the letters on the neglected side of the word affected neglect errors: When an affix appeared on the neglected side, it was neglected significantly more often than when the neglected side was part of the root; root letters on the neglected side were never omitted, whereas affixes were. Perceptual effects of length and final letter form were found for words with an affix on the neglected side, but not for words in which a root letter appeared in the neglected side. Semantic and lexical factors did not affect the participants' reading and error pattern, and neglect errors did not preserve the morpho-lexical characteristics of the target words. These findings indicate that an early morphological decomposition of words to their root and affixes occurs before access to the lexicon and to semantics, at the orthographic-visual analysis stage, and that the effects did not result from lexical feedback. The same effects of morphological structure on reading were manifested by the participants with left- and right-sided neglexia. Since neglexia is a deficit at the orthographic-visual analysis level, the effect of morphology on reading patterns in neglexia further supports that morphological decomposition occurs in the orthographic-visual analysis stage, prelexically, and that the search for the three letters of the root in Hebrew is a trigger for attention shift in neglexia. PMID:26528159

Analysis of the flow property of aluminum alloy AA6016 based on the fracture morphology using the hydroforming technology

NASA Astrophysics Data System (ADS)

Lang, Lihui; Zhang, Quanda; Sun, Zhiying; Wang, Yao

2017-09-01

In this paper, the hydraulic bulging experiments were respectively carried out using AA6016-T4 aluminum alloy and AA6016-O aluminum alloy, and the deformation properties and fracture mechanism of aluminum alloy under the conditions of thermal and hydraulic were analyzed. Firstly, the aluminum alloy AA6016 was dealt with two kinds of heat treatment systems such as solid solution heat treatment adding natural ageing and full annealing, then the aluminum alloy such as AA6016-T4 and AA6016-O were obtained. In the same working environment, the two kinds of materials were used in the process of hydraulic bulging experiments, according to the observation and measurement of the deformation sizes of grid circles and material thicknesses near the fracture region, the flow properties and development trend of fracture defect of the materials were analyzed comprehensively from the perspective of qualitative analysis and quantitative analysis; Secondly, the two kinds of materials were sampled in different regions of the fracture area and the microstructure morphology of the fracture was observed by the scanning electron microscope (SEM). The influence laws of the heat treatment systems on the fracture defect of the aluminum alloy under the condition of the liquid pressure were studied preliminarily by observing the distribution characteristics of the fracture microstructure morphology of dimple. At the same time, the experimental research on the ordinary stamping forming process of AA6016-O was carried out and the influence law of different forming process on the fracture defect of the aluminum alloy material was studied by observing the distribution of the fracture microstructure morphology; Finally, the development process of the fracture defect of aluminum alloy sheet was described theoretically from the view of the stress state.

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture.

PubMed

Mander, Luke; Li, Mao; Mio, Washington; Fowlkes, Charless C; Punyasena, Surangi W

2013-11-07

Taxonomic identification of pollen and spores uses inherently qualitative descriptions of morphology. Consequently, identifications are restricted to categories that can be reliably classified by multiple analysts, resulting in the coarse taxonomic resolution of the pollen and spore record. Grass pollen represents an archetypal example; it is not routinely identified below family level. To address this issue, we developed quantitative morphometric methods to characterize surface ornamentation and classify grass pollen grains. This produces a means of quantifying morphological features that are traditionally described qualitatively. We used scanning electron microscopy to image 240 specimens of pollen from 12 species within the grass family (Poaceae). We classified these species by developing algorithmic features that quantify the size and density of sculptural elements on the pollen surface, and measure the complexity of the ornamentation they form. These features yielded a classification accuracy of 77.5%. In comparison, a texture descriptor based on modelling the statistical distribution of brightness values in image patches yielded a classification accuracy of 85.8%, and seven human subjects achieved accuracies between 68.33 and 81.67%. The algorithmic features we developed directly relate to biologically meaningful features of grass pollen morphology, and could facilitate direct interpretation of unsupervised classification results from fossil material.

Spotsizer: High-throughput quantitative analysis of microbial growth.

PubMed

Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

2016-10-01

Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

Clavicle anatomical osteosynthesis plate breakage - failure analysis report based on patient morphological parameters.

PubMed

Marinescu, Rodica; Antoniac, Vasile Iulian; Stoia, Dan Ioan; Lăptoiu, Dan Constantin

2017-01-01

Clavicle fracture reported incidence is about 5% of fractures in adult; among them, those located in the middle third of the shaft represent more than 80% from the total of cases. Due to the special morphological and biomechanical constraints of the clavicle, several methods for restoring morphological integrity in these fractures are described, including conservative, non-surgical treatment. The last 10 years of clinical studies in the field have favored the surgical treatment for selected cases; several osteosynthesis implants are in use - mostly anatomical plates with specific advantages and documented complications. A failed anatomical clavicle plate was explanted and analyzed after a protocol using stereomicroscopy, scanning electron microscopy and energy dispersive spectrometry. Based on the computed tomography (CT) scan determination of patient morphological parameters, a finite elements analysis of the failure scenario was completed. The failure analysis has proved that the plate breakage had occurred in the point of maximal elastic stress and minor deformation. The clinical implication is that no hole should remain free of screw during clavicle plate fixation and the implant should be chosen based on patient morphological parameters. In comminuted clavicle fracture, anatomic bridging with locked plate technique may lead to implant failure due to increase of the stress in the midshaft area. Thorough knowledge of anatomy and morphology of complex bones like the clavicle is necessary. Modern osteosynthesis anatomical implants are still to be improved.

Quantitative correlation between the void morphology of niobium-tin wires and their irreversible critical current degradation upon mechanical loading

DOE PAGES

Barth, Christian; Seeber, B.; Rack, A.; ...

2018-04-26

Understanding the critical current performance variation of Nb 3Sn superconducting wires under mechanical loading is a crucial issue for the design of next generation accelerator and fusion magnets. In these applications, the mechanical properties of the conductors may become a limiting factor due to the strong electro-magnetic forces resulting from the combination of large magnets and intense magnetic fields. In particular, the presence of voids in the superconducting filament structure, which are formed during the fabrication and the reaction heat treatment, determines localized stress concentrations and possibly the formation of cracks. In this work, we demonstrate a quantitative correlation betweenmore » the void morphology and the electro-mechanical limits measured on different Bronze route Nb 3Sn wires. Hot Isostatic Pressing (HIP) prior to the reaction heat treatment is utilized to partially eliminate the voids. The wires’ void distributions - with and without HIP treatment - are detected and statistically analyzed using high energy X-ray micro tomography. The stress concentration due to the shape and distribution of the voids as well as their impact on the electro-mechanical properties are determined through finite element method modeling. Lastly, the results are quantitatively correlated with the experimentally determined limits of the irreversible critical current degradation upon mechanical loading.« less

Quantitative correlation between the void morphology of niobium-tin wires and their irreversible critical current degradation upon mechanical loading

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

Barth, Christian; Seeber, B.; Rack, A.

Understanding the critical current performance variation of Nb 3Sn superconducting wires under mechanical loading is a crucial issue for the design of next generation accelerator and fusion magnets. In these applications, the mechanical properties of the conductors may become a limiting factor due to the strong electro-magnetic forces resulting from the combination of large magnets and intense magnetic fields. In particular, the presence of voids in the superconducting filament structure, which are formed during the fabrication and the reaction heat treatment, determines localized stress concentrations and possibly the formation of cracks. In this work, we demonstrate a quantitative correlation betweenmore » the void morphology and the electro-mechanical limits measured on different Bronze route Nb 3Sn wires. Hot Isostatic Pressing (HIP) prior to the reaction heat treatment is utilized to partially eliminate the voids. The wires’ void distributions - with and without HIP treatment - are detected and statistically analyzed using high energy X-ray micro tomography. The stress concentration due to the shape and distribution of the voids as well as their impact on the electro-mechanical properties are determined through finite element method modeling. Lastly, the results are quantitatively correlated with the experimentally determined limits of the irreversible critical current degradation upon mechanical loading.« less

Quantitative correlation between the void morphology of niobium-tin wires and their irreversible critical current degradation upon mechanical loading.

PubMed

Barth, C; Seeber, B; Rack, A; Calzolaio, C; Zhai, Y; Matera, D; Senatore, C

2018-04-26

Understanding the critical current performance variation of Nb 3 Sn superconducting wires under mechanical loading is a crucial issue for the design of next generation accelerator and fusion magnets. In these applications, the mechanical properties of the conductors may become a limiting factor due to the strong electro-magnetic forces resulting from the combination of large magnets and intense magnetic fields. In particular, the presence of voids in the superconducting filament structure, which are formed during the fabrication and the reaction heat treatment, determines localized stress concentrations and possibly the formation of cracks. In this work, we demonstrate a quantitative correlation between the void morphology and the electro-mechanical limits measured on different Bronze route Nb 3 Sn wires. Hot Isostatic Pressing (HIP) prior to the reaction heat treatment is utilized to partially eliminate the voids. The wires' void distributions - with and without HIP treatment - are detected and statistically analyzed using high energy X-ray micro tomography. The stress concentration due to the shape and distribution of the voids as well as their impact on the electro-mechanical properties are determined through finite element method modeling. Finally, the results are quantitatively correlated with the experimentally determined limits of the irreversible critical current degradation upon mechanical loading.

Influence analysis in quantitative trait loci detection.

PubMed

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

2014-07-01

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

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

PubMed Central

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

2011-01-01

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

Quantitative high-resolution genomic analysis of single cancer cells.

PubMed

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

2011-01-01

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

[Pyramidal syndrome in lateral amyotrophic sclerosis: clinico-morphological analysis].

PubMed

Musaeva, L S; Zavalishin, I A; Gulevskaia, T S

2003-01-01

Retrospective clinical analysis with a special focus on pyramidal syndrome expression in the disease course as well as morphological study of brain and spinal structures in all levels of cortical-spinal projection (from brain motor cortex to spinal lumbar segments) have been conducted for 11 section cases of lateral amyotrophic sclerosis (LAS), sporadic type. Two groups of patients were studied: with pronounced pyramidal syndrome (spasticity, hyperreflexia, etc)--7 cases and with some signs of pyramidal deficiency (anisoreflexia, stability of peritoneal reflexes)--4 cases. Pyramidal syndrome in LAS is considered as an emergence of current neurodegenerative process, embracing a significant part of upper motor neurons of both precentral convolution and its axons along the whole length of cerebrospinal axis in the form of cytoplasmic inclusions and axonal spheroids. A presence of pathomorphological changes in other upper segmental structures of motor control reveals their role in pyramidal deficiency. Comparative analysis showed that expression of pyramidal syndrome signs and its correlation to atrophic paresis appearances is specifically determined by the severity of upper and lower motor neurons lesions. With regard to morphological changes in CNS structures, the peculiarities of some pyramidal syndrome appearances in LAS are analyzed.

Benefit-risk analysis : a brief review and proposed quantitative approaches.

PubMed

Holden, William L

2003-01-01

Given the current status of benefit-risk analysis as a largely qualitative method, two techniques for a quantitative synthesis of a drug's benefit and risk are proposed to allow a more objective approach. The recommended methods, relative-value adjusted number-needed-to-treat (RV-NNT) and its extension, minimum clinical efficacy (MCE) analysis, rely upon efficacy or effectiveness data, adverse event data and utility data from patients, describing their preferences for an outcome given potential risks. These methods, using hypothetical data for rheumatoid arthritis drugs, demonstrate that quantitative distinctions can be made between drugs which would better inform clinicians, drug regulators and patients about a drug's benefit-risk profile. If the number of patients needed to treat is less than the relative-value adjusted number-needed-to-harm in an RV-NNT analysis, patients are willing to undergo treatment with the experimental drug to derive a certain benefit knowing that they may be at risk for any of a series of potential adverse events. Similarly, the results of an MCE analysis allow for determining the worth of a new treatment relative to an older one, given not only the potential risks of adverse events and benefits that may be gained, but also by taking into account the risk of disease without any treatment. Quantitative methods of benefit-risk analysis have a place in the evaluative armamentarium of pharmacovigilance, especially those that incorporate patients' perspectives.

Quantitative analysis of osteoblast behavior on microgrooved hydroxyapatite and titanium substrata.

PubMed

Lu, Xiong; Leng, Yang

2003-09-01

The effects of implant surface topography and chemistry on osteoblast behavior have been a research focus because of their potential importance in orthopedic and dental applications. This work focused on the topographic effects of hydroxyapatite (HA) and titanium (Ti) surface that had identical micropatterns to determine whether there was synergistic interaction between surface chemistry and surface topography. Surface microgrooves with six different groove widths (4, 8, 16, 24, 30, and 38 microm) and three different groove depths (2, 4, and 10 microm) were made on single crystalline silicon wafers using microfabrication techniques. Ti and HA thin films were coated on the microgrooves by radio-frequency magnetron sputtering. After that, human osteoblast-like cells were seeded and cultured on the microgrooved surfaces for up to 7 days. The cells' behavior was examined using scanning electron microscopy after cells were fixed and dehydrated. Statistical analysis was based on quantitative data of orientation angle, evaluating the contact guidance, and form index, describing cell shape or cell morphology changes. The contact guidance and cell shape changes were observed on the HA and Ti microgrooves. No difference in orientation angle between HA and Ti microgrooves was found. This might suggest that surface chemistry was not a significant influence on cell guidance. However, the form index analysis indicated an interaction between topographic effects and surface chemistry. Thus, conclusions about surface topographic effects on cell behavior drawn from one type of material cannot simply be applied to another type of material. Copyright 2003 Wiley Periodicals, Inc. J Biomed Mater Res 66A: 677-687, 2003

Quantitative Ultrasound for Measuring Obstructive Severity in Children with Hydronephrosis.

PubMed

Cerrolaza, Juan J; Peters, Craig A; Martin, Aaron D; Myers, Emmarie; Safdar, Nabile; Linguraru, Marius George

2016-04-01

We define sonographic biomarkers for hydronephrotic renal units that can predict the necessity of diuretic nuclear renography. We selected a cohort of 50 consecutive patients with hydronephrosis of varying severity in whom 2-dimensional sonography and diuretic mercaptoacetyltriglycine renography had been performed. A total of 131 morphological parameters were computed using quantitative image analysis algorithms. Machine learning techniques were then applied to identify ultrasound based safety thresholds that agreed with the t½ for washout. A best fit model was then derived for each threshold level of t½ that would be clinically relevant at 20, 30 and 40 minutes. Receiver operating characteristic curve analysis was performed. Sensitivity, specificity and area under the receiver operating characteristic curve were determined. Improvement obtained by the quantitative imaging method compared to the Society for Fetal Urology grading system and the hydronephrosis index was statistically verified. For the 3 thresholds considered and at 100% sensitivity the specificities of the quantitative imaging method were 94%, 70% and 74%, respectively. Corresponding area under the receiver operating characteristic curve values were 0.98, 0.94 and 0.94, respectively. Improvement obtained by the quantitative imaging method over the Society for Fetal Urology grade and hydronephrosis index was statistically significant (p <0.05 in all cases). Quantitative imaging analysis of renal sonograms in children with hydronephrosis can identify thresholds of clinically significant washout times with 100% sensitivity to decrease the number of diuretic renograms in up to 62% of children. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Looking into the puparium: Micro‐CT visualization of the internal morphological changes during metamorphosis of the blow fly, Calliphora vicina, with the first quantitative analysis of organ development in cyclorrhaphous dipterans

PubMed Central

Simonsen, Thomas J.; Hall, Martin J. R.

2017-01-01

Abstract Metamorphosis of cyclorrhaphous flies takes place inside a barrel‐like puparium, formed by the shrinking, hardening and darkening of the third‐instar larval cuticle. The opacity of this structure hampers the visualization of the morphological changes occurring inside and therefore a full understanding of the metamorphosis process. Here, we use micro‐computed tomography (micro‐CT) to describe the internal morphological changes that occur during metamorphosis of the blow fly, Calliphora vicina Robineau‐Desvoidy 1830 (Diptera: Calliphoridae) at a greater temporal resolution than anything hitherto published. The morphological changes were documented at 10% intervals of the total intra‐puparial period, and down to 2.5% intervals during the first 20% interval, when the most dramatic morphological changes occur. Moreover, the development of an internal gas bubble, which plays an essential role during early metamorphosis, was further investigated with X‐ray images and micro‐CT virtual sections. The origin of this gas bubble has been largely unknown, but micro‐CT virtual sections show that it is connected to one of the main tracheal trunks. Micro‐CT virtual sections also provided enough resolution for determining the completion of the larval‐pupal and pupal‐adult apolyses, thus enabling an accurate timing of the different intra‐puparial life stages. The prepupal, pupal, and pharate adult stages last for 7.5%, 22.5%, and 70% of the total intra‐puparial development, respectively. Furthermore, we provide for the first time quantitative data on the development of two organ systems of the blow fly: the alimentary canal and the indirect flight muscles. There is a significant and negative correlation between the volume of the indirect flight muscles and the pre‐helicoidal region of the midgut during metamorphosis. The latter occupies a large portion of the thorax during the pupal stage but narrows progressively as the indirect flight muscles

Quantitative risk analysis of oil storage facilities in seismic areas.

PubMed

Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto

2005-08-31

Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID

Mapping Candidate Ecological Restoration Areas Using Morphological Spatial Pattern Analysis (MSPA)

EPA Science Inventory

Morphological Spatial Pattern Analysis (MSPA) has been widely adopted by landscape ecologists over the past decade. A few examples of its many uses include: 1) quantifying landscape indicators and fragmentation in continental forest assessments, 2) explaining interior-exterior p...

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

PubMed

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

2016-12-21

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Ecomorphology of morpho-functional relationships in the family of Sparidae: a quantitative statistic approach.

PubMed

Antonucci, Francesca; Costa, Corrado; Aguzzi, Jacopo; Cataudella, Stefano

2009-07-01

In many fish species, morphological similarity can be considered as a proxy for similarities in habitat use. The Sparidae family includes species that are recognized for common morphological features such as structure and positioning of the fins and specialized dentition. The aim of this study was to quantitatively describe the relationship of body shape morphology with habitat use, trophic level, and systematics in the majority of known Sparidae species (N = 92). This ecomorphological comparison was performed with a geometric morphometric approach considering as variables the Trophic Index (TROPH), the habitat (i.e., classified as demersal, benthopelagic and reef associated) and the phylogenetic relationship of species at the subfamily level. The analysis by the TROPH variable showed a positive relation with shape because the morphological features of all the species are strongly correlated with their trophic behavior (e.g., herbivore species have a smaller mouth gap that make them able to feed upon sessile resources). The morphological analysis according to the Habitat variable was used to classify species according to a feeding-habitat niche in terms of portion of the water column and seabed space where species mostly perform their behavioral activities. We described three kinds of morphological designs in relation to a benthopelagic, demersal and reef-associated habit. The six subfamily groups were morphologically well distinguishable and the cladogram relative to Mahalanobis' morphological distances was compared with those proposed by other authors. We also quantified the phylogenetic relationship among the different subfamilies based on the analysis of shape in relation to trophic ecology, confirming the observations of the authors. (c) 2009 Wiley-Liss, Inc.

Comparative study of standard space and real space analysis of quantitative MR brain data.

PubMed

Aribisala, Benjamin S; He, Jiabao; Blamire, Andrew M

2011-06-01

To compare the robustness of region of interest (ROI) analysis of magnetic resonance imaging (MRI) brain data in real space with analysis in standard space and to test the hypothesis that standard space image analysis introduces more partial volume effect errors compared to analysis of the same dataset in real space. Twenty healthy adults with no history or evidence of neurological diseases were recruited; high-resolution T(1)-weighted, quantitative T(1), and B(0) field-map measurements were collected. Algorithms were implemented to perform analysis in real and standard space and used to apply a simple standard ROI template to quantitative T(1) datasets. Regional relaxation values and histograms for both gray and white matter tissues classes were then extracted and compared. Regional mean T(1) values for both gray and white matter were significantly lower using real space compared to standard space analysis. Additionally, regional T(1) histograms were more compact in real space, with smaller right-sided tails indicating lower partial volume errors compared to standard space analysis. Standard space analysis of quantitative MRI brain data introduces more partial volume effect errors biasing the analysis of quantitative data compared to analysis of the same dataset in real space. Copyright © 2011 Wiley-Liss, Inc.

Statistical shape analysis using 3D Poisson equation--A quantitatively validated approach.

PubMed

Gao, Yi; Bouix, Sylvain

2016-05-01

Statistical shape analysis has been an important area of research with applications in biology, anatomy, neuroscience, agriculture, paleontology, etc. Unfortunately, the proposed methods are rarely quantitatively evaluated, and as shown in recent studies, when they are evaluated, significant discrepancies exist in their outputs. In this work, we concentrate on the problem of finding the consistent location of deformation between two population of shapes. We propose a new shape analysis algorithm along with a framework to perform a quantitative evaluation of its performance. Specifically, the algorithm constructs a Signed Poisson Map (SPoM) by solving two Poisson equations on the volumetric shapes of arbitrary topology, and statistical analysis is then carried out on the SPoMs. The method is quantitatively evaluated on synthetic shapes and applied on real shape data sets in brain structures. Copyright © 2016 Elsevier B.V. All rights reserved.

Mathematical morphology for automated analysis of remotely sensed objects in radar images

NASA Technical Reports Server (NTRS)

Daida, Jason M.; Vesecky, John F.

1991-01-01

A symbiosis of pyramidal segmentation and morphological transmission is described. The pyramidal segmentation portion of the symbiosis has resulted in low (2.6 percent) misclassification error rate for a one-look simulation. Other simulations indicate lower error rates (1.8 percent for a four-look image). The morphological transformation portion has resulted in meaningful partitions with a minimal loss of fractal boundary information. An unpublished version of Thicken, suitable for watersheds transformations of fractal objects, is also presented. It is demonstrated that the proposed symbiosis works with SAR (synthetic aperture radar) images: in this case, a four-look Seasat image of sea ice. It is concluded that the symbiotic forms of both segmentation and morphological transformation seem well suited for unsupervised geophysical analysis.

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

PubMed Central

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

2013-01-01

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

Role Of Social Networks In Resilience Of Naval Recruits: A Quantitative Analysis

DTIC Science & Technology

2016-06-01

comprises 1,297 total surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network... surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network data examine the effects...NETWORKS IN RESILIENCE OF NAVAL RECRUITS: A QUANTITATIVE ANALYSIS by Andrea M. Watling June 2016 Thesis Advisor: Edward H. Powley Co

Predicting Raters’ Transparency Judgments of English and Chinese Morphological Constituents using Latent Semantic Analysis

PubMed Central

Wang, Hsueh-Cheng; Hsu, Li-Chuan; Tien, Yi-Min; Pomplun, Marc

2013-01-01

The morphological constituents of English compounds (e.g., “butter” and “fly” for “butterfly”) and two-character Chinese compounds may differ in meaning from the whole word. Subjective differences and ambiguity of transparency make the judgments difficult, and a computational alternative based on a general model may be a way to average across subjective differences. The current study proposes two approaches based on Latent Semantic Analysis (Landauer & Dumais, 1997): Model 1 compares the semantic similarity between a compound word and each of its constituents, and Model 2 derives the dominant meaning of a constituent based on a clustering analysis of morphological family members (e.g., “butterfingers” or “buttermilk” for “butter”). The proposed models successfully predicted participants’ transparency ratings, and we recommend that experimenters use Model 1 for English compounds and Model 2 for Chinese compounds, due to raters’ morphological processing in different writing systems. The dominance of lexical meaning, semantic transparency, and the average similarity between all pairs within a morphological family are provided, and practical applications for future studies are discussed. PMID:23784009

Improvements to direct quantitative analysis of multiple microRNAs facilitating faster analysis.

PubMed

Ghasemi, Farhad; Wegman, David W; Kanoatov, Mirzo; Yang, Burton B; Liu, Stanley K; Yousef, George M; Krylov, Sergey N

2013-11-05

Studies suggest that patterns of deregulation in sets of microRNA (miRNA) can be used as cancer diagnostic and prognostic biomarkers. Establishing a "miRNA fingerprint"-based diagnostic technique requires a suitable miRNA quantitation method. The appropriate method must be direct, sensitive, capable of simultaneous analysis of multiple miRNAs, rapid, and robust. Direct quantitative analysis of multiple microRNAs (DQAMmiR) is a recently introduced capillary electrophoresis-based hybridization assay that satisfies most of these criteria. Previous implementations of the method suffered, however, from slow analysis time and required lengthy and stringent purification of hybridization probes. Here, we introduce a set of critical improvements to DQAMmiR that address these technical limitations. First, we have devised an efficient purification procedure that achieves the required purity of the hybridization probe in a fast and simple fashion. Second, we have optimized the concentrations of the DNA probe to decrease the hybridization time to 10 min. Lastly, we have demonstrated that the increased probe concentrations and decreased incubation time removed the need for masking DNA, further simplifying the method and increasing its robustness. The presented improvements bring DQAMmiR closer to use in a clinical setting.

Automated classification of cell morphology by coherence-controlled holographic microscopy.

PubMed

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

PubMed

Ishikawa, Akira

2017-11-27

Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

Quantitative analysis of diffusion tensor orientation: theoretical framework.

PubMed

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

2004-11-01

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

Galaxy Zoo: quantitative visual morphological classifications for 48 000 galaxies from CANDELS

NASA Astrophysics Data System (ADS)

Simmons, B. D.; Lintott, Chris; Willett, Kyle W.; Masters, Karen L.; Kartaltepe, Jeyhan S.; Häußler, Boris; Kaviraj, Sugata; Krawczyk, Coleman; Kruk, S. J.; McIntosh, Daniel H.; Smethurst, R. J.; Nichol, Robert C.; Scarlata, Claudia; Schawinski, Kevin; Conselice, Christopher J.; Almaini, Omar; Ferguson, Henry C.; Fortson, Lucy; Hartley, William; Kocevski, Dale; Koekemoer, Anton M.; Mortlock, Alice; Newman, Jeffrey A.; Bamford, Steven P.; Grogin, N. A.; Lucas, Ray A.; Hathi, Nimish P.; McGrath, Elizabeth; Peth, Michael; Pforr, Janine; Rizer, Zachary; Wuyts, Stijn; Barro, Guillermo; Bell, Eric F.; Castellano, Marco; Dahlen, Tomas; Dekel, Avishai; Ownsworth, Jamie; Faber, Sandra M.; Finkelstein, Steven L.; Fontana, Adriano; Galametz, Audrey; Grützbauch, Ruth; Koo, David; Lotz, Jennifer; Mobasher, Bahram; Mozena, Mark; Salvato, Mara; Wiklind, Tommy

2017-02-01

We present quantified visual morphologies of approximately 48 000 galaxies observed in three Hubble Space Telescope legacy fields by the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) and classified by participants in the Galaxy Zoo project. 90 per cent of galaxies have z ≤ 3 and are observed in rest-frame optical wavelengths by CANDELS. Each galaxy received an average of 40 independent classifications, which we combine into detailed morphological information on galaxy features such as clumpiness, bar instabilities, spiral structure, and merger and tidal signatures. We apply a consensus-based classifier weighting method that preserves classifier independence while effectively down-weighting significantly outlying classifications. After analysing the effect of varying image depth on reported classifications, we also provide depth-corrected classifications which both preserve the information in the deepest observations and also enable the use of classifications at comparable depths across the full survey. Comparing the Galaxy Zoo classifications to previous classifications of the same galaxies shows very good agreement; for some applications, the high number of independent classifications provided by Galaxy Zoo provides an advantage in selecting galaxies with a particular morphological profile, while in others the combination of Galaxy Zoo with other classifications is a more promising approach than using any one method alone. We combine the Galaxy Zoo classifications of `smooth' galaxies with parametric morphologies to select a sample of featureless discs at 1 ≤ z ≤ 3, which may represent a dynamically warmer progenitor population to the settled disc galaxies seen at later epochs.

Microglia Morphological Categorization in a Rat Model of Neuroinflammation by Hierarchical Cluster and Principal Components Analysis

PubMed Central

Fernández-Arjona, María del Mar; Grondona, Jesús M.; Granados-Durán, Pablo; Fernández-Llebrez, Pedro; López-Ávalos, María D.

2017-01-01

It is known that microglia morphology and function are closely related, but only few studies have objectively described different morphological subtypes. To address this issue, morphological parameters of microglial cells were analyzed in a rat model of aseptic neuroinflammation. After the injection of a single dose of the enzyme neuraminidase (NA) within the lateral ventricle (LV) an acute inflammatory process occurs. Sections from NA-injected animals and sham controls were immunolabeled with the microglial marker IBA1, which highlights ramifications and features of the cell shape. Using images obtained by section scanning, individual microglial cells were sampled from various regions (septofimbrial nucleus, hippocampus and hypothalamus) at different times post-injection (2, 4 and 12 h). Each cell yielded a set of 15 morphological parameters by means of image analysis software. Five initial parameters (including fractal measures) were statistically different in cells from NA-injected rats (most of them IL-1β positive, i.e., M1-state) compared to those from control animals (none of them IL-1β positive, i.e., surveillant state). However, additional multimodal parameters were revealed more suitable for hierarchical cluster analysis (HCA). This method pointed out the classification of microglia population in four clusters. Furthermore, a linear discriminant analysis (LDA) suggested three specific parameters to objectively classify any microglia by a decision tree. In addition, a principal components analysis (PCA) revealed two extra valuable variables that allowed to further classifying microglia in a total of eight sub-clusters or types. The spatio-temporal distribution of these different morphotypes in our rat inflammation model allowed to relate specific morphotypes with microglial activation status and brain location. An objective method for microglia classification based on morphological parameters is proposed. Main points Microglia undergo a quantifiable

Microglia Morphological Categorization in a Rat Model of Neuroinflammation by Hierarchical Cluster and Principal Components Analysis.

PubMed

Fernández-Arjona, María Del Mar; Grondona, Jesús M; Granados-Durán, Pablo; Fernández-Llebrez, Pedro; López-Ávalos, María D

2017-01-01

It is known that microglia morphology and function are closely related, but only few studies have objectively described different morphological subtypes. To address this issue, morphological parameters of microglial cells were analyzed in a rat model of aseptic neuroinflammation. After the injection of a single dose of the enzyme neuraminidase (NA) within the lateral ventricle (LV) an acute inflammatory process occurs. Sections from NA-injected animals and sham controls were immunolabeled with the microglial marker IBA1, which highlights ramifications and features of the cell shape. Using images obtained by section scanning, individual microglial cells were sampled from various regions (septofimbrial nucleus, hippocampus and hypothalamus) at different times post-injection (2, 4 and 12 h). Each cell yielded a set of 15 morphological parameters by means of image analysis software. Five initial parameters (including fractal measures) were statistically different in cells from NA-injected rats (most of them IL-1β positive, i.e., M1-state) compared to those from control animals (none of them IL-1β positive, i.e., surveillant state). However, additional multimodal parameters were revealed more suitable for hierarchical cluster analysis (HCA). This method pointed out the classification of microglia population in four clusters. Furthermore, a linear discriminant analysis (LDA) suggested three specific parameters to objectively classify any microglia by a decision tree. In addition, a principal components analysis (PCA) revealed two extra valuable variables that allowed to further classifying microglia in a total of eight sub-clusters or types. The spatio-temporal distribution of these different morphotypes in our rat inflammation model allowed to relate specific morphotypes with microglial activation status and brain location. An objective method for microglia classification based on morphological parameters is proposed. Main points Microglia undergo a quantifiable

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

PubMed

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

2013-01-21

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

A Quantitative Diffuse Reflectance Imaging (QDRI) System for Comprehensive Surveillance of the Morphological Landscape in Breast Tumor Margins.

PubMed

Nichols, Brandon S; Schindler, Christine E; Brown, Jonathon Q; Wilke, Lee G; Mulvey, Christine S; Krieger, Marlee S; Gallagher, Jennifer; Geradts, Joseph; Greenup, Rachel A; Von Windheim, Jesko A; Ramanujam, Nirmala

2015-01-01

function (eCDF) analysis is used to reduce optical property maps to quantitative distributions representing the morphological landscape of breast tumor margins. The optimizations presented in this work provide an avenue to rapidly survey large tissue areas on intra-operative time scales with improved sensitivity to regions of focal disease that may otherwise be overlooked.

Procedure for quantitative determination of effectiveness of photoinduced destruction of malignant tumors

NASA Astrophysics Data System (ADS)

Bizyuk, S. A.; Istomin, Yu. P.; Dzhagarov, B. M.

2006-07-01

We have developed a procedure for analysis of the functional status of blood vessels in tumor tissues using computer-assisted color scanning of tumor slices and also for a quantitative assessment of the effectiveness of photoinduced destruction of tumor tissues in animal experiments. Its major advantage is direct determination of the size of the tumor necrosis zone. The procedure has been tested in an experiment on three strains of malignant tumors with different morphologies.

A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

ERIC Educational Resources Information Center

Katharaki, Maria; Katharakis, George

2010-01-01

In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

SNIa detection in the SNLS photometric analysis using Morphological Component Analysis

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

Möller, A.; Ruhlmann-Kleider, V.; Neveu, J.

2015-04-01

Detection of supernovae (SNe) and, more generally, of transient events in large surveys can provide numerous false detections. In the case of a deferred processing of survey images, this implies reconstructing complete light curves for all detections, requiring sizable processing time and resources. Optimizing the detection of transient events is thus an important issue for both present and future surveys. We present here the optimization done in the SuperNova Legacy Survey (SNLS) for the 5-year data deferred photometric analysis. In this analysis, detections are derived from stacks of subtracted images with one stack per lunation. The 3-year analysis provided 300,000more » detections dominated by signals of bright objects that were not perfectly subtracted. Allowing these artifacts to be detected leads not only to a waste of resources but also to possible signal coordinate contamination. We developed a subtracted image stack treatment to reduce the number of non SN-like events using morphological component analysis. This technique exploits the morphological diversity of objects to be detected to extract the signal of interest. At the level of our subtraction stacks, SN-like events are rather circular objects while most spurious detections exhibit different shapes. A two-step procedure was necessary to have a proper evaluation of the noise in the subtracted image stacks and thus a reliable signal extraction. We also set up a new detection strategy to obtain coordinates with good resolution for the extracted signal. SNIa Monte-Carlo (MC) generated images were used to study detection efficiency and coordinate resolution. When tested on SNLS 3-year data this procedure decreases the number of detections by a factor of two, while losing only 10% of SN-like events, almost all faint ones. MC results show that SNIa detection efficiency is equivalent to that of the original method for bright events, while the coordinate resolution is improved.« less

Material and morphology parameter sensitivity analysis in particulate composite materials

NASA Astrophysics Data System (ADS)

Zhang, Xiaoyu; Oskay, Caglar

2017-12-01

This manuscript presents a novel parameter sensitivity analysis framework for damage and failure modeling of particulate composite materials subjected to dynamic loading. The proposed framework employs global sensitivity analysis to study the variance in the failure response as a function of model parameters. In view of the computational complexity of performing thousands of detailed microstructural simulations to characterize sensitivities, Gaussian process (GP) surrogate modeling is incorporated into the framework. In order to capture the discontinuity in response surfaces, the GP models are integrated with a support vector machine classification algorithm that identifies the discontinuities within response surfaces. The proposed framework is employed to quantify variability and sensitivities in the failure response of polymer bonded particulate energetic materials under dynamic loads to material properties and morphological parameters that define the material microstructure. Particular emphasis is placed on the identification of sensitivity to interfaces between the polymer binder and the energetic particles. The proposed framework has been demonstrated to identify the most consequential material and morphological parameters under vibrational and impact loads.

A quantitative comparison of morphological and histological characteristics of collagen in the rabbit medial collateral ligament.

PubMed

Wan, Chao; Hao, Zhixiu; Wen, Shizhu

2013-12-01

Collagen fiber is one of the critical factors in determining mechanical properties of ligaments and both the morphological and histological characteristics of collagen have been widely studied. However, there was still no consensus about whether the morphological characteristics of collagen correlated with its histological characteristics in physiological ligaments. Rabbit medial collateral ligaments (MCLs) were measured under a transmission electron microscope and a polarized light microscope plus picrosirius red-staining to obtain the distributions of collagen fibril diameters and types at different anatomical sites of rabbit MCLs, respectively. The correlation between the fibril diameter and type was determined by a correlation analysis. The collagen fibril diameters at the different anatomical sites had different distributions (unimodal or bimodal) and mean fibril diameters were found to increase significantly from the anterior part to the posterior part (P=0.0482) as well as from the proximal to the distal sections (P=0.0208). Type I collagen in the core portion of MCLs was significantly less than at the other four peripheral areas (P<0.005) but no significant variation was found in each respective portion (P>0.05). The low coefficient in the correlation analysis (r=0.3759) demonstrated collagen fibril diameters had no correlation with collagen types. This may provide a new view of collagen types in studying the mechanical behavior of ligaments. Copyright © 2013 Elsevier GmbH. All rights reserved.

Arsenic distribution and valence state variation studied by fast hierarchical length-scale morphological, compositional, and speciation imaging at the Nanoscopium, Synchrotron Soleil

NASA Astrophysics Data System (ADS)

Somogyi, Andrea; Medjoubi, Kadda; Sancho-Tomas, Maria; Visscher, P. T.; Baranton, Gil; Philippot, Pascal

2017-09-01

The understanding of real complex geological, environmental and geo-biological processes depends increasingly on in-depth non-invasive study of chemical composition and morphology. In this paper we used scanning hard X-ray nanoprobe techniques in order to study the elemental composition, morphology and As speciation in complex highly heterogeneous geological samples. Multivariate statistical analytical techniques, such as principal component analysis and clustering were used for data interpretation. These measurements revealed the quantitative and valance state inhomogeneity of As and its relation to the total compositional and morphological variation of the sample at sub-μm scales.

[Correspondence analysis between traditional commercial specifications and quantitative quality indices of Notopterygii Rhizoma et Radix].

PubMed

Jiang, Shun-Yuan; Sun, Hong-Bing; Sun, Hui; Ma, Yu-Ying; Chen, Hong-Yu; Zhu, Wen-Tao; Zhou, Yi

2016-03-01

This paper aims to explore a comprehensive assessment method combined traditional Chinese medicinal material specifications with quantitative quality indicators. Seventy-six samples of Notopterygii Rhizoma et Radix were collected on market and at producing areas. Traditional commercial specifications were described and assigned, and 10 chemical components and volatile oils were determined for each sample. Cluster analysis, Fisher discriminant analysis and correspondence analysis were used to establish the relationship between the traditional qualitative commercial specifications and quantitative chemical indices for comprehensive evaluating quality of medicinal materials, and quantitative classification of commercial grade and quality grade. A herb quality index (HQI) including traditional commercial specifications and chemical components for quantitative grade classification were established, and corresponding discriminant function were figured out for precise determination of quality grade and sub-grade of Notopterygii Rhizoma et Radix. The result showed that notopterol, isoimperatorin and volatile oil were the major components for determination of chemical quality, and their dividing values were specified for every grade and sub-grade of the commercial materials of Notopterygii Rhizoma et Radix. According to the result, essential relationship between traditional medicinal indicators, qualitative commercial specifications, and quantitative chemical composition indicators can be examined by K-mean cluster, Fisher discriminant analysis and correspondence analysis, which provide a new method for comprehensive quantitative evaluation of traditional Chinese medicine quality integrated traditional commodity specifications and quantitative modern chemical index. Copyright© by the Chinese Pharmaceutical Association.

A comparison of 3D poly(ε-caprolactone) tissue engineering scaffolds produced with conventional and additive manufacturing techniques by means of quantitative analysis of SR μ-CT images

NASA Astrophysics Data System (ADS)

Brun, F.; Intranuovo, F.; Mohammadi, S.; Domingos, M.; Favia, P.; Tromba, G.

2013-07-01

The technique used to produce a 3D tissue engineering (TE) scaffold is of fundamental importance in order to guarantee its proper morphological characteristics. An accurate assessment of the resulting structural properties is therefore crucial in order to evaluate the effectiveness of the produced scaffold. Synchrotron radiation (SR) computed microtomography (μ-CT) combined with further image analysis seems to be one of the most effective techniques to this aim. However, a quantitative assessment of the morphological parameters directly from the reconstructed images is a non trivial task. This study considers two different poly(ε-caprolactone) (PCL) scaffolds fabricated with a conventional technique (Solvent Casting Particulate Leaching, SCPL) and an additive manufacturing (AM) technique (BioCell Printing), respectively. With the first technique it is possible to produce scaffolds with random, non-regular, rounded pore geometry. The AM technique instead is able to produce scaffolds with square-shaped interconnected pores of regular dimension. Therefore, the final morphology of the AM scaffolds can be predicted and the resulting model can be used for the validation of the applied imaging and image analysis protocols. It is here reported a SR μ-CT image analysis approach that is able to effectively and accurately reveal the differences in the pore- and throat-size distributions as well as connectivity of both AM and SCPL scaffolds.

Influence of sample preparation and reliability of automated numerical refocusing in stain-free analysis of dissected tissues with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

2015-05-01

Digital holographic microscopy (DHM) has been demonstrated to be a versatile tool for high resolution non-destructive quantitative phase imaging of surfaces and multi-modal minimally-invasive monitoring of living cell cultures in-vitro. DHM provides quantitative monitoring of physiological processes through functional imaging and structural analysis which, for example, gives new insight into signalling of cellular water permeability and cell morphology changes due to toxins and infections. Also the analysis of dissected tissues quantitative DHM phase contrast prospects application fields by stain-free imaging and the quantification of tissue density changes. We show that DHM allows imaging of different tissue layers with high contrast in unstained tissue sections. As the investigation of fixed samples represents a very important application field in pathology, we also analyzed the influence of the sample preparation. The retrieved data demonstrate that the quality of quantitative DHM phase images of dissected tissues depends strongly on the fixing method and common staining agents. As in DHM the reconstruction is performed numerically, multi-focus imaging is achieved from a single digital hologram. Thus, we evaluated the automated refocussing feature of DHM for application on different types of dissected tissues and revealed that on moderately stained samples highly reproducible holographic autofocussing can be achieved. Finally, it is demonstrated that alterations of the spatial refractive index distribution in murine and human tissue samples represent a reliable absolute parameter that is related of different degrees of inflammation in experimental colitis and Crohn's disease. This paves the way towards the usage of DHM in digital pathology for automated histological examinations and further studies to elucidate the translational potential of quantitative phase microscopy for the clinical management of patients, e.g., with inflammatory bowel disease.

Dielectric inspection of erythrocyte morphology.

PubMed

Hayashi, Yoshihito; Oshige, Ikuya; Katsumoto, Yoichi; Omori, Shinji; Yasuda, Akio; Asami, Koji

2008-05-21

We performed a systematic study of the sensitivity of dielectric spectroscopy to erythrocyte morphology. Namely, rabbit erythrocytes of four different shapes were prepared by precisely controlling the pH of the suspending medium, and their complex permittivities over the frequency range from 0.1 to 110 MHz were measured and analyzed. Their quantitative analysis shows that the characteristic frequency and the broadening parameter of the dielectric relaxation of interfacial polarization are highly specific to the erythrocyte shape, while they are insensitive to the cell volume fraction. Therefore, these two dielectric parameters can be used to differentiate erythrocytes of different shapes, if dielectric spectroscopy is applied to flow-cytometric inspection of single blood cells. In addition, we revealed the applicability and limitations of the analytical theory of interfacial polarization to explain the experimental permittivities of non-spherical erythrocytes.

Use of MRI in Differentiation of Papillary Renal Cell Carcinoma Subtypes: Qualitative and Quantitative Analysis.

PubMed

Doshi, Ankur M; Ream, Justin M; Kierans, Andrea S; Bilbily, Matthew; Rusinek, Henry; Huang, William C; Chandarana, Hersh

2016-03-01

The purpose of this study was to determine whether qualitative and quantitative MRI feature analysis is useful for differentiating type 1 from type 2 papillary renal cell carcinoma (PRCC). This retrospective study included 21 type 1 and 17 type 2 PRCCs evaluated with preoperative MRI. Two radiologists independently evaluated various qualitative features, including signal intensity, heterogeneity, and margin. For the quantitative analysis, a radiology fellow and a medical student independently drew 3D volumes of interest over the entire tumor on T2-weighted HASTE images, apparent diffusion coefficient parametric maps, and nephrographic phase contrast-enhanced MR images to derive first-order texture metrics. Qualitative and quantitative features were compared between the groups. For both readers, qualitative features with greater frequency in type 2 PRCC included heterogeneous enhancement, indistinct margin, and T2 heterogeneity (all, p < 0.035). Indistinct margins and heterogeneous enhancement were independent predictors (AUC, 0.822). Quantitative analysis revealed that apparent diffusion coefficient, HASTE, and contrast-enhanced entropy were greater in type 2 PRCC (p < 0.05; AUC, 0.682-0.716). A combined quantitative and qualitative model had an AUC of 0.859. Qualitative features within the model had interreader concordance of 84-95%, and the quantitative data had intraclass coefficients of 0.873-0.961. Qualitative and quantitative features can help discriminate between type 1 and type 2 PRCC. Quantitative analysis may capture useful information that complements the qualitative appearance while benefiting from high interobserver agreement.

The influence of low frequency sound on the changes of EEG signal morphology

NASA Astrophysics Data System (ADS)

Damijan, Z.; Wiciak, J.

2006-11-01

The effects of low frequency sound on the changes of morphology of the spectral power density function of EEG signals were studied as a part of the research program f = 40 Hz, Lp = 110 dB HP. The research program involved 33 experiments. A quantitative analysis was conducted of the driving response effect for the fundamental frequency and its harmonics to find the frequency of the driving response effect occurrence depending on the sex of participants.

Morphological Decomposition Based on the Analysis of Orthography

ERIC Educational Resources Information Center

Rastle, Kathleen; Davis, Matthew H.

2008-01-01

Recent theories of morphological processing have been dominated by the notion that morphologically complex words are decomposed into their constituents on the basis of their semantic properties. In this article we argue that the weight of evidence now suggests that the recognition of morphologically complex words begins with a rapid morphemic…

Clinical impact of quantitative left atrial vortex flow analysis in patients with atrial fibrillation: a comparison with invasive left atrial voltage mapping.

PubMed

Lee, Jung Myung; Hong, Geu-Ru; Pak, Hui-Nam; Shim, Chi Young; Houle, Helene; Vannan, Mani A; Kim, Minji; Chung, Namsik

2015-08-01

Recently, left atrial (LA) vortex flow analysis using contrast transesophageal echocardiography (TEE) has been shown to be feasible and has demonstrated significant differences in vortex flow morphology and pulsatility between normal subjects and patients with atrial fibrillation (AF). However, the relationship between LA vortex flow and electrophysiological properties and the clinical significance of LA vortex flow are unknown. The aims of this study were (1) to compare LA vortex flow parameters with LA voltage and (2) to assess the predictive value of LA vortex flow parameters for the recurrence of AF after radiofrequency catheter ablation (RFCA). Thirty-nine patients with symptomatic non-valvular AF underwent contrast TEE before undergoing RFCA for AF. Quantitative LA vortex flow parameters were analyzed by Omega flow (Siemens Medical Solution, Mountain View, CA, USA). The morphology and pulsatility of LA vortex flow were compared with electrophysiologic parameters that were measured invasively. Hemodynamic, electrophysiological, and vortex flow parameters were compared between patients with and without early recurrence of AF after RFCA. Morphologic parameters, including LA vortex depth, length, width, and sphericity index were not associated with LA voltage or hemodynamic parameters. The relative strength (RS), which represents the pulsatility power of LA, was positively correlated with LA voltage (R = 0.53, p = 0.01) and LA appendage flow velocity (R = 0.73, p < 0.001) and negatively correlated with LA volume index (R = -0.56, p < 0.001). Patients with recurrent AF after RFCA showed significantly lower RS (1.7 ± 0.2 vs 1.9 ± 0.4, p = 0.048) and LA voltage (0.9 ± 0.7 vs 1.7 ± 0.8, p = 0.004) than patients without AF recurrence. In the relatively small LA dimension group (LA volume index ≤ 33 ml/m(2)), RS was significantly lower (2.1 ± 0.3 vs 1.7 ± 0.1, p = 0.029) in patients with the recurrent AF. Quantitative LA vortex flow analysis, especially RS

Quantitative kinetic analysis of lung nodules by temporal subtraction technique in dynamic chest radiography with a flat panel detector

NASA Astrophysics Data System (ADS)

Tsuchiya, Yuichiro; Kodera, Yoshie; Tanaka, Rie; Sanada, Shigeru

2007-03-01

Early detection and treatment of lung cancer is one of the most effective means to reduce cancer mortality; chest X-ray radiography has been widely used as a screening examination or health checkup. The new examination method and the development of computer analysis system allow obtaining respiratory kinetics by the use of flat panel detector (FPD), which is the expanded method of chest X-ray radiography. Through such changes functional evaluation of respiratory kinetics in chest has become available. Its introduction into clinical practice is expected in the future. In this study, we developed the computer analysis algorithm for the purpose of detecting lung nodules and evaluating quantitative kinetics. Breathing chest radiograph obtained by modified FPD was converted into 4 static images drawing the feature, by sequential temporal subtraction processing, morphologic enhancement processing, kinetic visualization processing, and lung region detection processing, after the breath synchronization process utilizing the diaphragmatic analysis of the vector movement. The artificial neural network used to analyze the density patterns detected the true nodules by analyzing these static images, and drew their kinetic tracks. For the algorithm performance and the evaluation of clinical effectiveness with 7 normal patients and simulated nodules, both showed sufficient detecting capability and kinetic imaging function without statistically significant difference. Our technique can quantitatively evaluate the kinetic range of nodules, and is effective in detecting a nodule on a breathing chest radiograph. Moreover, the application of this technique is expected to extend computer-aided diagnosis systems and facilitate the development of an automatic planning system for radiation therapy.

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

DTIC Science & Technology

2017-05-10

repertoire-wide properties. Finally, through 75 the use of appropriate statistical analyses, the repertoire profiles can be quantitatively compared and 76...cell response to eVLP and 503 quantitatively compare GC B-cell repertoires from immunization conditions. We partitioned the 504 resulting clonotype... Quantitative analysis of repertoire-scale immunoglobulin properties in vaccine-induced B-cell responses Ilja V. Khavrutskii1, Sidhartha Chaudhury*1

Appreciating the difference between design-based and model-based sampling strategies in quantitative morphology of the nervous system.

PubMed

Geuna, S

2000-11-20

Quantitative morphology of the nervous system has undergone great developments over recent years, and several new technical procedures have been devised and applied successfully to neuromorphological research. However, a lively debate has arisen on some issues, and a great deal of confusion appears to exist that is definitely responsible for the slow spread of the new techniques among scientists. One such element of confusion is related to uncertainty about the meaning, implications, and advantages of the design-based sampling strategy that characterize the new techniques. In this article, to help remove this uncertainty, morphoquantitative methods are described and contrasted on the basis of the inferential paradigm of the sampling strategy: design-based vs model-based. Moreover, some recommendations are made to help scientists judge the appropriateness of a method used for a given study in relation to its specific goals. Finally, the use of the term stereology to label, more or less expressly, only some methods is critically discussed. Copyright 2000 Wiley-Liss, Inc.

Age determination by teeth examination: a comparison between different morphologic and quantitative analyses.

PubMed

Amariti, M L; Restori, M; De Ferrari, F; Paganelli, C; Faglia, R; Legnani, G

1999-06-01

Age determination by teeth examination is one of the main means of determining personal identification. Current studies have suggested different techniques for determining the age of a subject by means of the analysis of microscopic and macroscopic structural modifications of the tooth with ageing. The histological approach is useful among the various methodologies utilized for this purpose. It is still unclear as to what is the best technique, as almost all the authors suggest the use of the approach they themselves have tested. In the present study, age determination by means of microscopic techniques has been based on the quantitative analysis of three parameters, all well recognized in specialized literature: 1. dentinal tubules density/sclerosis 2. tooth translucency 3. analysis of the cementum thickness. After a description of the three methodologies (with automatic image processing of the dentinal sclerosis utilizing an appropriate computer program developed by the authors) the results obtained on cases using the three different approaches are presented, and the merits and failings of each technique are identified with the intention of identifying the one offering the least degree of error in age determination.

CUMULATIVE RISK ASSESSMENT: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS

EPA Science Inventory

INTRODUCTION: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS FOR CUMULATIVE RISK

Hugh A. Barton1 and Carey N. Pope2
1US EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC
2Department of...

Evaluation of shear wave elastography for differential diagnosis of breast lesions: A new qualitative analysis versus conventional quantitative analysis.

PubMed

Ren, Wei-Wei; Li, Xiao-Long; Wang, Dan; Liu, Bo-Ji; Zhao, Chong-Ke; Xu, Hui-Xiong

2018-04-13

To evaluate a special kind of ultrasound (US) shear wave elastography for differential diagnosis of breast lesions, using a new qualitative analysis (i.e. the elasticity score in the travel time map) compared with conventional quantitative analysis. From June 2014 to July 2015, 266 pathologically proven breast lesions were enrolled in this study. The maximum, mean, median, minimum, and standard deviation of shear wave speed (SWS) values (m/s) were assessed. The elasticity score, a new qualitative feature, was evaluated in the travel time map. The area under the receiver operating characteristic (AUROC) curves were plotted to evaluate the diagnostic performance of both qualitative and quantitative analyses for differentiation of breast lesions. Among all quantitative parameters, SWS-max showed the highest AUROC (0.805; 95% CI: 0.752, 0.851) compared with SWS-mean (0.786; 95% CI:0.732, 0.834; P = 0.094), SWS-median (0.775; 95% CI:0.720, 0.824; P = 0.046), SWS-min (0.675; 95% CI:0.615, 0.731; P = 0.000), and SWS-SD (0.768; 95% CI:0.712, 0.817; P = 0.074). The AUROC of qualitative analysis in this study obtained the best diagnostic performance (0.871; 95% CI: 0.825, 0.909, compared with the best parameter of SWS-max in quantitative analysis, P = 0.011). The new qualitative analysis of shear wave travel time showed the superior diagnostic performance in the differentiation of breast lesions in comparison with conventional quantitative analysis.

Quantitation of glycerophosphorylcholine by flow injection analysis using immobilized enzymes.

PubMed

Mancini, A; Del Rosso, F; Roberti, R; Caligiana, P; Vecchini, A; Binaglia, L

1996-09-20

A method for quantitating glycerophosphorylcholine by flow injection analysis is reported in the present paper. Glycerophosphorylcholine phosphodiesterase and choline oxidase, immobilized on controlled porosity glass beads, are packed in a small reactor inserted in a flow injection manifold. When samples containing glycerophosphorylcholine are injected, glycerophosphorylcholine is hydrolyzed into choline and sn-glycerol-3-phosphate. The free choline produced in this reaction is oxidized to betain and hydrogen peroxide. Hydrogen peroxide is detected amperometrically. Quantitation of glycerophosphorylcholine in samples containing choline and phosphorylcholine is obtained inserting ahead of the reactor a small column packed with a mixed bed ion exchange resin. The time needed for each determination does not exceed one minute. The present method, applied to quantitate glycerophosphorylcholine in samples of seminal plasma, gave results comparable with those obtained using the standard enzymatic-spectrophotometric procedure. An alternative procedure, making use of co-immobilized glycerophosphorylcholine phosphodiesterase and glycerol-3-phosphate oxidase for quantitating glycerophosphorylcholine, glycerophosphorylethanolamine and glycerophosphorylserine is also described.

Quantitative analysis of vascular parameters for micro-CT imaging of vascular networks with multi-resolution.

PubMed

Zhao, Fengjun; Liang, Jimin; Chen, Xueli; Liu, Junting; Chen, Dongmei; Yang, Xiang; Tian, Jie

2016-03-01

Previous studies showed that all the vascular parameters from both the morphological and topological parameters were affected with the altering of imaging resolutions. However, neither the sensitivity analysis of the vascular parameters at multiple resolutions nor the distinguishability estimation of vascular parameters from different data groups has been discussed. In this paper, we proposed a quantitative analysis method of vascular parameters for vascular networks of multi-resolution, by analyzing the sensitivity of vascular parameters at multiple resolutions and estimating the distinguishability of vascular parameters from different data groups. Combining the sensitivity and distinguishability, we designed a hybrid formulation to estimate the integrated performance of vascular parameters in a multi-resolution framework. Among the vascular parameters, degree of anisotropy and junction degree were two insensitive parameters that were nearly irrelevant with resolution degradation; vascular area, connectivity density, vascular length, vascular junction and segment number were five parameters that could better distinguish the vascular networks from different groups and abide by the ground truth. Vascular area, connectivity density, vascular length and segment number not only were insensitive to multi-resolution but could also better distinguish vascular networks from different groups, which provided guidance for the quantification of the vascular networks in multi-resolution frameworks.

Quantitative analysis to guide orphan drug development.

PubMed

Lesko, L J

2012-08-01

The development of orphan drugs for rare diseases has made impressive strides in the past 10 years. There has been a surge in orphan drug designations, but new drug approvals have not kept up. This article presents a three-pronged hierarchical strategy for quantitative analysis of data at the descriptive, mechanistic, and systems levels of the biological system that could represent a standardized and rational approach to orphan drug development. Examples are provided to illustrate the concept.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

Quantitative analysis of morphological changes in yeast colonies growing on solid medium: the eccentricity and Fourier indices.

PubMed

Gil de Prado, Elena; Rivas, Eva-María; de Silóniz, María-Isabel; Diezma, Belén; Barreiro, Pilar; Peinado, José M

2014-11-01

The colony shape of four yeast species growing on agar medium was measured for 116 days by image analysis. Initially, all the colonies are circular, with regular edges. The loss of circularity can be quantitatively estimated by the eccentricity index, Ei , calculated as the ratio between their orthogonal vertical and horizontal diameters. Ei can increase from 1 (complete circularity) to a maximum of 1.17-1.30, depending on the species. One colony inhibits its neighbour only when it has reached a threshold area. Then, Ei of the inhibited colony increases proportionally to the area of the inhibitory colony. The initial distance between colonies affects those threshold values but not the proportionality, Ei /area; this inhibition affects the shape but not the total surface of the colony. The appearance of irregularities in the edges is associated, in all the species, not with age but with nutrient exhaustion. The edge irregularity can be quantified by the Fourier index, Fi , calculated by the minimum number of Fourier coefficients that are needed to describe the colony contour with 99% fitness. An ad hoc function has been developed in Matlab v. 7.0 to automate the computation of the Fourier coefficients. In young colonies, Fi has a value between 2 (circumference) and 3 (ellipse). These values are maintained in mature colonies of Debaryomyces, but can reach values up to 14 in Saccharomyces. All the species studied showed the inhibition of growth in facing colony edges, but only three species showed edge irregularities associated with substrate exhaustion. Copyright © 2014 John Wiley & Sons, Ltd.

A kinetic model for the characteristic surface morphologies of thin films by directional vapor deposition

NASA Astrophysics Data System (ADS)

Li, Kun-Dar; Huang, Po-Yu

2017-12-01

In order to simulate a process of directional vapor deposition, in this study, a numerical approach was applied to model the growth and evolution of surface morphologies for the crystallographic structures of thin films. The critical factors affecting the surface morphologies in a deposition process, such as the crystallographic symmetry, anisotropic interfacial energy, shadowing effect, and deposition rate, were all enclosed in the theoretical model. By altering the parameters of crystallographic symmetry in the structures, the faceted nano-columns with rectangular and hexagonal shapes were established in the simulation results. Furthermore, for revealing the influences of the anisotropic strength and the deposition rate theoretically on the crystallographic structure formations, various parameters adjusted in the numerical calculations were also investigated. Not only the morphologies but also the surface roughnesses for different processing conditions were distinctly demonstrated with the quantitative analysis of the simulations.

'Ogura'-based 'CMS' lines with different nuclear backgrounds of cabbage revealed substantial diversity at morphological and molecular levels.

PubMed

Parkash, Chander; Kumar, Sandeep; Singh, Rajender; Kumar, Ajay; Kumar, Satish; Dey, Shyam Sundar; Bhatia, Reeta; Kumar, Raj

2018-01-01

A comprehensive study on characterization and genetic diversity analysis was carried out in 16 'Ogura'-based 'CMS' lines of cabbage using 14 agro-morphological traits and 29 SSR markers. Agro-morphological characterization depicted considerable variations for different horticultural traits studied. The genotype, ZHA-2, performed better for most of the economically important quantitative traits. Further, gross head weight (0.76), head length (0.60) and head width (0.83) revealed significant positive correlation with net head weight. Dendrogram based on 10 quantitative traits exhibited considerable diversity among different CMS lines and principle component analysis (PCA) indicated that net and gross head weight, and head length and width are the main components of divergence between 16 CMS lines of cabbage. In molecular study, a total of 58 alleles were amplified by 29 SSR primers, averaging to 2.0 alleles in each locus. High mean values of Shannon's Information index (0.62), expected (0.45) and observed (0.32) heterozygosity and polymorphic information content (0.35) depicted substantial polymorphism. Dendrogram based on Jaccard's similarity coefficient constructed two major groups and eight sub-groups, which revealed substantial diversity among different CMS lines. In overall, based on agro-morphological and molecular studies genotype RRMA, ZHA-2 and RCA were found most divergent. Hence, they have immense potential in future breeding programs for the high-yielding hybrid development in cabbage.

MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis

PubMed Central

Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

2016-01-01

ABSTRACT Introduction/Background: Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. Material and Methods: n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Results: Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Conclusion: Both Ki-67 and MCM-2 are

MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis.

PubMed

Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

2016-01-01

Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they

Quantitative Myocardial Perfusion Imaging Versus Visual Analysis in Diagnosing Myocardial Ischemia: A CE-MARC Substudy.

PubMed

Biglands, John D; Ibraheem, Montasir; Magee, Derek R; Radjenovic, Aleksandra; Plein, Sven; Greenwood, John P

2018-05-01

This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion. This retrospective study included 128 patients randomly selected from the CE-MARC (Clinical Evaluation of Magnetic Resonance Imaging in Coronary Heart Disease) study population such that the distribution of risk factors and disease status was proportionate to the full population. Visual analysis results of cardiovascular magnetic resonance perfusion images, by consensus of 2 expert readers, were taken from the original study reports. Quantitative myocardial blood flow estimates were obtained using Fermi-constrained deconvolution. The reference standard for myocardial ischemia was a quantitative coronary x-ray angiogram stenosis severity of ≥70% diameter in any coronary artery of >2 mm diameter, or ≥50% in the left main stem. Diagnostic performance was calculated using receiver-operating characteristic curve analysis. The area under the curve for visual analysis was 0.88 (95% confidence interval: 0.81 to 0.95) with a sensitivity of 81.0% (95% confidence interval: 69.1% to 92.8%) and specificity of 86.0% (95% confidence interval: 78.7% to 93.4%). For quantitative stress myocardial blood flow the area under the curve was 0.89 (95% confidence interval: 0.83 to 0.96) with a sensitivity of 87.5% (95% confidence interval: 77.3% to 97.7%) and specificity of 84.5% (95% confidence interval: 76.8% to 92.3%). There was no statistically significant difference between the diagnostic performance of quantitative and visual analyses (p = 0.72). Incorporating rest myocardial

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

PubMed Central

Bray, Mark-Anthony; Singh, Shantanu; Han, Han; Davis, Chadwick T.; Borgeson, Blake; Hartland, Cathy; Kost-Alimova, Maria; Gustafsdottir, Sigrun M.; Gibson, Christopher C.; Carpenter, Anne E.

2016-01-01

In morphological profiling, quantitative data are extracted from microscopy images of cells to identify biologically relevant similarities and differences among samples based on these profiles. This protocol describes the design and execution of experiments using Cell Painting, a morphological profiling assay multiplexing six fluorescent dyes imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Cells are plated in multi-well plates, perturbed with the treatments to be tested, stained, fixed, and imaged on a high-throughput microscope. Then, automated image analysis software identifies individual cells and measures ~1,500 morphological features (various measures of size, shape, texture, intensity, etc.) to produce a rich profile suitable for detecting subtle phenotypes. Profiles of cell populations treated with different experimental perturbations can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic perturbations, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. Cell culture and image acquisition takes two weeks; feature extraction and data analysis take an additional 1-2 weeks. PMID:27560178

Photogrammetric Analysis of Changes in Crater Morphology at Telica Volcano, Nicaragua from 1994 to 2016

NASA Astrophysics Data System (ADS)

Hanagan, C.; La Femina, P.

2017-12-01

Understanding processes that lead to volcanic eruptions is paramount for predicting future volcanic activity. Telica volcano, Nicaragua is a persistently active volcano with hundreds of daily, low magnitude and low frequency seismic events, high-temperature degassing, and sub-decadal VEI 1-3 eruptions. The phreatic vulcanian eruptions of 1999, 2011, and 2013, and phreatic to phreatomagmatic vulcanian eruption of 2015 are thought to have resulted by sealing of the hydrothermal system prior to the eruptions. Two mechanisms have been proposed for sealing of the volcanic system, hydrothermal mineralization and landslides covering the vent. These eruptions affect the crater morphology of Telica volcano, and therefore the exact mechanisms of change to the crater's form are of interest to provide data that may support or refute the proposed sealing mechanisms, improving our understanding of eruption mechanisms. We use a collection of photographs between February 1994 and May 2016 and a combination of qualitative and quantitative photogrammetry to detect the extent and type of changes in crater morphology associated with 2011, 2013, and 2015 eruptive activity. We produced dense point cloud models using Agisoft PhotoScan Professional for times with sufficient photographic coverage, including August 2011, March 2013, December 2015, March 2016, and May 2016. Our May 2016 model is georeferenced, and each other point cloud was differenced using the C2C tool in CloudCompare and the M3C2 method (CloudCompare plugin) Lague et al. (2013). Results of the qualitative observations and quantitative differencing reveal a general trend of material subtraction from the inner crater walls associated with eruptive activity and accumulation of material on the crater floor, often visibly sourced from the walls of the crater. Both daily activity and VEI 1-3 explosive events changed the crater morphology, and correlation between a landslide-covered vent and the 2011 and 2015 eruptive sequences

A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

PubMed Central

Meyer, Miriah; Wunderlich, Zeba; Simirenko, Lisa; Luengo Hendriks, Cris L.; Keränen, Soile V. E.; Henriquez, Clara; Knowles, David W.; Biggin, Mark D.; Eisen, Michael B.; DePace, Angela H.

2011-01-01

Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3–4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of

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

PubMed

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

2017-01-01

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

Quantitative analysis of culture using millions of digitized books

PubMed Central

Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

2011-01-01

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. ‘Culturomics’ extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities. PMID:21163965

Quantitative analysis of culture using millions of digitized books.

PubMed

Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K; Pickett, Joseph P; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A; Aiden, Erez Lieberman

2011-01-14

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

PubMed

Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

2015-01-01

Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Quantitative Doppler Analysis Using Conventional Color Flow Imaging Acquisitions.

PubMed

Karabiyik, Yucel; Ekroll, Ingvild Kinn; Eik-Nes, Sturla H; Lovstakken, Lasse

2018-05-01

Interleaved acquisitions used in conventional triplex mode result in a tradeoff between the frame rate and the quality of velocity estimates. On the other hand, workflow becomes inefficient when the user has to switch between different modes, and measurement variability is increased. This paper investigates the use of power spectral Capon estimator in quantitative Doppler analysis using data acquired with conventional color flow imaging (CFI) schemes. To preserve the number of samples used for velocity estimation, only spatial averaging was utilized, and clutter rejection was performed after spectral estimation. The resulting velocity spectra were evaluated in terms of spectral width using a recently proposed spectral envelope estimator. The spectral envelopes were also used for Doppler index calculations using in vivo and string phantom acquisitions. In vivo results demonstrated that the Capon estimator can provide spectral estimates with sufficient quality for quantitative analysis using packet-based CFI acquisitions. The calculated Doppler indices were similar to the values calculated using spectrograms estimated on a commercial ultrasound scanner.

High-throughput quantitative analysis by desorption electrospray ionization mass spectrometry.

PubMed

Manicke, Nicholas E; Kistler, Thomas; Ifa, Demian R; Cooks, R Graham; Ouyang, Zheng

2009-02-01

A newly developed high-throughput desorption electrospray ionization (DESI) source was characterized in terms of its performance in quantitative analysis. A 96-sample array, containing pharmaceuticals in various matrices, was analyzed in a single run with a total analysis time of 3 min. These solution-phase samples were examined from a hydrophobic PTFE ink printed on glass. The quantitative accuracy, precision, and limit of detection (LOD) were characterized. Chemical background-free samples of propranolol (PRN) with PRN-d(7) as internal standard (IS) and carbamazepine (CBZ) with CBZ-d(10) as IS were examined. So were two other sample sets consisting of PRN/PRN-d(7) at varying concentration in a biological milieu of 10% urine or porcine brain total lipid extract, total lipid concentration 250 ng/microL. The background-free samples, examined in a total analysis time of 1.5 s/sample, showed good quantitative accuracy and precision, with a relative error (RE) and relative standard deviation (RSD) generally less than 3% and 5%, respectively. The samples in urine and the lipid extract required a longer analysis time (2.5 s/sample) and showed RSD values of around 10% for the samples in urine and 4% for the lipid extract samples and RE values of less than 3% for both sets. The LOD for PRN and CBZ when analyzed without chemical background was 10 and 30 fmol, respectively. The LOD of PRN increased to 400 fmol analyzed in 10% urine, and 200 fmol when analyzed in the brain lipid extract.

On the Need for Quantitative Bias Analysis in the Peer-Review Process.

PubMed

Fox, Matthew P; Lash, Timothy L

2017-05-15

Peer review is central to the process through which epidemiologists generate evidence to inform public health and medical interventions. Reviewers thereby act as critical gatekeepers to high-quality research. They are asked to carefully consider the validity of the proposed work or research findings by paying careful attention to the methodology and critiquing the importance of the insight gained. However, although many have noted problems with the peer-review system for both manuscripts and grant submissions, few solutions have been proposed to improve the process. Quantitative bias analysis encompasses all methods used to quantify the impact of systematic error on estimates of effect in epidemiologic research. Reviewers who insist that quantitative bias analysis be incorporated into the design, conduct, presentation, and interpretation of epidemiologic research could substantially strengthen the process. In the present commentary, we demonstrate how quantitative bias analysis can be used by investigators and authors, reviewers, funding agencies, and editors. By utilizing quantitative bias analysis in the peer-review process, editors can potentially avoid unnecessary rejections, identify key areas for improvement, and improve discussion sections by shifting from speculation on the impact of sources of error to quantification of the impact those sources of bias may have had. © The Author 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cranial base morphology and temporal bone pneumatization in Asian Homo erectus.

PubMed

Balzeau, Antoine; Grimaud-Hervé, Dominique

2006-10-01

The external morphological features of the temporal bone are used frequently to determine taxonomic affinities of fossils of the genus Homo. Temporal bone pneumatization has been widely studied in great apes and in early hominids. However, this feature is rarely examined in the later hominids, particularly in Asian Homo erectus. We provide a comparative morphological and quantitative analysis of Asian Homo erectus from the sites of Ngandong, Sambungmacan, and Zhoukoudian, and of Neandertals and anatomically modern Homo sapiens in order to discuss causes and modalities of temporal bone pneumatization during hominid evolution. The evolution of temporal bone pneumatization in the genus Homo is more complex than previously described. Indeed, the Zhoukoudian fossils have a unique pattern of temporal bone pneumatization, whereas Ngandong and Sambungmacan fossils, as well as the Neandertals, more closely resemble the modern human pattern. Moreover, these Chinese fossils are characterized by a wide midvault and a relatively narrow occipital bone. Our results support the point of view that cell development does not play an active role in determining cranial base morphology. Instead, pneumatization is related to available space and to temporal bone morphology, and its development is related to correlated morphology and the relative disposition of the bones and cerebral lobes. Because variation in pneumatization is extensive within the same species, the phyletic implications of pneumatization are limited in the taxa considered here.

A Multivariate Analysis of Unilateral Cleft Lip and Palate Facial Skeletal Morphology.

PubMed

Starbuck, John M; Ghoneima, Ahmed; Kula, Katherine

2015-07-01

Unilateral cleft lip and palate (UCLP) occurs when the maxillary and nasal facial prominences fail to fuse correctly during development, resulting in a palatal cleft and clefted soft and hard tissues of the dentoalveolus. The UCLP deformity may compromise an individual's ability to eat, chew, and speak. In this retrospective cross-sectional study, cone beam computed tomography (CBCT) images of 7-17-year-old individuals born with UCLP (n = 24) and age- and sex-matched controls (n = 24) were assessed. Coordinate values of three-dimensional anatomical landmarks (n = 32) were recorded from each CBCT image. Data were evaluated using principal coordinates analysis (PCOORD) and Euclidean distance matrix analysis (EDMA). Approximately 40% of morphometric variation is captured by PCOORD axes 1-3, and the negative and positive ends of each axis are associated with specific patterns of morphological differences. Approximately 36% of facial skeletal measures significantly differ by confidence interval testing (α = 0.10) between samples. Although significant form differences occur across the facial skeleton, strong patterns of morphological differences were localized to the lateral and superioinferior aspects of the nasal aperture, particularly on the clefted side of the face. The UCLP deformity strongly influences facial skeletal morphology of the midface and oronasal facial regions, and to a lesser extent the upper and lower facial skeletons. The pattern of strong morphological differences in the oronasal region combined with differences across the facial complex suggests that craniofacial bones are integrated and covary, despite influences from the congenital cleft.

Quantitative analysis of professionally trained versus untrained voices.

PubMed

Siupsinskiene, Nora

2003-01-01

The aim of this study was to compare healthy trained and untrained voices as well as healthy and dysphonic trained voices in adults using combined voice range profile and aerodynamic tests, to define the normal range limiting values of quantitative voice parameters and to select the most informative quantitative voice parameters for separation between healthy and dysphonic trained voices. Three groups of persons were evaluated. One hundred eighty six healthy volunteers were divided into two groups according to voice training: non-professional speakers group consisted of 106 untrained voices persons (36 males and 70 females) and professional speakers group--of 80 trained voices persons (21 males and 59 females). Clinical group consisted of 103 dysphonic professional speakers (23 males and 80 females) with various voice disorders. Eighteen quantitative voice parameters from combined voice range profile (VRP) test were analyzed: 8 of voice range profile, 8 of speaking voice, overall vocal dysfunction degree and coefficient of sound, and aerodynamic maximum phonation time. Analysis showed that healthy professional speakers demonstrated expanded vocal abilities in comparison to healthy non-professional speakers. Quantitative voice range profile parameters- pitch range, high frequency limit, area of high frequencies and coefficient of sound differed significantly between healthy professional and non-professional voices, and were more informative than speaking voice or aerodynamic parameters in showing the voice training. Logistic stepwise regression revealed that VRP area in high frequencies was sufficient to discriminate between healthy and dysphonic professional speakers for male subjects (overall discrimination accuracy--81.8%) and combination of three quantitative parameters (VRP high frequency limit, maximum voice intensity and slope of speaking curve) for female subjects (overall model discrimination accuracy--75.4%). We concluded that quantitative voice assessment

Quantitative Determination of Aluminum in Deodorant Brands: A Guided Inquiry Learning Experience in Quantitative Analysis Laboratory

ERIC Educational Resources Information Center

Sedwick, Victoria; Leal, Anne; Turner, Dea; Kanu, A. Bakarr

2018-01-01

The monitoring of metals in commercial products is essential for protecting public health against the hazards of metal toxicity. This article presents a guided inquiry (GI) experimental lab approach in a quantitative analysis lab class that enabled students' to determine the levels of aluminum in deodorant brands. The utility of a GI experimental…

Quantitative genetics

USDA-ARS?s Scientific Manuscript database

The majority of economically important traits targeted for cotton improvement are quantitatively inherited. In this chapter, the current state of cotton quantitative genetics is described and separated into four components. These components include: 1) traditional quantitative inheritance analysis, ...

New insights in morphological analysis for managing activated sludge systems.

PubMed

Oliveira, Pedro; Alliet, Marion; Coufort-Saudejaud, Carole; Frances, Christine

2018-06-01

In activated sludge (AS) process, the impact of the operational parameters on process efficiency is assumed to be correlated with the sludge properties. This study provides a better insight into these interactions by subjecting a laboratory-scale AS system to a sequence of operating condition modifications enabling typical situations of a wastewater treatment plant to be represented. Process performance was assessed and AS floc morphology (size, circularity, convexity, solidity and aspect ratio) was quantified by measuring 100,000 flocs per sample with an automated image analysis technique. Introducing 3D distributions, which combine morphological properties, allowed the identification of a filamentous bulking characterized by a floc population shift towards larger sizes and lower solidity and circularity values. Moreover, a washout phenomenon was characterized by smaller AS flocs and an increase in their solidity. Recycle ratio increase and COD:N ratio decrease both promoted a slight reduction of floc sizes and a constant evolution of circularity and convexity values. The analysis of the volume-based 3D distributions turned out to be a smart tool to combine size and shape data, allowing a deeper understanding of the dynamics of floc structure under process disturbances.

Quantitative analysis on electrooculography (EOG) for neurodegenerative disease

NASA Astrophysics Data System (ADS)

Liu, Chang-Chia; Chaovalitwongse, W. Art; Pardalos, Panos M.; Seref, Onur; Xanthopoulos, Petros; Sackellares, J. C.; Skidmore, Frank M.

2007-11-01

Many studies have documented abnormal horizontal and vertical eye movements in human neurodegenerative disease as well as during altered states of consciousness (including drowsiness and intoxication) in healthy adults. Eye movement measurement may play an important role measuring the progress of neurodegenerative diseases and state of alertness in healthy individuals. There are several techniques for measuring eye movement, Infrared detection technique (IR). Video-oculography (VOG), Scleral eye coil and EOG. Among those available recording techniques, EOG is a major source for monitoring the abnormal eye movement. In this real-time quantitative analysis study, the methods which can capture the characteristic of the eye movement were proposed to accurately categorize the state of neurodegenerative subjects. The EOG recordings were taken while 5 tested subjects were watching a short (>120 s) animation clip. In response to the animated clip the participants executed a number of eye movements, including vertical smooth pursued (SVP), horizontal smooth pursued (HVP) and random saccades (RS). Detection of abnormalities in ocular movement may improve our diagnosis and understanding a neurodegenerative disease and altered states of consciousness. A standard real-time quantitative analysis will improve detection and provide a better understanding of pathology in these disorders.

Electroencephalography reactivity for prognostication of post-anoxic coma after cardiopulmonary resuscitation: A comparison of quantitative analysis and visual analysis.

PubMed

Liu, Gang; Su, Yingying; Jiang, Mengdi; Chen, Weibi; Zhang, Yan; Zhang, Yunzhou; Gao, Daiquan

2016-07-28

Electroencephalogram reactivity (EEG-R) is a positive predictive factor for assessing outcomes in comatose patients. Most studies assess the prognostic value of EEG-R utilizing visual analysis; however, this method is prone to subjectivity. We sought to categorize EEG-R with a quantitative approach. We retrospectively studied consecutive comatose patients who had an EEG-R recording performed 1-3 days after cardiopulmonary resuscitation (CPR) or during normothermia after therapeutic hypothermia. EEG-R was assessed via visual analysis and quantitative analysis separately. Clinical outcomes were followed-up at 3-month and dichotomized as recovery of awareness or no recovery of awareness. A total of 96 patients met the inclusion criteria, and 38 (40%) patients recovered awareness at 3-month followed-up. Of 27 patients with EEG-R measured with visual analysis, 22 patients recovered awareness; and of the 69 patients who did not demonstrated EEG-R, 16 patients recovered awareness. The sensitivity and specificity of visually measured EEG-R were 58% and 91%, respectively. The area under the receiver operating characteristic curve for the quantitative analysis was 0.92 (95% confidence interval, 0.87-0.97), with the best cut-off value of 0.10. EEG-R through quantitative analysis might be a good method in predicting the recovery of awareness in patients with post-anoxic coma after CPR. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Systematic Analysis of Rocky Shore Morphology along 700km of Coastline Using LiDAR-derived DEMs

NASA Astrophysics Data System (ADS)

Matsumoto, H.; Dickson, M. E.; Masselink, G.

2016-12-01

Rock shore platforms occur along much of the world's coast and have a long history of study; however, uncertainty remains concerning the relative importance of various formative controls in different settings (e.g. wave erosion, weathering, tidal range, rock resistance, inheritance). Ambiguity is often attributed to intrinsic natural variability and the lack of preserved evidence on eroding rocky shores, but it could also be argued that previous studies are limited in scale, focusing on a small number of local sites, which restricts the potential for insights from broad, regional analyses. Here we describe a method, using LiDAR-derived digital elevation models (DEMs), for analysing shore platform morphology over an unprecedentedly wide area in which there are large variations in environmental conditions. The new method semi-automatically extracts shore platform profiles and systematically conducts morphometric analysis. We apply the method to 700 km of coast in the SW UK that is exposed to (i) highly energetic swell waves to local wind waves, (ii) macro to mega tidal ranges, and (iii) highly resistant igneous rocks to moderately hard sedimentary rocks. Computer programs are developed to estimate mean sea level, mean spring tidal range, wave height, and rock strength along the coastline. Filtering routines automatically select and remove profiles that are unsuitable for analysis. The large data-set of remaining profiles supports broad and systematic investigation of possible controls on platform morphology. Results, as expected, show wide scatter, because many formative controls are in play, but several trends exist that are generally consistent with relationships that have been inferred from local site studies. This paper will describe correlation analysis on platform morphology in relation to environmental conditions and also present a multi-variable empirical model derived from multi linear regression analysis. Interesting matches exist between platform gradients

Morphological Perspectives on Galaxy Evolution since z~1.5

NASA Astrophysics Data System (ADS)

Rutkowski, Michael

Galaxies represent a fundamental catalyst in the "lifecycle'' of matter in the Universe, and the study of galaxy assembly and evolution provides unique insight into the physical processes governing the transformation of matter from atoms to gas to stars. With the Hubble Space Telescope, the astrophysical community is able to study the formation and evolution of galaxies, at an unrivaled spatial resolution, over more than 90% of cosmic time. Here, I present results from two complementary studies of galaxy evolution in the local and intermediate redshift Universe which used new and archival HST images. First, I use archival broad-band HST WFPC2 optical images of local (d < 63 Mpc) Seyfert-type galaxies to test the observed correlation between visually-classified host galaxy dust morphology and AGN class. Using quantitative parameters for classifying galaxy morphology, I do not measure a strong correlation between the galaxy morphology and AGN class. This result could imply that the Unified Model of AGN provides a sufficient model for the observed diversity of AGN, but this result could also indicate the quantitative techniques are insufficient for characterizing the dust morphology of local galaxies. To address the latter, I develop a new automated method using an inverse unsharp masking technique coupled to Source Extractor to detect and measure dust morphology. I measure no strong trends with dust-morphology and AGN class using this method, and conclude that the Unified Model remains sufficient to explain the diversity of AGN. Second, I use new UV-optical-near IR broad-band images obtained with the HST WFC3 in the Early Release Science (ERS) program to study the evolution of massive, early-type galaxies. These galaxies were once considered to be "red and dead'', as a class uniformly devoid of recent star formation, but observations of these galaxies in the local Universe at UV wavelengths have revealed a significant fraction (30%) of ETGs to have recently formed a

Comparison of DNA fragmentation and color thresholding for objective quantitation of apoptotic cells

NASA Technical Reports Server (NTRS)

Plymale, D. R.; Ng Tang, D. S.; Fermin, C. D.; Lewis, D. E.; Martin, D. S.; Garry, R. F.

1995-01-01

Apoptosis is a process of cell death characterized by distinctive morphological changes and fragmentation of cellular DNA. Using video imaging and color thresholding techniques, we objectively quantitated the number of cultured CD4+ T-lymphoblastoid cells (HUT78 cells, RH9 subclone) displaying morphological signs of apoptosis before and after exposure to gamma-irradiation. The numbers of apoptotic cells measured by objective video imaging techniques were compared to numbers of apoptotic cells measured in the same samples by sensitive apoptotic assays that quantitate DNA fragmentation. DNA fragmentation assays gave consistently higher values compared with the video imaging assays that measured morphological changes associated with apoptosis. These results suggest that substantial DNA fragmentation can precede or occur in the absence of the morphological changes which are associated with apoptosis in gamma-irradiated RH9 cells.

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

PubMed

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

2013-03-01

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

Three-dimensional morphological analysis of intracranial aneurysms: a fully automated method for aneurysm sac isolation and quantification.

PubMed

Larrabide, Ignacio; Cruz Villa-Uriol, Maria; Cárdenes, Rubén; Pozo, Jose Maria; Macho, Juan; San Roman, Luis; Blasco, Jordi; Vivas, Elio; Marzo, Alberto; Hose, D Rod; Frangi, Alejandro F

2011-05-01

Morphological descriptors are practical and essential biomarkers for diagnosis and treatment selection for intracranial aneurysm management according to the current guidelines in use. Nevertheless, relatively little work has been dedicated to improve the three-dimensional quantification of aneurysmal morphology, to automate the analysis, and hence to reduce the inherent intra and interobserver variability of manual analysis. In this paper we propose a methodology for the automated isolation and morphological quantification of saccular intracranial aneurysms based on a 3D representation of the vascular anatomy. This methodology is based on the analysis of the vasculature skeleton's topology and the subsequent application of concepts from deformable cylinders. These are expanded inside the parent vessel to identify different regions and discriminate the aneurysm sac from the parent vessel wall. The method renders as output the surface representation of the isolated aneurysm sac, which can then be quantified automatically. The proposed method provides the means for identifying the aneurysm neck in a deterministic way. The results obtained by the method were assessed in two ways: they were compared to manual measurements obtained by three independent clinicians as normally done during diagnosis and to automated measurements from manually isolated aneurysms by three independent operators, nonclinicians, experts in vascular image analysis. All the measurements were obtained using in-house tools. The results were qualitatively and quantitatively compared for a set of the saccular intracranial aneurysms (n = 26). Measurements performed on a synthetic phantom showed that the automated measurements obtained from manually isolated aneurysms where the most accurate. The differences between the measurements obtained by the clinicians and the manually isolated sacs were statistically significant (neck width: p <0.001, sac height: p = 0.002). When comparing clinicians

The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

PubMed Central

Kahlert, Maria; Fink, Patrick

2017-01-01

An increasing number of studies use next generation sequencing (NGS) to analyze complex communities, but is the method sensitive enough when it comes to identification and quantification of species? We compared NGS with morphology-based identification methods in an analysis of microalgal (periphyton) communities. We conducted a mesocosm experiment in which we allowed two benthic grazer species to feed upon benthic biofilms, which resulted in altered periphyton communities. Morphology-based identification and 454 (Roche) pyrosequencing of the V4 region in the small ribosomal unit (18S) rDNA gene were used to investigate the community change caused by grazing. Both the NGS-based data and the morphology-based method detected a marked shift in the biofilm composition, though the two methods varied strongly in their abilities to detect and quantify specific taxa, and neither method was able to detect all species in the biofilms. For quantitative analysis, we therefore recommend using both metabarcoding and microscopic identification when assessing the community composition of eukaryotic microorganisms. PMID:28234997

Quantitative analysis of eyes and other optical systems in linear optics.

PubMed

Harris, William F; Evans, Tanya; van Gool, Radboud D

2017-05-01

To show that 14-dimensional spaces of augmented point P and angle Q characteristics, matrices obtained from the ray transference, are suitable for quantitative analysis although only the latter define an inner-product space and only on it can one define distances and angles. The paper examines the nature of the spaces and their relationships to other spaces including symmetric dioptric power space. The paper makes use of linear optics, a three-dimensional generalization of Gaussian optics. Symmetric 2 × 2 dioptric power matrices F define a three-dimensional inner-product space which provides a sound basis for quantitative analysis (calculation of changes, arithmetic means, etc.) of refractive errors and thin systems. For general systems the optical character is defined by the dimensionally-heterogeneous 4 × 4 symplectic matrix S, the transference, or if explicit allowance is made for heterocentricity, the 5 × 5 augmented symplectic matrix T. Ordinary quantitative analysis cannot be performed on them because matrices of neither of these types constitute vector spaces. Suitable transformations have been proposed but because the transforms are dimensionally heterogeneous the spaces are not naturally inner-product spaces. The paper obtains 14-dimensional spaces of augmented point P and angle Q characteristics. The 14-dimensional space defined by the augmented angle characteristics Q is dimensionally homogenous and an inner-product space. A 10-dimensional subspace of the space of augmented point characteristics P is also an inner-product space. The spaces are suitable for quantitative analysis of the optical character of eyes and many other systems. Distances and angles can be defined in the inner-product spaces. The optical systems may have multiple separated astigmatic and decentred refracting elements. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

Quantitative proteomic analysis of intact plastids.

PubMed

Shiraya, Takeshi; Kaneko, Kentaro; Mitsui, Toshiaki

2014-01-01

Plastids are specialized cell organelles in plant cells that are differentiated into various forms including chloroplasts, chromoplasts, and amyloplasts, and fulfill important functions in maintaining the overall cell metabolism and sensing environmental factors such as sunlight. It is therefore important to grasp the mechanisms of differentiation and functional changes of plastids in order to enhance the understanding of vegetality. In this chapter, details of a method for the extraction of intact plastids that makes analysis possible while maintaining the plastid functions are provided; in addition, a quantitative shotgun method for analyzing the composition and changes in the content of proteins in plastids as a result of environmental impacts is described.

Renal geology (quantitative renal stone analysis) by 'Fourier transform infrared spectroscopy'.

PubMed

Singh, Iqbal

2008-01-01

To prospectively determine the precise stone composition (quantitative analysis) by using infrared spectroscopy in patients with urinary stone disease presenting to our clinic. To determine an ideal method for stone analysis suitable for use in a clinical setting. After routine and a detailed metabolic workup of all patients of urolithiasis, stone samples of 50 patients of urolithiasis satisfying the entry criteria were subjected to the Fourier transform infrared spectroscopic analysis after adequate sample homogenization at a single testing center. Calcium oxalate monohydrate and dihydrate stone mixture was most commonly encountered in 35 (71%) followed by calcium phosphate, carbonate apatite, magnesium ammonium hexahydrate and xanthine stones. Fourier transform infrared spectroscopy allows an accurate, reliable quantitative method of stone analysis. It also helps in maintaining a computerized large reference library. Knowledge of precise stone composition may allow the institution of appropriate prophylactic therapy despite the absence of any detectable metabolic abnormalities. This may prevent and or delay stone recurrence.

Toward Monitoring Parkinson's Through Analysis of Static Handwriting Samples: A Quantitative Analytical Framework.

PubMed

Zhi, Naiqian; Jaeger, Beverly Kris; Gouldstone, Andrew; Sipahi, Rifat; Frank, Samuel

2017-03-01

Detection of changes in micrographia as a manifestation of symptomatic progression or therapeutic response in Parkinson's disease (PD) is challenging as such changes can be subtle. A computerized toolkit based on quantitative analysis of handwriting samples would be valuable as it could supplement and support clinical assessments, help monitor micrographia, and link it to PD. Such a toolkit would be especially useful if it could detect subtle yet relevant changes in handwriting morphology, thus enhancing resolution of the detection procedure. This would be made possible by developing a set of metrics sensitive enough to detect and discern micrographia with specificity. Several metrics that are sensitive to the characteristics of micrographia were developed, with minimal sensitivity to confounding handwriting artifacts. These metrics capture character size-reduction, ink utilization, and pixel density within a writing sample from left to right. They are used here to "score" handwritten signatures of 12 different individuals corresponding to healthy and symptomatic PD conditions, and sample control signatures that had been artificially reduced in size for comparison purposes. Moreover, metric analyses of samples from ten of the 12 individuals for which clinical diagnosis time is known show considerable informative variations when applied to static signature samples obtained before and after diagnosis. In particular, a measure called pixel density variation showed statistically significant differences ( ) between two comparison groups of remote signature recordings: earlier versus recent, based on independent and paired t-test analyses on a total of 40 signature samples. The quantitative framework developed here has the potential to be used in future controlled experiments to study micrographia and links to PD from various aspects, including monitoring and assessment of applied interventions and treatments. The inherent value in this methodology is further enhanced by

Quantitative trait loci × environment interactions for plant morphology vary over ontogeny in Brassica rapa.

PubMed

Dechaine, Jennifer M; Brock, Marcus T; Iniguez-Luy, Federico L; Weinig, Cynthia

2014-01-01

Growth in plants occurs via the addition of repeating modules, suggesting that the genetic architecture of similar subunits may vary between earlier- and later-developing modules. These complex environment × ontogeny interactions are not well elucidated, as studies examining quantitative trait loci (QTLs) expression over ontogeny have not included multiple environments. Here, we characterized the genetic architecture of vegetative traits and onset of reproduction over ontogeny in recombinant inbred lines of Brassica rapa in the field and glasshouse. The magnitude of genetic variation in plasticity of seedling internodes was greater than in those produced later in ontogeny. We correspondingly detected that QTLs for seedling internode length were environment-specific, whereas later in ontogeny the majority of QTLs affected internode lengths in all treatments. The relationship between internode traits and onset of reproduction varied with environment and ontogenetic stage. This relationship was observed only in the glasshouse environment and was largely attributable to one environment-specific QTL. Our results provide the first evidence of a QTL × environment × ontogeny interaction, and provide QTL resolution for differences between early- and later-stage plasticity for stem elongation. These results also suggest potential constraints on morphological evolution in early vs later modules as a result of associations with reproductive timing. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Patient-specific coronary blood supply territories for quantitative perfusion analysis

PubMed Central

Zakkaroff, Constantine; Biglands, John D.; Greenwood, John P.; Plein, Sven; Boyle, Roger D.; Radjenovic, Aleksandra; Magee, Derek R.

2018-01-01

Abstract Myocardial perfusion imaging, coupled with quantitative perfusion analysis, provides an important diagnostic tool for the identification of ischaemic heart disease caused by coronary stenoses. The accurate mapping between coronary anatomy and under-perfused areas of the myocardium is important for diagnosis and treatment. However, in the absence of the actual coronary anatomy during the reporting of perfusion images, areas of ischaemia are allocated to a coronary territory based on a population-derived 17-segment (American Heart Association) AHA model of coronary blood supply. This work presents a solution for the fusion of 2D Magnetic Resonance (MR) myocardial perfusion images and 3D MR angiography data with the aim to improve the detection of ischaemic heart disease. The key contribution of this work is a novel method for the mediated spatiotemporal registration of perfusion and angiography data and a novel method for the calculation of patient-specific coronary supply territories. The registration method uses 4D cardiac MR cine series spanning the complete cardiac cycle in order to overcome the under-constrained nature of non-rigid slice-to-volume perfusion-to-angiography registration. This is achieved by separating out the deformable registration problem and solving it through phase-to-phase registration of the cine series. The use of patient-specific blood supply territories in quantitative perfusion analysis (instead of the population-based model of coronary blood supply) has the potential of increasing the accuracy of perfusion analysis. Quantitative perfusion analysis diagnostic accuracy evaluation with patient-specific territories against the AHA model demonstrates the value of the mediated spatiotemporal registration in the context of ischaemic heart disease diagnosis. PMID:29392098

An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

NASA Astrophysics Data System (ADS)

Guldner, Ian H.; Yang, Lin; Cowdrick, Kyle R.; Wang, Qingfei; Alvarez Barrios, Wendy V.; Zellmer, Victoria R.; Zhang, Yizhe; Host, Misha; Liu, Fang; Chen, Danny Z.; Zhang, Siyuan

2016-04-01

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining, and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis, and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.

Quantitative Proteomic Analysis of Differentially Expressed Protein Profiles Involved in Pancreatic Ductal Adenocarcinoma

PubMed Central

Kuo, Kung-Kai; Kuo, Chao-Jen; Chiu, Chiang-Yen; Liang, Shih-Shin; Huang, Chun-Hao; Chi, Shu-Wen; Tsai, Kun-Bow; Chen, Chiao-Yun; Hsi, Edward; Cheng, Kuang-Hung; Chiou, Shyh-Horng

2016-01-01

Objectives The aim of this study was to identify differentially expressed proteins among various stages of pancreatic ductal adenocarcinoma (PDAC) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry and stable isotope dimethyl labeling. Methods Differentially expressed proteins were identified and compared based on the mass spectral differences of their isotope-labeled peptide fragments generated from protease digestion. Results Our quantitative proteomic analysis of the differentially expressed proteins with stable isotope (deuterium/hydrogen ratio, ≥2) identified a total of 353 proteins, with at least 5 protein biomarker proteins that were significantly differentially expressed between cancer and normal mice by at least a 2-fold alteration. These 5 protein biomarker candidates include α-enolase, α-catenin, 14-3-3 β, VDAC1, and calmodulin with high confidence levels. The expression levels were also found to be in agreement with those examined by Western blot and histochemical staining. Conclusions The systematic decrease or increase of these identified marker proteins may potentially reflect the morphological aberrations and diseased stages of pancreas carcinoma throughout progressive developments leading to PDAC. The results would form a firm foundation for future work concerning validation and clinical translation of some identified biomarkers into targeted diagnosis and therapy for various stages of PDAC. PMID:26262590

Phase composition and morphological characterization of human kidney stones using IR spectroscopy, scanning electron microscopy and X-ray Rietveld analysis.

PubMed

Chatterjee, Paramita; Chakraborty, Arup; Mukherjee, Alok K

2018-07-05

Pathological calcification in human urinary tract (kidney stones) is a common problem affecting an increasing number of people around the world. Analysis of such minerals or compounds is of fundamental importance for understanding their etiology and for the development of prophylactic measures. In the present study, structural characterization, phase quantification and morphological behaviour of thirty three (33) human kidney stones from eastern India have been carried out using IR spectroscopy (FT-IR), powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM). Quantitative phase composition of kidney stones has been analyzed following the Rietveld method. Based on the quantitative estimates of constituent phases, the calculi samples have been classified into oxalate (OX), uric acid (UA), phosphate (PH) and mixed (MX) groups. Rietveld analysis of PXRD patterns showed that twelve (36%) of the renal calculi were composed exclusively of whewellite (calcium oxalate monohydrate, COM). The remaining twenty one (64%) stones were mixture of phases with oxalate as the major constituent in fourteen (67%) of these stones. The average crystallite size of whewellite in oxalate stones, as determined from the PXRD analysis, varies between 93 (1) nm and 202 (3) nm, whereas the corresponding sizes for the uric acid and struvite crystallites in UA and PH stones are 79 (1)-155 (4) nm and 69 (1)-123(1) nm, respectively. The size of hydroxyapatite crystallites, 10 (1)-21 (1) nm, is smaller by about one order of magnitude compared to other minerals in the kidney stones. A statistical analysis using fifty (50) kidney stones (33 calculi from the present study and 17 calculi reported earlier from our laboratory) revealed that the oxalate group (whewellite, weddellite or mixture of whewellite and weddellite as the major constituent) is the most prevalent (82%) kidney stone type in eastern India. Copyright © 2018 Elsevier B.V. All rights reserved.

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

ERIC Educational Resources Information Center

Parker, Richard H.

2011-01-01

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

The study on the parallel processing based time series correlation analysis of RBC membrane flickering in quantitative phase imaging

NASA Astrophysics Data System (ADS)

Lee, Minsuk; Won, Youngjae; Park, Byungjun; Lee, Seungrag

2017-02-01

Not only static characteristics but also dynamic characteristics of the red blood cell (RBC) contains useful information for the blood diagnosis. Quantitative phase imaging (QPI) can capture sample images with subnanometer scale depth resolution and millisecond scale temporal resolution. Various researches have been used QPI for the RBC diagnosis, and recently many researches has been developed to decrease the process time of RBC information extraction using QPI by the parallel computing algorithm, however previous studies are interested in the static parameters such as morphology of the cells or simple dynamic parameters such as root mean square (RMS) of the membrane fluctuations. Previously, we presented a practical blood test method using the time series correlation analysis of RBC membrane flickering with QPI. However, this method has shown that there is a limit to the clinical application because of the long computation time. In this study, we present an accelerated time series correlation analysis of RBC membrane flickering using the parallel computing algorithm. This method showed consistent fractal scaling exponent results of the surrounding medium and the normal RBC with our previous research.

Morphological Integration of Soft-Tissue Facial Morphology in Down Syndrome and Siblings

PubMed Central

Starbuck, John; Reeves, Roger H.; Richtsmeier, Joan

2011-01-01

Down syndrome (DS), resulting from trisomy of chromosome 21, is the most common live-born human aneuploidy. The phenotypic expression of trisomy 21 produces variable, though characteristic, facial morphology. Although certain facial features have been documented quantitatively and qualitatively as characteristic of DS (e.g., epicanthic folds, macroglossia, and hypertelorism), all of these traits occur in other craniofacial conditions with an underlying genetic cause. We hypothesize that the typical DS face is integrated differently than the face of non-DS siblings, and that the pattern of morphological integration unique to individuals with DS will yield information about underlying developmental associations between facial regions. We statistically compared morphological integration patterns of immature DS faces (N = 53) with those of non-DS siblings (N = 54), aged 6–12 years using 31 distances estimated from 3D coordinate data representing 17 anthropometric landmarks recorded on 3D digital photographic images. Facial features are affected differentially in DS, as evidenced by statistically significant differences in integration both within and between facial regions. Our results suggest a differential affect of trisomy on facial prominences during craniofacial development. PMID:21996933

Morphological integration of soft-tissue facial morphology in Down Syndrome and siblings.

PubMed

Starbuck, John; Reeves, Roger H; Richtsmeier, Joan

2011-12-01

Down syndrome (DS), resulting from trisomy of chromosome 21, is the most common live-born human aneuploidy. The phenotypic expression of trisomy 21 produces variable, though characteristic, facial morphology. Although certain facial features have been documented quantitatively and qualitatively as characteristic of DS (e.g., epicanthic folds, macroglossia, and hypertelorism), all of these traits occur in other craniofacial conditions with an underlying genetic cause. We hypothesize that the typical DS face is integrated differently than the face of non-DS siblings, and that the pattern of morphological integration unique to individuals with DS will yield information about underlying developmental associations between facial regions. We statistically compared morphological integration patterns of immature DS faces (N = 53) with those of non-DS siblings (N = 54), aged 6-12 years using 31 distances estimated from 3D coordinate data representing 17 anthropometric landmarks recorded on 3D digital photographic images. Facial features are affected differentially in DS, as evidenced by statistically significant differences in integration both within and between facial regions. Our results suggest a differential affect of trisomy on facial prominences during craniofacial development. 2011 Wiley Periodicals, Inc.

QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

PubMed Central

Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

2015-01-01

Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.

PubMed

Rigbolt, Kristoffer T G; Vanselow, Jens T; Blagoev, Blagoy

2011-08-01

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.

GProX, a User-Friendly Platform for Bioinformatics Analysis and Visualization of Quantitative Proteomics Data*

PubMed Central

Rigbolt, Kristoffer T. G.; Vanselow, Jens T.; Blagoev, Blagoy

2011-01-01

Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)1. The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net. PMID:21602510

Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis.

PubMed

Davolos, Domenico; Pietrangeli, Biancamaria; Persiani, Anna Maria; Maggi, Oriana

2012-02-01

The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1-5.8S-ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591(T)  = CBS 129191(T)). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

Wavelength Selection Method Based on Differential Evolution for Precise Quantitative Analysis Using Terahertz Time-Domain Spectroscopy.

PubMed

Li, Zhi; Chen, Weidong; Lian, Feiyu; Ge, Hongyi; Guan, Aihong

2017-12-01

Quantitative analysis of component mixtures is an important application of terahertz time-domain spectroscopy (THz-TDS) and has attracted broad interest in recent research. Although the accuracy of quantitative analysis using THz-TDS is affected by a host of factors, wavelength selection from the sample's THz absorption spectrum is the most crucial component. The raw spectrum consists of signals from the sample and scattering and other random disturbances that can critically influence the quantitative accuracy. For precise quantitative analysis using THz-TDS, the signal from the sample needs to be retained while the scattering and other noise sources are eliminated. In this paper, a novel wavelength selection method based on differential evolution (DE) is investigated. By performing quantitative experiments on a series of binary amino acid mixtures using THz-TDS, we demonstrate the efficacy of the DE-based wavelength selection method, which yields an error rate below 5%.

[Achene morphology cluster analysis of Taraxacum F. H. Wigg. from northeast China and molecule systematics evidence determined by SRAP].

PubMed

Li, Hai-juan; Zhao, Xin; Jia, Qing-fei; Li, Tian-lai; Ning, Wei

2012-08-01

The achenes morphological and micro-morphological characteristics of six species of genus Taraxacum from northeastern China as well as SRAP cluster analysis were observed for their classification evidences. The achenes were observed by microscope and EPMA. Cluster analysis was given on the basis of the size, shape, cone proportion, color and surface sculpture of achenes. The Taraxacum inter-species achene shape characteristic difference is obvious, particularly spinulose distribution and size, achene color and achene size; with the Taraxacum plant achene shape the cluster method T. antungense Kitag. and the T. urbanum Kitag. should combine for the identical kind; the achene morphology cluster analysis and the SRAP tagged molecule systematics's cluster result retrieves in the table with "the Chinese flora". The class group to divide the result is consistent. Taraxacum plant achene shape characteristic stable conservative, may carry on the inter-species division and the sibship analysis according to the achene shape characteristic combination difference; the achene morphology cluster analysis as well as the SRAP tagged molecule systematics confirmation support dandelion classification result of "the Chinese flora".

Quantitative imaging of fibrotic and morphological changes in liver of non-alcoholic steatohepatitis (NASH) model mice by second harmonic generation (SHG) and auto-fluorescence (AF) imaging using two-photon excitation microscopy (TPEM).

PubMed

Yamamoto, Shin; Oshima, Yusuke; Saitou, Takashi; Watanabe, Takao; Miyake, Teruki; Yoshida, Osamu; Tokumoto, Yoshio; Abe, Masanori; Matsuura, Bunzo; Hiasa, Yoichi; Imamura, Takeshi

2016-12-01

Non-alcoholic steatohepatitis (NASH) is a common liver disorder caused by fatty liver. Because NASH is associated with fibrotic and morphological changes in liver tissue, a direct imaging technique is required for accurate staging of liver tissue. For this purpose, in this study we took advantage of two label-free optical imaging techniques, second harmonic generation (SHG) and auto-fluorescence (AF), using two-photon excitation microscopy (TPEM). Three-dimensional ex vivo imaging of tissues from NASH model mice, followed by image processing, revealed that SHG and AF are sufficient to quantitatively characterize the hepatic capsule at an early stage and parenchymal morphologies associated with liver disease progression, respectively.

A quantitative study of peculiarities in galaxy morphology

NASA Astrophysics Data System (ADS)

Wu, Katherine Liang-Kai

I have developed a refined version of the asymmetry parameter first presented by Abraham et al. (1996). Coupled with a simple concentration index, this pair of indices, AW-CW, is compared to Abraham et al.'s log(AA)-log(C A) algorithm. These indices are then applied to a large sample of galaxies in the Hubble Deep Field with photometric redshifts from Connolly (1999). This allows investigation of trends at redshifts which have been largely inaccessible until now. The final sample consists of ~350 objects detected by the AW-CW algorithms with first-moment radii, r1 >= 0'.2 (corresponding to F814WAB ~ 26). The distribution of objects in the AW- CW plane is found to change with redshift. The region of the AW - CW plane populated by objects out to z ~ 1.2 is roughly constant. Accounting for bandpass shifting effects, this region resembles that populated by local bright galaxies (Frei et al. 1996) cosmologically simulated at z = 0.8. Beyond z ~ 1.2, the distribution of galaxies undergoes a significant change. Highly concentrated objects disappear from the AW-C W plane, while high asymmetry objects appear. The high concentration objects below z ~ 1.2 all have early-type morphologies. Very low resolution SEDs of these galaxies created using colors from Williams et al. (1996) are used to calculate the expected appearance of these objects at higher redshifts (z = 1.5 and 2.3). Assuming their luminosities and SEDs have not changed, one-third of the z ~ 0.8 objects would be undetected at z = 1.5, and 97% would disappear by z = 2.3. Any true drop in the number density of these objects would be completely masked by such strong selection effects. An increase in the number and degree of asymmetric objects is also seen beyond z ~ 1.2. Many of these objects exhibit multiple condensations, consistent with merging. Though the shifting of the ultraviolet galaxy spectrum into the F814W-band may be partially responsible, the majority of the increase in both number and degree of

Joint analysis of binary and quantitative traits with data sharing and outcome-dependent sampling.

PubMed

Zheng, Gang; Wu, Colin O; Kwak, Minjung; Jiang, Wenhua; Joo, Jungnam; Lima, Joao A C

2012-04-01

We study the analysis of a joint association between a genetic marker with both binary (case-control) and quantitative (continuous) traits, where the quantitative trait values are only available for the cases due to data sharing and outcome-dependent sampling. Data sharing becomes common in genetic association studies, and the outcome-dependent sampling is the consequence of data sharing, under which a phenotype of interest is not measured for some subgroup. The trend test (or Pearson's test) and F-test are often, respectively, used to analyze the binary and quantitative traits. Because of the outcome-dependent sampling, the usual F-test can be applied using the subgroup with the observed quantitative traits. We propose a modified F-test by also incorporating the genotype frequencies of the subgroup whose traits are not observed. Further, a combination of this modified F-test and Pearson's test is proposed by Fisher's combination of their P-values as a joint analysis. Because of the correlation of the two analyses, we propose to use a Gamma (scaled chi-squared) distribution to fit the asymptotic null distribution for the joint analysis. The proposed modified F-test and the joint analysis can also be applied to test single trait association (either binary or quantitative trait). Through simulations, we identify the situations under which the proposed tests are more powerful than the existing ones. Application to a real dataset of rheumatoid arthritis is presented. © 2012 Wiley Periodicals, Inc.

Extracting hurricane eye morphology from spaceborne SAR images using morphological analysis

NASA Astrophysics Data System (ADS)

Lee, Isabella K.; Shamsoddini, Ali; Li, Xiaofeng; Trinder, John C.; Li, Zeyu

2016-07-01

Hurricanes are among the most destructive global natural disasters. Thus recognizing and extracting their morphology is important for understanding their dynamics. Conventional optical sensors, due to cloud cover associated with hurricanes, cannot reveal the intense air-sea interaction occurring at the sea surface. In contrast, the unique capabilities of spaceborne synthetic aperture radar (SAR) data for cloud penetration, and its backscattering signal characteristics enable the extraction of the sea surface roughness. Therefore, SAR images enable the measurement of the size and shape of hurricane eyes, which reveal their evolution and strength. In this study, using six SAR hurricane images, we have developed a mathematical morphology method for automatically extracting the hurricane eyes from C-band SAR data. Skeleton pruning based on discrete skeleton evolution (DSE) was used to ensure global and local preservation of the hurricane eye shape. This distance weighted algorithm applied in a hierarchical structure for extraction of the edges of the hurricane eyes, can effectively avoid segmentation errors by reducing redundant skeletons attributed to speckle noise along the edges of the hurricane eye. As a consequence, the skeleton pruning has been accomplished without deficiencies in the key hurricane eye skeletons. A morphology-based analyses of the subsequent reconstructions of the hurricane eyes shows a high degree of agreement with the hurricane eye areas derived from reference data based on NOAA manual work.

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

ERIC Educational Resources Information Center

Cochran, Beverly; Lunday, Deborah; Miskevich, Frank

2008-01-01

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

Investment appraisal using quantitative risk analysis.

PubMed

Johansson, Henrik

2002-07-01

Investment appraisal concerned with investments in fire safety systems is discussed. Particular attention is directed at evaluating, in terms of the Bayesian decision theory, the risk reduction that investment in a fire safety system involves. It is shown how the monetary value of the change from a building design without any specific fire protection system to one including such a system can be estimated by use of quantitative risk analysis, the results of which are expressed in terms of a Risk-adjusted net present value. This represents the intrinsic monetary value of investing in the fire safety system. The method suggested is exemplified by a case study performed in an Avesta Sheffield factory.

Morphological Variation among Betula nana (diploid), B. pubescens (tetraploid) and their Triploid Hybrids in Iceland

PubMed Central

Thórsson, Æ. Th.; Pálsson, S.; Sigurgeirsson, A.; Anamthawat-Jónsson, K.

2007-01-01

Background and Aims Introgressive hybridization between two co-existing Betula species in Iceland, diploid dwarf birch B. nana and tetraploid downy birch B. pubescens, has been well documented. The two species are highly variable morphologically, making taxonomic delineation difficult despite stable ploidy levels. Here an analysis is made of morphological variation within each ploidy group with an aim to establishing a reliable means to distinguish the species. Methods Plant materials were collected from 14 woodlands in Iceland. The plants were identified based on 2n chromosome numbers. Morphological variation in species-specific characters within each ploidy group was analysed qualitatively and quantitatively. The morphological index was based on eight discrete characters, whereas the multivariate analysis was based on nine leaf variables. Key Results Of the 461 plants examined, 9·5 % were found to be triploid hybrids. The three ploidy groups were morphologically distinguishable but their variation overlapped. The diploid, triploid and tetraploid groups had average scores of 1·3, 4·1 and 8·3, respectively, in the morphology index scale from 0 (B. nana) to 13 (B. pubescens). A linear discriminant analysis also revealed significant separation among the three ploidy groups and the model assigned 96 % and 97 % of the B. nana and B. pubescens individuals correctly. The triploid hybrids were difficult to predict since only half of them could be assigned correctly. Leaf length was the most useful variable identifying triploid hybrids. Geographical patterns within the ploidy groups could partly be explained by differences in mean July temperature. Conclusions Hybridization between B. nana and B. pubescens is widespread in Iceland. The species can be distinguished from each other morphologically, and from the triploid hybrids. The overlapping morphological variation indicates bidirectional introgression between the two species via triploid hybrids. Iceland could be

Portable image analysis system for characterizing aggregate morphology.

DOT National Transportation Integrated Search

2008-01-01

In the last decade, the application of image-based evaluation of particle shape, angularity and texture has been widely researched to characterize aggregate morphology. These efforts have been driven by the knowledge that the morphologic characterist...

Three-dimensional analysis of facial morphology.

PubMed

Liu, Yun; Kau, Chung How; Talbert, Leslie; Pan, Feng

2014-09-01

The objectives of this study were to evaluate sexual dimorphism for facial features within Chinese and African American populations and to compare the facial morphology by sex between these 2 populations. Three-dimensional facial images were acquired by using the portable 3dMDface System, which captured 189 subjects from 2 population groups of Chinese (n = 72) and African American (n = 117). Each population was categorized into male and female groups for evaluation. All subjects in the groups were aged between 18 and 30 years and had no apparent facial anomalies. A total of 23 anthropometric landmarks were identified on the three-dimensional faces of each subject. Twenty-one measurements in 4 regions, including 19 distances and 2 angles, were not only calculated but also compared within and between the Chinese and African American populations. The Student's t-test was used to analyze each data set obtained within each subgroup. Distinct facial differences were presented between the examined subgroups. When comparing the sex differences of facial morphology in the Chinese population, significant differences were noted in 71.43% of the parameters calculated, and the same proportion was found in the African American group. The facial morphologic differences between the Chinese and African American populations were evaluated by sex. The proportion of significant differences in the parameters calculated was 90.48% for females and 95.24% for males between the 2 populations. The African American population had a more convex profile and greater face width than those of the Chinese population. Sexual dimorphism for facial features was presented in both the Chinese and African American populations. In addition, there were significant differences in facial morphology between these 2 populations.

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

PubMed

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

2018-04-01

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

Automated kidney morphology measurements from ultrasound images using texture and edge analysis

NASA Astrophysics Data System (ADS)

Ravishankar, Hariharan; Annangi, Pavan; Washburn, Michael; Lanning, Justin

2016-04-01

In a typical ultrasound scan, a sonographer measures Kidney morphology to assess renal abnormalities. Kidney morphology can also help to discriminate between chronic and acute kidney failure. The caliper placements and volume measurements are often time consuming and an automated solution will help to improve accuracy, repeatability and throughput. In this work, we developed an automated Kidney morphology measurement solution from long axis Ultrasound scans. Automated kidney segmentation is challenging due to wide variability in kidney shape, size, weak contrast of the kidney boundaries and presence of strong edges like diaphragm, fat layers. To address the challenges and be able to accurately localize and detect kidney regions, we present a two-step algorithm that makes use of edge and texture information in combination with anatomical cues. First, we use an edge analysis technique to localize kidney region by matching the edge map with predefined templates. To accurately estimate the kidney morphology, we use textural information in a machine learning algorithm framework using Haar features and Gradient boosting classifier. We have tested the algorithm on 45 unseen cases and the performance against ground truth is measured by computing Dice overlap, % error in major and minor axis of kidney. The algorithm shows successful performance on 80% cases.

Aneurysm Morphology and Prediction of Rupture: An International Study of Unruptured Intracranial Aneurysms Analysis.

PubMed

Mocco, J; Brown, Robert D; Torner, James C; Capuano, Ana W; Fargen, Kyle M; Raghavan, Madhavan L; Piepgras, David G; Meissner, Irene; Huston, John

2018-04-01

There are conflicting data between natural history studies suggesting a very low risk of rupture for small, unruptured intracranial aneurysms and retrospective studies that have identified a much higher frequency of small, ruptured aneurysms than expected. To use the prospective International Study of Unruptured Intracranial Aneurysms cohort to identify morphological characteristics predictive of unruptured intracranial aneurysm rupture. A case-control design was used to analyze morphological characteristics associated with aneurysm rupture in the International Study of Unruptured Intracranial Aneurysms database. Fifty-seven patients with ruptured aneurysms during follow-up were matched (by size and location) with 198 patients with unruptured intracranial aneurysms without rupture during follow-up. Twelve morphological metrics were measured from cerebral angiograms in a blinded fashion. Perpendicular height (P = .008) and size ratio (ratio of maximum diameter to the parent vessel diameter; P = .01) were predictors of aneurysm rupture on univariate analysis. Aspect ratio, daughter sacs, multiple lobes, aneurysm angle, neck diameter, parent vessel diameter, and calculated aneurysm volume were not statistically significant predictors of rupture. On multivariate analysis, perpendicular height was the only significant predictor of rupture (Chi-square 7.1, P-value .008). This study underscores the importance of other morphological factors, such as perpendicular height and size ratio, that may influence unruptured intracranial aneurysm rupture risk in addition to greatest diameter and anterior vs posterior location.

Eurytemora carolleeae in the Laurentian Great Lakes revealed by phylogenetic and morphological analysis

USGS Publications Warehouse

Vasquez, Adrian A.; Hudson, Patrick L.; Fujimoto, Masanori; Keeler, Kevin M.; Armenio, Patricia M.; Ram, Jeffrey L.

2016-01-01

In the Laurentian Great Lakes, specimens of Eurytemora have been reported asEurytemora affinis since its invasion in the late 1950s. During an intensive collection of aquatic invertebrates for morphological and molecular identification in Western Lake Erie in 2012-2013, several specimens of Eurytemora were collected. Analysis of these specimens identified them as the recently described species Eurytemora carolleeaeAlekseev and Souissi 2011. This result led us to assess E. carolleeae’s identifying features, geographic distribution and historical presence in the Laurentian Great Lakes in view of its recent description in 2011. Cytochrome oxidase I (COI) DNA sequences ofEurytemora specimens were identified as closer (2 - 4% different) to recently describedE. carolleeae than to most E. affinis sequences (14% different). Eurytemora from other areas of the Great Lakes and from North American rivers as far west as South Dakota (Missouri River) and east to Delaware (Christina River) also keyed to E. carolleeae. Morphological analysis of archival specimens from 1962 and from all the Great Lakes was identified as E. carolleeae. Additionally, Eurytemora drawings in previous publications were reassessed to determine if the species was E. carolleeae and are reported here. Additional morphological characters that may distinguish North AmericanE. carolleeae from other taxa are also described. We conclude that E. carolleeae is the correct name for the species of Eurytemora that has inhabited the Great Lakes since its invasion, as established by both morphological and COI sequence comparisons to reference keys and sequence databases in present and archival specimens.

Morphology of the ferritin iron core by aberration corrected scanning transmission electron microscopy

NASA Astrophysics Data System (ADS)

Jian, Nan; Dowle, Miriam; Horniblow, Richard D.; Tselepis, Chris; Palmer, Richard E.

2016-11-01

As the major iron storage protein, ferritin stores and releases iron for maintaining the balance of iron in fauna, flora, and bacteria. We present an investigation of the morphology and iron loading of ferritin (from equine spleen) using aberration-corrected high angle annular dark field scanning transmission electron microscopy. Atom counting method, with size selected Au clusters as mass standards, was employed to determine the number of iron atoms in the nanoparticle core of each ferritin protein. Quantitative analysis shows that the nuclearity of iron atoms in the mineral core varies from a few hundred iron atoms to around 5000 atoms. Moreover, a relationship between the iron loading and iron core morphology is established, in which mineral core nucleates from a single nanoparticle, then grows along the protein shell before finally forming either a solid or hollow core structure.

Glioma grading using cell nuclei morphologic features in digital pathology images

NASA Astrophysics Data System (ADS)

Reza, Syed M. S.; Iftekharuddin, Khan M.

2016-03-01

This work proposes a computationally efficient cell nuclei morphologic feature analysis technique to characterize the brain gliomas in tissue slide images. In this work, our contributions are two-fold: 1) obtain an optimized cell nuclei segmentation method based on the pros and cons of the existing techniques in literature, 2) extract representative features by k-mean clustering of nuclei morphologic features to include area, perimeter, eccentricity, and major axis length. This clustering based representative feature extraction avoids shortcomings of extensive tile [1] [2] and nuclear score [3] based methods for brain glioma grading in pathology images. Multilayer perceptron (MLP) is used to classify extracted features into two tumor types: glioblastoma multiforme (GBM) and low grade glioma (LGG). Quantitative scores such as precision, recall, and accuracy are obtained using 66 clinical patients' images from The Cancer Genome Atlas (TCGA) [4] dataset. On an average ~94% accuracy from 10 fold crossvalidation confirms the efficacy of the proposed method.

Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging

NASA Astrophysics Data System (ADS)

Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.

2010-02-01

We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.

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

PubMed

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

2016-07-01

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

[Quantitative Analysis of Heavy Metals in Water with LIBS Based on Signal-to-Background Ratio].

PubMed

Hu, Li; Zhao, Nan-jing; Liu, Wen-qing; Fang, Li; Zhang, Da-hai; Wang, Yin; Meng, De Shuo; Yu, Yang; Ma, Ming-jun

2015-07-01

There are many influence factors in the precision and accuracy of the quantitative analysis with LIBS technology. According to approximately the same characteristics trend of background spectrum and characteristic spectrum along with the change of temperature through in-depth analysis, signal-to-background ratio (S/B) measurement and regression analysis could compensate the spectral line intensity changes caused by system parameters such as laser power, spectral efficiency of receiving. Because the measurement dates were limited and nonlinear, we used support vector machine (SVM) for regression algorithm. The experimental results showed that the method could improve the stability and the accuracy of quantitative analysis of LIBS, and the relative standard deviation and average relative error of test set respectively were 4.7% and 9.5%. Data fitting method based on signal-to-background ratio(S/B) is Less susceptible to matrix elements and background spectrum etc, and provides data processing reference for real-time online LIBS quantitative analysis technology.

Non-invasive microstructure and morphology investigation of the mouse lung: qualitative description and quantitative measurement.

PubMed

Zhang, Lu; Li, Dongyue; Luo, Shuqian

2011-02-25

Early detection of lung cancer is known to improve the chances of successful treatment. However, lungs are soft tissues with complex three-dimensional configuration. Conventional X-ray imaging is based purely on absorption resulting in very low contrast when imaging soft tissues without contrast agents. It is difficult to obtain adequate information of lung lesions from conventional X-ray imaging. In this study, a recently emerged imaging technique, in-line X-ray phase contrast imaging (IL-XPCI) was used. This powerful technique enabled high-resolution investigations of soft tissues without contrast agents. We applied IL-XPCI to observe the lungs in an intact mouse for the purpose of defining quantitatively the micro-structures in lung. The three-dimensional model of the lung was successfully established, which provided an excellent view of lung airways. We highlighted the use of IL-XPCI in the visualization and assessment of alveoli which had rarely been studied in three dimensions (3D). The precise view of individual alveolus was achieved. The morphological parameters, such as diameter and alveolar surface area were measured. These parameters were of great importance in the diagnosis of diseases related to alveolus and alveolar scar. Our results indicated that IL-XPCI had the ability to represent complex anatomical structures in lung. This offered a new perspective on the diagnosis of respiratory disease and may guide future work in the study of respiratory mechanism on the alveoli level.

Mutual information analysis and detection of interictal morphological differences in interictal epileptiform discharges of patients with partial epilepsies.

PubMed

Varma, N K; Kushwaha, R; Beydoun, A; Williams, W J; Drury, I

1997-10-01

The purpose of this paper is to compare the morphological features of interictal epileptiform discharges (IED) in patients with benign epilepsy of childhood with centrotemporal spikes to IED of those with symptomatic localization related epilepsies using information theory. Three patients from each clinical group were selected. Two-second epochs centered at the peak negativity of the sharp waves were analyzed from a referential montage during stage I sleep. The epochs from the two groups were compared using parametric and information theory analysis. Information analysis determined the likelihood of correctly identifying the clinical group based on the IED. Standard parametric, morphological and spectral analyses were also performed. We found no significant difference in the morphology of the sharp wave between the two groups. The after-going slow wave contained the greatest information that separated the two groups. This result was supported by morphological and spectral differences in the after-going slow wave. Greater distinguishing information is held in the after-going slow wave than the sharp wave for the identification of clinical groups. Information analysis may assist in differentiating clinical syndromes from EEG signals.

Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

PubMed

Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

2015-01-01

The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics.

Identification and quantitation of semi-crystalline microplastics using image analysis and differential scanning calorimetry.

PubMed

Rodríguez Chialanza, Mauricio; Sierra, Ignacio; Pérez Parada, Andrés; Fornaro, Laura

2018-06-01

There are several techniques used to analyze microplastics. These are often based on a combination of visual and spectroscopic techniques. Here we introduce an alternative workflow for identification and mass quantitation through a combination of optical microscopy with image analysis (IA) and differential scanning calorimetry (DSC). We studied four synthetic polymers with environmental concern: low and high density polyethylene (LDPE and HDPE, respectively), polypropylene (PP), and polyethylene terephthalate (PET). Selected experiments were conducted to investigate (i) particle characterization and counting procedures based on image analysis with open-source software, (ii) chemical identification of microplastics based on DSC signal processing, (iii) dependence of particle size on DSC signal, and (iv) quantitation of microplastics mass based on DSC signal. We describe the potential and limitations of these techniques to increase reliability for microplastic analysis. Particle size demonstrated to have particular incidence in the qualitative and quantitative performance of DSC signals. Both, identification (based on characteristic onset temperature) and mass quantitation (based on heat flow) showed to be affected by particle size. As a result, a proper sample treatment which includes sieving of suspended particles is particularly required for this analytical approach.

Quantitative refractive index distribution of single cell by combining phase-shifting interferometry and AFM imaging.

PubMed

Zhang, Qinnan; Zhong, Liyun; Tang, Ping; Yuan, Yingjie; Liu, Shengde; Tian, Jindong; Lu, Xiaoxu

2017-05-31

Cell refractive index, an intrinsic optical parameter, is closely correlated with the intracellular mass and concentration. By combining optical phase-shifting interferometry (PSI) and atomic force microscope (AFM) imaging, we constructed a label free, non-invasive and quantitative refractive index of single cell measurement system, in which the accurate phase map of single cell was retrieved with PSI technique and the cell morphology with nanoscale resolution was achieved with AFM imaging. Based on the proposed AFM/PSI system, we achieved quantitative refractive index distributions of single red blood cell and Jurkat cell, respectively. Further, the quantitative change of refractive index distribution during Daunorubicin (DNR)-induced Jurkat cell apoptosis was presented, and then the content changes of intracellular biochemical components were achieved. Importantly, these results were consistent with Raman spectral analysis, indicating that the proposed PSI/AFM based refractive index system is likely to become a useful tool for intracellular biochemical components analysis measurement, and this will facilitate its application for revealing cell structure and pathological state from a new perspective.

Relationship between increasing concentrations of two carcinogens and statistical image descriptors of foci morphology in the cell transformation assay.

PubMed

Callegaro, Giulia; Corvi, Raffaella; Salovaara, Susan; Urani, Chiara; Stefanini, Federico M

2017-06-01

Cell Transformation Assays (CTAs) have long been proposed for the identification of chemical carcinogenicity potential. The endpoint of these in vitro assays is represented by the phenotypic alterations in cultured cells, which are characterized by the change from the non-transformed to the transformed phenotype. Despite the wide fields of application and the numerous advantages of CTAs, their use in regulatory toxicology has been limited in part due to concerns about the subjective nature of visual scoring, i.e. the step in which transformed colonies or foci are evaluated through morphological features. An objective evaluation of morphological features has been previously obtained through automated digital processing of foci images to extract the value of three statistical image descriptors. In this study a further potential of the CTA using BALB/c 3T3 cells is addressed by analysing the effect of increasing concentrations of two known carcinogens, benzo[a]pyrene and NiCl 2 , with different modes of action on foci morphology. The main result of our quantitative evaluation shows that the concentration of the considered carcinogens has an effect on foci morphology that is statistically significant for the mean of two among the three selected descriptors. Statistical significance also corresponds to visual relevance. The statistical analysis of variations in foci morphology due to concentration allowed to quantify morphological changes that can be visually appreciated but not precisely determined. Therefore, it has the potential of providing new quantitative parameters in CTAs, and of exploiting all the information encoded in foci. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea

PubMed Central

2011-01-01

Background Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. Results We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. Conclusions The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our

A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.

PubMed

Geisler, Jonathan H; McGowen, Michael R; Yang, Guang; Gatesy, John

2011-04-25

Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti

A novel image-based quantitative method for the characterization of NETosis

PubMed Central

Zhao, Wenpu; Fogg, Darin K.; Kaplan, Mariana J.

2015-01-01

NETosis is a newly recognized mechanism of programmed neutrophil death. It is characterized by a stepwise progression of chromatin decondensation, membrane rupture, and release of bactericidal DNA-based structures called neutrophil extracellular traps (NETs). Conventional ‘suicidal’ NETosis has been described in pathogenic models of systemic autoimmune disorders. Recent in vivo studies suggest that a process of ‘vital’ NETosis also exists, in which chromatin is condensed and membrane integrity is preserved. Techniques to assess ‘suicidal’ or ‘vital’ NET formation in a specific, quantitative, rapid and semiautomated way have been lacking, hindering the characterization of this process. Here we have developed a new method to simultaneously assess both ‘suicidal’ and ‘vital’ NETosis, using high-speed multi-spectral imaging coupled to morphometric image analysis, to quantify spontaneous NET formation observed ex-vivo or stimulus-induced NET formation triggered in vitro. Use of imaging flow cytometry allows automated, quantitative and rapid analysis of subcellular morphology and texture, and introduces the potential for further investigation using NETosis as a biomarker in pre-clinical and clinical studies. PMID:26003624

Uncertainty in the use of MAMA software to measure particle morphological parameters from SEM images

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

Schwartz, Daniel S.; Tandon, Lav

The MAMA software package developed at LANL is designed to make morphological measurements on a wide variety of digital images of objects. At LANL, we have focused on using MAMA to measure scanning electron microscope (SEM) images of particles, as this is a critical part of our forensic analysis of interdicted radiologic materials. In order to successfully use MAMA to make such measurements, we must understand the level of uncertainty involved in the process, so that we can rigorously support our quantitative conclusions.

Morphological and Genetic Analysis of Four Color Morphs of Bean Leaf Beetle.

PubMed

Tiroesele, Bamphitlhi; Skoda, Steven R; Hunt, Thomas E; Lee, Donald J; Ullah, Muhammad Irfan; Molina-Ochoa, Jaime; Foster, John E

2018-03-01

Bean leaf beetle (BLB), Cerotoma trifurcata (Forster; Coleoptera: Chrysomelidae), exhibits considerable color variation but little is known about the underlying genetic structure and gene flow among color phenotypes. Genetic and morphological variation among four color phenotypes-green with spots (G+S), green without spots (G-S), red with spots (R+S) and red without spots (R-S)-were analyzed using amplified fragment length polymorphisms (AFLP) and morphometrics, respectively. AFLP generated 175 markers that showed ≥80% polymorphism. Analysis of molecular variance (AMOVA) indicated that genetic variation was greatest within phenotypes (82.6-84.0%); gene flow among the four phenotypes was relatively high (Nm = 3.82). The dendrogram and STRUCTURE analysis indicated some population divergence of G-S from the other phenotypes. Morphological parameters were similar among phenotypes except that R+S showed significant differences in weight and body-length. Canonical variables 1 and 2, based on average morphometric characters, accounted for 98% of the total variation; some divergence was indicated between G+S and R+S from each other and from the G-S/R-S BLB color morphs. The pattern of genetic variation indicated potential divergence of G-S and G+S from each other and from R-S and R+S. Although these results indicate that the four different color morphs are not genetically or reproductively isolated, there is some genetic differentiation/structure and morphological dissimilarity suggesting weak/incomplete isolation.

Gender identification of Caspian Terns using external morphology and discriminant function analysis

USGS Publications Warehouse

Ackerman, Joshua T.; Takekawa, John Y.; Bluso, J.D.; Yee, J.L.; Eagles-Smith, Collin A.

2008-01-01

Caspian Tern (Sterna caspia) plumage characteristics are sexually monochromatic and gender cannot easily be distinguished in the field without extensive behavioral observations. We assessed sexual size dimorphism and developed a discriminant function to assign gender in Caspian Terns based on external morphology. We collected and measured Caspian Terns in San Francisco Bay, California, and confirmed their gender based on necropsy and genetic analysis. Of the eight morphological measurements we examined, only bill depth at the gonys and head plus bill length differed between males and females with males being larger than females. A discriminant function using both bill depth at the gonys and head plus bill length accurately assigned gender of 83% of terns for which gender was known. We improved the accuracy of our discriminant function to 90% by excluding individuals that had less than a 75% posterior probability of correctly being assigned to gender. Caspian Terns showed little sexual size dimorphism in many morphometries, but our results indicate they can be reliably assigned to gender in the field using two morphological measurements.

Nanoscale analysis of the morphology and surface stability of calcium carbonate polymorphs

NASA Astrophysics Data System (ADS)

Sekkal, W.; Zaoui, A.

2013-04-01

Under earth surface conditions, in ocean and natural water, calcium carbonate is ubiquitous, forming anhydrous and hydrous minerals. These hydrous phases are of considerable interest for their role as precursors to stable carbonate minerals. Atomistic simulation techniques have been employed here to perform a comprehensive and quantitative study of the structural and energetic stability of dry and hydrous surfaces of calcium carbonate polymorphs using two recently developed forcefields. Results show that the dry forms are prone to ductility; while hydrous phases are found to be brittle. The (001) surface of monohydrocalcite appears to be the most stable (0.99 J/m2) whereas for the ikaite phase, the (001) surface is the most stable. The corresponding value is 0.2 J/m2, i.e. even lower than the surface energy of the Beautiful computed morphology pictures are obtained with Xiao's model and are very similar to the observed SEM images.

Quantitative analysis of fracture surface by roughness and fractal method

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

Li, X.W.; Tian, J.F.; Kang, Y.

1995-09-01

In recent years there has been extensive research and great development in Quantitative Fractography, which acts as an integral part of fractographic analysis. A prominent technique for studying the fracture surface is based on fracture profile generation and the major means for characterizing the profile quantitatively are roughness and fractal methods. By this way, some quantitative indexes such as the roughness parameters R{sub L} for profile and R{sub S} for surface, fractal dimensions D{sub L} for profile and D{sub S} for surface can be measured. Given the relationships between the indexes and the mechanical properties of materials, it is possiblemore » to achieve the goal of protecting materials from fracture. But, as the case stands, the theory and experimental technology of quantitative fractography are still imperfect and remain to be studied further. Recently, Gokhale and Underwood et al have proposed an assumption-free method for estimating the surface roughness by vertically sectioning the fracture surface with sections at an angle of 120 deg with each other, which could be expressed as follows: R{sub S} = {ovr R{sub L}{center_dot}{Psi}} where {Psi} is the profile structure factor. This method is based on the classical sterological principles and verified with the aid of computer simulations for some ruled surfaces. The results are considered to be applicable to fracture surfaces with any arbitrary complexity and anisotropy. In order to extend the detail applications to this method in quantitative fractography, the authors made a study on roughness and fractal methods dependent on this method by performing quantitative measurements on some typical low-temperature impact fractures.« less

Automated analysis of non-mass-enhancing lesions in breast MRI based on morphological, kinetic, and spatio-temporal moments and joint segmentation-motion compensation technique

NASA Astrophysics Data System (ADS)

Hoffmann, Sebastian; Shutler, Jamie D.; Lobbes, Marc; Burgeth, Bernhard; Meyer-Bäse, Anke

2013-12-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) represents an established method for the detection and diagnosis of breast lesions. While mass-like enhancing lesions can be easily categorized according to the Breast Imaging Reporting and Data System (BI-RADS) MRI lexicon, a majority of diagnostically challenging lesions, the so called non-mass-like enhancing lesions, remain both qualitatively as well as quantitatively difficult to analyze. Thus, the evaluation of kinetic and/or morphological characteristics of non-masses represents a challenging task for an automated analysis and is of crucial importance for advancing current computer-aided diagnosis (CAD) systems. Compared to the well-characterized mass-enhancing lesions, non-masses have no well-defined and blurred tumor borders and a kinetic behavior that is not easily generalizable and thus discriminative for malignant and benign non-masses. To overcome these difficulties and pave the way for novel CAD systems for non-masses, we will evaluate several kinetic and morphological descriptors separately and a novel technique, the Zernike velocity moments, to capture the joint spatio-temporal behavior of these lesions, and additionally consider the impact of non-rigid motion compensation on a correct diagnosis.

Morphometric Analysis of Chemoreception Organ in Male and Female Ticks (Acari: Ixodidae).

PubMed

Josek, Tanya; Allan, Brian F; Alleyne, Marianne

2018-05-04

The Haller's organ plays a crucial role in a tick's ability to detect hosts. Even though this sensory organ is vital to tick survival, the morphology of this organ is not well understood. The objective of this study was to characterize variation in the morphological components of the Haller's organ of three medically important tick species using quantitative methods. The Haller's organs of Ixodes scapularis Say (Ixodida: Ixodidae) (black-legged tick), Amblyomma americanum (L.) (Ixodida: Ixodidae) (lone star tick), and Dermacentor variabilis (Say) (Ixodida: Ixodidae) (American dog tick) were morphologically analyzed using environmental scanning electron microscopy and geometric morphometrics, and the results were statistically interpreted using canonical variate analysis. Our data reveal significant, quantitative differences in the morphology of the Haller's organ among all three tick species and that in D. variabilis the sensory structure is sexually dimorphic. Studies like this can serve as a quantitative basis for further studies on sensor physiology, behavior, and tick species life history, potentially leading to novel methods for the prevention of tick-borne disease.

The correlation of sperm morphology with unexplained recurrent spontaneous abortion: A systematic review and meta-analysis

PubMed Central

Cao, Xiaodan; Cui, Yun; Zhang, Xiaoxia; Lou, Jiangtao; Zhou, Jun; Wei, Renxiong

2017-01-01

Sperm morphology displays a potential impact on sperm function and may ultimately impact reproductive function. Current studies have investigated the correlation between sperm morphology with unexplained recurrent spontaneous abortion (RSA) but have shown inconsistent results. Hence, we systematically searched MEDLINE, EMBASE, CNKI databases, as well as the Cochrane Library for studies that examined the association between sperm morphology and unexplained RSA. Fifteen studies were identified, including 883 cases and 530 controls. Our meta-analysis results indicated that the percentage of normal sperm morphology from men with RSA partners was significantly lower than those from normal controls(SMD [95% CI]: − 0.60 [−0.81, −0.40]; P<0.00001) and the percentage of sperm morphologic alterations was significantly higher in patients with RSA compared with the control group (SMD [95% CI]: 0.92 [0.42, 1.43]; P=0.0004). The present study suggested that the percentage of normal sperm morphology may indeed decrease in men from RSA group compared with controls. However, there were some limitations in the study such as the differences in stain techniques and classification criteria. Further evidences are needed to better elucidate the relationship between sperm morphology and unexplained RSA. PMID:28903451

Quantitative analysis of regional myocardial performance in coronary artery disease

NASA Technical Reports Server (NTRS)

Stewart, D. K.; Dodge, H. T.; Frimer, M.

1975-01-01

Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.

Undecalcified temporal bone morphology: a methodology useful for gross to fine observation and three-dimensional reconstruction.

PubMed

Fujiyoshi, T; Mogi, G; Watanabe, T; Matsushita, F

1992-01-01

Using a novel method of cutting undecalcified temporal bone specimens, quantitative structural analysis in the human and the Japanese monkey was undertaken. One millimeter thick serial slices made from unembedded temporal bones retained fine structure. Therefore, gross to fine observation could be performed systematically at the macroscopic, light, scanning, and transmission electron microscopic levels. The entire temporal bone three-dimensional reconstruction was completed from embedded sections; consequently, the volume of the tubotympanum and air cell system could be calculated. Available methods by embedding, tungsten carbide sectioning, grinding, and microwave irradiation for decalcification were also examined. These morphologic studies suggest that these novel methods offer timesaving advantages over any presently available techniques, and allow for elucidation of temporal bone morphology with only a few specimens.

Variable selection based near infrared spectroscopy quantitative and qualitative analysis on wheat wet gluten

NASA Astrophysics Data System (ADS)

Lü, Chengxu; Jiang, Xunpeng; Zhou, Xingfan; Zhang, Yinqiao; Zhang, Naiqian; Wei, Chongfeng; Mao, Wenhua

2017-10-01

Wet gluten is a useful quality indicator for wheat, and short wave near infrared spectroscopy (NIRS) is a high performance technique with the advantage of economic rapid and nondestructive test. To study the feasibility of short wave NIRS analyzing wet gluten directly from wheat seed, 54 representative wheat seed samples were collected and scanned by spectrometer. 8 spectral pretreatment method and genetic algorithm (GA) variable selection method were used to optimize analysis. Both quantitative and qualitative model of wet gluten were built by partial least squares regression and discriminate analysis. For quantitative analysis, normalization is the optimized pretreatment method, 17 wet gluten sensitive variables are selected by GA, and GA model performs a better result than that of all variable model, with R2V=0.88, and RMSEV=1.47. For qualitative analysis, automatic weighted least squares baseline is the optimized pretreatment method, all variable models perform better results than those of GA models. The correct classification rates of 3 class of <24%, 24-30%, >30% wet gluten content are 95.45, 84.52, and 90.00%, respectively. The short wave NIRS technique shows potential for both quantitative and qualitative analysis of wet gluten for wheat seed.

Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR

PubMed Central

Morisset, Dany; Štebih, Dejan; Milavec, Mojca; Gruden, Kristina; Žel, Jana

2013-01-01

In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed. PMID:23658750

Identification among morphologically similar Argyreia (Convolvulaceae) based on leaf anatomy and phenetic analyses.

PubMed

Traiperm, Paweena; Chow, Janene; Nopun, Possathorn; Staples, G; Swangpol, Sasivimon C

2017-12-01

The genus Argyreia Lour. is one of the species-rich Asian genera in the family Convolvulaceae. Several species complexes were recognized in which taxon delimitation was imprecise, especially when examining herbarium materials without fully developed open flowers. The main goal of this study is to investigate and describe leaf anatomy for some morphologically similar Argyreia using epidermal peeling, leaf and petiole transverse sections, and scanning electron microscopy. Phenetic analyses including cluster analysis and principal component analysis were used to investigate the similarity of these morpho-types. Anatomical differences observed between the morpho-types include epidermal cell walls and the trichome types on the leaf epidermis. Additional differences in the leaf and petiole transverse sections include the epidermal cell shape of the adaxial leaf blade, the leaf margins, and the petiole transverse sectional outline. The phenogram from cluster analysis using the UPGMA method represented four groups with an R value of 0.87. Moreover, the important quantitative and qualitative leaf anatomical traits of the four groups were confirmed by the principal component analysis of the first two components. The results from phenetic analyses confirmed the anatomical differentiation between the morpho-types. Leaf anatomical features regarded as particularly informative for morpho-type differentiation can be used to supplement macro morphological identification.

Race and Older Mothers’ Differentiation: A Sequential Quantitative and Qualitative Analysis

PubMed Central

Sechrist, Jori; Suitor, J. Jill; Riffin, Catherine; Taylor-Watson, Kadari; Pillemer, Karl

2011-01-01

The goal of this paper is to demonstrate a process by which qualitative and quantitative approaches are combined to reveal patterns in the data that are unlikely to be detected and confirmed by either method alone. Specifically, we take a sequential approach to combining qualitative and quantitative data to explore race differences in how mothers differentiate among their adult children. We began with a standard multivariate analysis examining race differences in mothers’ differentiation among their adult children regarding emotional closeness and confiding. Finding no race differences in this analysis, we conducted an in-depth comparison of the Black and White mothers’ narratives to determine whether there were underlying patterns that we had been unable to detect in our first analysis. Using this method, we found that Black mothers were substantially more likely than White mothers to emphasize interpersonal relationships within the family when describing differences among their children. In our final step, we developed a measure of familism based on the qualitative data and conducted a multivariate analysis to confirm the patterns revealed by the in-depth comparison of the mother’s narratives. We conclude that using such a sequential mixed methods approach to data analysis has the potential to shed new light on complex family relations. PMID:21967639

Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia)

NASA Astrophysics Data System (ADS)

Stefani, Fabrizio; Benzoni, F.; Yang, S.-Y.; Pichon, M.; Galli, P.; Chen, C. A.

2011-12-01

A combined morphological and genetic study of the coral genus Stylophora investigated species boundaries in the Gulf of Aden, Yemen. Two mitochondrial regions, including the hypervariable IGS9 spacer and the control region, and a fragment of rDNA were used for phylogenetic analysis. Results were compared by multivariate analysis on the basis of branch morphology and corallite morphometry. Two species were clearly discriminated by both approaches. The first species was characterised by small corallites and a low morphological variability and was ascribed to a new geographical record of Stylophora madagascarensis on the basis of its phylogenetic distinction and its morphological similarity to the type material. The second species was characterised by larger corallite size and greater morphological variability and was ascribed to Stylophora pistillata. The analysis was extended to the intrageneric level for other S. pistillata populations from the Red Sea and the Pacific Ocean. Strong internal divergence was evident in the genus Sty lophora. S. pistillata populations were split into two highly divergent Red Sea/Gulf of Aden and western Pacific lineages with significant morphological overlap, which suggests they represent two distinct cryptic species. The combined use of morphological and molecular approaches, so far proved to be a powerful tool for the re-delineation of species boundaries in corals, provided novel evidence of cryptic divergence in this group of marine metazoans.

A thioacidolysis method tailored for higher‐throughput quantitative analysis of lignin monomers

PubMed Central

Foster, Cliff; Happs, Renee M.; Doeppke, Crissa; Meunier, Kristoffer; Gehan, Jackson; Yue, Fengxia; Lu, Fachuang; Davis, Mark F.

2016-01-01

Abstract Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β‐O‐4 linkages. Current thioacidolysis methods are low‐throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non‐chlorinated organic solvent and is tailored for higher‐throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1–2 mg of biomass per assay and has been quantified using fast‐GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, including standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day‐to‐day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. The method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses. PMID:27534715

A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

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

Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.

Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

DOE PAGES

Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.; ...

2016-09-14

Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

QuASAR: quantitative allele-specific analysis of reads.

PubMed

Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-04-15

Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

QuASAR: quantitative allele-specific analysis of reads

PubMed Central

Harvey, Chris T.; Moyerbrailean, Gregory A.; Davis, Gordon O.; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-01-01

Motivation: Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. Results: We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. Availability and implementation: http://github.com/piquelab/QuASAR. Contact: fluca@wayne.edu or rpique@wayne.edu Supplementary information: Supplementary Material is available at Bioinformatics online. PMID:25480375

Morphological diagnostics of star formation in molecular clouds

NASA Astrophysics Data System (ADS)

Beaumont, Christopher Norris

Molecular clouds are the birth sites of all star formation in the present-day universe. They represent the initial conditions of star formation, and are the primary medium by which stars transfer energy and momentum back to parsec scales. Yet, the physical evolution of molecular clouds remains poorly understood. This is not due to a lack of observational data, nor is it due to an inability to simulate the conditions inside molecular clouds. Instead, the physics and structure of the interstellar medium are sufficiently complex that interpreting molecular cloud data is very difficult. This dissertation mitigates this problem, by developing more sophisticated ways to interpret morphological information in molecular cloud observations and simulations. In particular, I have focused on leveraging machine learning techniques to identify physically meaningful substructures in the interstellar medium, as well as techniques to inter-compare molecular cloud simulations to observations. These contributions make it easier to understand the interplay between molecular clouds and star formation. Specific contributions include: new insight about the sheet-like geometry of molecular clouds based on observations of stellar bubbles; a new algorithm to disambiguate overlapping yet morphologically distinct cloud structures; a new perspective on the relationship between molecular cloud column density distributions and the sizes of cloud substructures; a quantitative analysis of how projection effects affect measurements of cloud properties; and an automatically generated, statistically-calibrated catalog of bubbles identified from their infrared morphologies.

Quantitative analysis of NMR spectra with chemometrics

NASA Astrophysics Data System (ADS)

Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

2008-01-01

The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

Thesis Abstract Morphological and phylogeographic analysis of Brazilian tortoises (Testudinidae).

PubMed

Silva, T L; Venancio, L P R; Bonini-Domingos, C R

2015-12-29

distribution of C. carbonarius can partially be explained by the fact that all the morphotypes are considered as a single taxonomic unit. Behavioral aspects such as intraspecific communication may be as reliable as morphological or molecular data for inferring evolutionary relationships. Analysis of the physical characteristics of vocalization [fundamental frequency (Hz), interval between notes (s), duration of each note (s), and number of notes from each vocalization] between C. carbonarius and morphotype 1 revealed statistically significant differences in the interval between notes (s) (P = 0.0000); duration of each note (s) (P = 0.0000); frequency of notes (Hz) (P = 0.0009); and number of notes (P = 0.0002). The results of preference experiments using sound stimulus were inconclusive with respect to species-specific vocalization preference; only females of C. carbonarius showed intraspecific vocalization preference, indicating possible reproductive isolation mechanisms. To explore the presence of sexual dimorphism and morphological differences between C. denticulatus, C. carbonarius, and morphotype 1, descriptive statistics to analyze the data obtained for the investigated measures were used. Two sets of analysis were conducted - the first for each group, to compare the sexes; and the second for each sex, to compare the groups. To examine the interspecific variation in size and shape, a correlation matrix inprincipal component analysis was used. Next, I used factor analysis to rank the features showing >0.75 correlation in the differentiation between the sexes. The results were consistent with the hypothesis that morphotype 1 corresponds to a new species, because it differs from the species pattern in terms of morphology, coloring, and sexual dimorphism. The results of classical cytogenetic analysis - to differentiate C. denticulatus, C. carbonarius, and morphotype 1 - revealed no consistent data that would enable its use as a taxonomic parameter. Conventional Giemsa

A Removal of Eye Movement and Blink Artifacts from EEG Data Using Morphological Component Analysis

PubMed Central

Wagatsuma, Hiroaki

2017-01-01

EEG signals contain a large amount of ocular artifacts with different time-frequency properties mixing together in EEGs of interest. The artifact removal has been substantially dealt with by existing decomposition methods known as PCA and ICA based on the orthogonality of signal vectors or statistical independence of signal components. We focused on the signal morphology and proposed a systematic decomposition method to identify the type of signal components on the basis of sparsity in the time-frequency domain based on Morphological Component Analysis (MCA), which provides a way of reconstruction that guarantees accuracy in reconstruction by using multiple bases in accordance with the concept of “dictionary.” MCA was applied to decompose the real EEG signal and clarified the best combination of dictionaries for this purpose. In our proposed semirealistic biological signal analysis with iEEGs recorded from the brain intracranially, those signals were successfully decomposed into original types by a linear expansion of waveforms, such as redundant transforms: UDWT, DCT, LDCT, DST, and DIRAC. Our result demonstrated that the most suitable combination for EEG data analysis was UDWT, DST, and DIRAC to represent the baseline envelope, multifrequency wave-forms, and spiking activities individually as representative types of EEG morphologies. PMID:28194221

The importance of metadata to assess information content in digital reconstructions of neuronal morphology.

PubMed

Parekh, Ruchi; Armañanzas, Rubén; Ascoli, Giorgio A

2015-04-01

Digital reconstructions of axonal and dendritic arbors provide a powerful representation of neuronal morphology in formats amenable to quantitative analysis, computational modeling, and data mining. Reconstructed files, however, require adequate metadata to identify the appropriate animal species, developmental stage, brain region, and neuron type. Moreover, experimental details about tissue processing, neurite visualization and microscopic imaging are essential to assess the information content of digital morphologies. Typical morphological reconstructions only partially capture the underlying biological reality. Tracings are often limited to certain domains (e.g., dendrites and not axons), may be incomplete due to tissue sectioning, imperfect staining, and limited imaging resolution, or can disregard aspects irrelevant to their specific scientific focus (such as branch thickness or depth). Gauging these factors is critical in subsequent data reuse and comparison. NeuroMorpho.Org is a central repository of reconstructions from many laboratories and experimental conditions. Here, we introduce substantial additions to the existing metadata annotation aimed to describe the completeness of the reconstructed neurons in NeuroMorpho.Org. These expanded metadata form a suitable basis for effective description of neuromorphological data.

Amorphous material of the skin in amyotrophic lateral sclerosis: a morphologic and biochemical study

NASA Technical Reports Server (NTRS)

Ono, S.; Nagao, K.; Yamauchi, M.

1994-01-01

We performed morphologic studies on skin from seven patients with ALS and seven control subjects. By light microscopy, the wide spaces that separated collagen bundles reacted strongly with colloidal iron and alcian blue in ALS patients. Electron microscopy revealed markedly increased amorphous material that was positive for ruthenium red in the ground substance. These findings were not present in controls. Quantitative amino acid analysis showed that the amount of total amino acids (nmoles per mg dry weight) was significantly decreased (p < 0.01) in ALS patients compared with that of controls, and there was a significant negative correlation between skin amino acid content and duration of illness in ALS patients (r = -0.83, p < 0.001). These morphologic findings and biochemical data indicate that the amorphous material, which is markedly increased in ALS skin, includes glycosaminoglycans.

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis.

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches.

Character analysis and the integration of molecular and morphological data in an understanding of sand dollar phylogeny.

PubMed

Marshall, C R

1992-03-01

Reconciling discordant morphological and molecular phylogenies remains a problem in modern systematics. By examining conflicting DNA-hybridization and morphological phylogenies of sand dollars, I show that morphological criteria may be used to help evaluate the reliability of molecular phylogenies where they differ from morphological trees. All available criteria for assessing the reliability of DNA-hybridization phylogenies suggest that the sand dollar DNA-hybridization phylogeny is robust. Standard homology-recognition criteria are used to assess the a priori reliabilities of the morphological attributes associated with the node drawn into question by the DNA data, and it is shown that these attributes are among the least phylogenetically informative of all the morphological characters. Moreover, the questioned node has the smallest number of supporting characters, and most of these characters are associated with the food grooves, which suggests that they may be functionally correlated. Thus, on the basis of the analysis of the morphological data and given the robustness of the DNA tree, the DNA phylogeny is preferred. Further, paleobiogeographic data support the DNA tree rather than the morphological tree, and a plausible heterochronic mechanism has been proposed that may account for the homoplasious morphological evolution that must have occurred if the DNA tree is correct.

Low-dose CT for quantitative analysis in acute respiratory distress syndrome

PubMed Central

2013-01-01

Introduction The clinical use of serial quantitative computed tomography (CT) to characterize lung disease and guide the optimization of mechanical ventilation in patients with acute respiratory distress syndrome (ARDS) is limited by the risk of cumulative radiation exposure and by the difficulties and risks related to transferring patients to the CT room. We evaluated the effects of tube current-time product (mAs) variations on quantitative results in healthy lungs and in experimental ARDS in order to support the use of low-dose CT for quantitative analysis. Methods In 14 sheep chest CT was performed at baseline and after the induction of ARDS via intravenous oleic acid injection. For each CT session, two consecutive scans were obtained applying two different mAs: 60 mAs was paired with 140, 15 or 7.5 mAs. All other CT parameters were kept unaltered (tube voltage 120 kVp, collimation 32 × 0.5 mm, pitch 0.85, matrix 512 × 512, pixel size 0.625 × 0.625 mm). Quantitative results obtained at different mAs were compared via Bland-Altman analysis. Results Good agreement was observed between 60 mAs and 140 mAs and between 60 mAs and 15 mAs (all biases less than 1%). A further reduction of mAs to 7.5 mAs caused an increase in the bias of poorly aerated and nonaerated tissue (-2.9% and 2.4%, respectively) and determined a significant widening of the limits of agreement for the same compartments (-10.5% to 4.8% for poorly aerated tissue and -5.9% to 10.8% for nonaerated tissue). Estimated mean effective dose at 140, 60, 15 and 7.5 mAs corresponded to 17.8, 7.4, 2.0 and 0.9 mSv, respectively. Image noise of scans performed at 140, 60, 15 and 7.5 mAs corresponded to 10, 16, 38 and 74 Hounsfield units, respectively. Conclusions A reduction of effective dose up to 70% has been achieved with minimal effects on lung quantitative results. Low-dose computed tomography provides accurate quantitative results and could be used to characterize lung compartment distribution and

Morphological imaging and quantification of axial xylem tissue in Fraxinus excelsior L. through X-ray micro-computed tomography.

PubMed

Koddenberg, Tim; Militz, Holger

2018-05-05

The popularity of X-ray based imaging methods has continued to increase in research domains. In wood research, X-ray micro-computed tomography (XμCT) is useful for structural studies examining the three-dimensional and complex xylem tissue of trees qualitatively and quantitatively. In this study, XμCT made it possible to visualize and quantify the spatial xylem organization of the angiosperm species Fraxinus excelsior L. on the microscopic level. Through image analysis, it was possible to determine morphological characteristics of the cellular axial tissue (vessel elements, fibers, and axial parenchyma cells) three-dimensionally. X-ray imaging at high resolutions provides very distinct visual insight into the xylem structure. Numerical analyses performed through semi-automatic procedures made it possible to quickly quantify cell characteristics (length, diameter, and volume of cells). Use of various spatial resolutions (0.87-5 μm) revealed boundaries users should be aware of. Nevertheless, our findings, both qualitative and quantitative, demonstrate XμCT to be a valuable tool for studying the spatial cell morphology of F. excelsior. Copyright © 2018. Published by Elsevier Ltd.

Selection of reference genes for quantitative real-time RT-PCR assays in different morphological forms of dimorphic zygomycetous fungus Benjaminiella poitrasii.

PubMed

Pathan, Ejaj K; Ghormade, Vandana; Deshpande, Mukund V

2017-01-01

Benjaminiella poitrasii, a dimorphic non-pathogenic zygomycetous fungus, exhibits a morphological yeast (Y) to hypha (H) reversible transition in the vegetative phase, sporangiospores (S) in the asexual phase and zygospores (Z) in the sexual phase. To study the gene expression across these diverse morphological forms, suitable reference genes are required. In the present study, 13 genes viz. ACT, 18S rRNA, eEF1α, eEF-Tu,eIF-1A, Tub-α, Tub-b, Ubc, GAPDH, Try, WS-21, NADGDH and NADPGDH were evaluated for their potential as a reference, particularly for studying gene expression during the Y-H reversible transition and also for other asexual and sexual life stages of B. poitrasii. Analysis of RT-qPCR data using geNorm, normFinder and BestKeeper software revealed that genes such as Ubc, 18S rRNA and WS-21 were expressed at constant levels in each given subset of RNA samples from all the morphological phases of B. poitrasii. Therefore, these reference genes can be used to elucidate the role of morpho-genes in B. poitrasii. Further, use of the two most stably expressed genes (Ubc and WS-21) to normalize the expression of the ornithine decarboxylase gene (Bpodc) in different morphological forms of B. poitrasii, generated more reliable results, indicating that our selection of reference genes was appropriate.

Selective Weighted Least Squares Method for Fourier Transform Infrared Quantitative Analysis.

PubMed

Wang, Xin; Li, Yan; Wei, Haoyun; Chen, Xia

2017-06-01

Classical least squares (CLS) regression is a popular multivariate statistical method used frequently for quantitative analysis using Fourier transform infrared (FT-IR) spectrometry. Classical least squares provides the best unbiased estimator for uncorrelated residual errors with zero mean and equal variance. However, the noise in FT-IR spectra, which accounts for a large portion of the residual errors, is heteroscedastic. Thus, if this noise with zero mean dominates in the residual errors, the weighted least squares (WLS) regression method described in this paper is a better estimator than CLS. However, if bias errors, such as the residual baseline error, are significant, WLS may perform worse than CLS. In this paper, we compare the effect of noise and bias error in using CLS and WLS in quantitative analysis. Results indicated that for wavenumbers with low absorbance, the bias error significantly affected the error, such that the performance of CLS is better than that of WLS. However, for wavenumbers with high absorbance, the noise significantly affected the error, and WLS proves to be better than CLS. Thus, we propose a selective weighted least squares (SWLS) regression that processes data with different wavenumbers using either CLS or WLS based on a selection criterion, i.e., lower or higher than an absorbance threshold. The effects of various factors on the optimal threshold value (OTV) for SWLS have been studied through numerical simulations. These studies reported that: (1) the concentration and the analyte type had minimal effect on OTV; and (2) the major factor that influences OTV is the ratio between the bias error and the standard deviation of the noise. The last part of this paper is dedicated to quantitative analysis of methane gas spectra, and methane/toluene mixtures gas spectra as measured using FT-IR spectrometry and CLS, WLS, and SWLS. The standard error of prediction (SEP), bias of prediction (bias), and the residual sum of squares of the errors

Quantitative analysis of rib movement based on dynamic chest bone images: preliminary results

NASA Astrophysics Data System (ADS)

Tanaka, R.; Sanada, S.; Oda, M.; Mitsutaka, M.; Suzuki, K.; Sakuta, K.; Kawashima, H.

2014-03-01

Rib movement during respiration is one of the diagnostic criteria in pulmonary impairments. In general, the rib movement is assessed in fluoroscopy. However, the shadows of lung vessels and bronchi overlapping ribs prevent accurate quantitative analysis of rib movement. Recently, an image-processing technique for separating bones from soft tissue in static chest radiographs, called "bone suppression technique", has been developed. Our purpose in this study was to evaluate the usefulness of dynamic bone images created by the bone suppression technique in quantitative analysis of rib movement. Dynamic chest radiographs of 10 patients were obtained using a dynamic flat-panel detector (FPD). Bone suppression technique based on a massive-training artificial neural network (MTANN) was applied to the dynamic chest images to create bone images. Velocity vectors were measured in local areas on the dynamic bone images, which formed a map. The velocity maps obtained with bone and original images for scoliosis and normal cases were compared to assess the advantages of bone images. With dynamic bone images, we were able to quantify and distinguish movements of ribs from those of other lung structures accurately. Limited rib movements of scoliosis patients appeared as reduced rib velocity vectors. Vector maps in all normal cases exhibited left-right symmetric distributions, whereas those in abnormal cases showed nonuniform distributions. In conclusion, dynamic bone images were useful for accurate quantitative analysis of rib movements: Limited rib movements were indicated as a reduction of rib movement and left-right asymmetric distribution on vector maps. Thus, dynamic bone images can be a new diagnostic tool for quantitative analysis of rib movements without additional radiation dose.

Retinal ganglion cells in the eastern newt Notophthalmus viridescens: topography, morphology, and diversity.

PubMed

Pushchin, Igor I; Karetin, Yuriy A

2009-10-20

The topography and morphology of retinal ganglion cells (RGCs) in the eastern newt were studied. Cells were retrogradely labeled with tetramethylrhodamine-conjugated dextran amines or horseradish peroxidase and examined in retinal wholemounts. Their total number was 18,025 +/- 3,602 (mean +/- SEM). The spatial density of RGCs varied from 2,100 cells/mm(2) in the retinal periphery to 4,500 cells/mm(2) in the dorsotemporal retina. No prominent retinal specializations were found. The spatial resolution estimated from the spatial density of RGCs varied from 1.4 cycles per degree in the periphery to 1.95 cycles per degree in the region of the peak RGC density. A sample of 68 cells was camera lucida drawn and subjected to quantitative analysis. A total of 21 parameters related to RGC morphology and stratification in the retina were estimated. Partitionings obtained by using different clustering algorithms combined with automatic variable weighting and dimensionality reduction techniques were compared, and an effective solution was found by using silhouette analysis. A total of seven clusters were identified and associated with potential cell types. Kruskal-Wallis ANOVA-on-Ranks with post hoc Mann-Whitney U tests showed significant pairwise between-cluster differences in one or more of the clustering variables. The average silhouette values of the clusters were reasonably high, ranging from 0.52 to 0.79. Cells assigned to the same cluster displayed similar morphology and stratification in the retina. The advantages and limitations of the methodology adopted are discussed. The present classification is compared with known morphological and physiological RGC classifications in other salamanders.

Quantitative analysis of multiple sclerosis: a feasibility study

NASA Astrophysics Data System (ADS)

Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

2006-03-01

Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

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

Zhou, Jian-Ying; Chen, Lijun; Zhang, Bai

The identification of protein biomarkers requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics strategy using one channel for universal normalization across all samples. A total of 307 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 107 one-dimensional (1D) LC-MS/MS datasets and 8 offline two-dimensional (2D) LC-MS/MS datasets (25 fractions for each set) for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assessmore » the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we developed a quantification confidence score based on the quality of each peptide-spectrum match (PSM) to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS datasets collected over a 16 month period.« less

Morphological and molecular analysis of the collagen fibers in inflammatory process

NASA Astrophysics Data System (ADS)

de Carvalho, Luis Felipe das Chagas e. Silva; Alves, Mônica Ghislaine Oliveira; Soares, Carlos Alexandre; Almeida, Janete Dias; da Silva Martinho, Herculano

2011-07-01

Collagen makes up one third of the total protein in humans, being formed by the connection of three polypeptide chains arranged in a triple helix. This protein has fundamental importance in the formation of extracellular matrix of connective tissue. This study aimed to analyze the structural changes of collagen, which are resulting from inflammatory processes in oral mucosa, and to make the comparative analysis between the histopathology and the Raman spectra. The samples of tissues with inflammatory fibrous hyperplasia (IFH) and normal mucosa (NM) were evaluated by Raman Spectroscopy, hematoxylin-eosin and Massons trichrome stain. The histological analysis in both stains showed differences in collagen fibers, which was presented as thin fibers and arranged in parallel direction in NM and as collagen fibers are thick, mature and not organized, showing that these types of stain show morphological changes of collagen in IFH. The Raman Spectroscopy discriminate the groups of NM and IFH based on vibrational modes of proline, hydroxiproline and CH3, CH2. The histological stains only shows information from morphological data, and can be complemented by Raman spectra. This technique could demonstrate that inflammatory process caused some changes in collagen structure which is related to aminoacids such as proline and hidroxyproline.

Quantitative gene expression deregulation in mantle-cell lymphoma: correlation with clinical and biologic factors.

PubMed

Kienle, Dirk; Katzenberger, Tiemo; Ott, German; Saupe, Doreen; Benner, Axel; Kohlhammer, Holger; Barth, Thomas F E; Höller, Sylvia; Kalla, Jörg; Rosenwald, Andreas; Müller-Hermelink, Hans Konrad; Möller, Peter; Lichter, Peter; Döhner, Hartmut; Stilgenbauer, Stephan

2007-07-01

There is evidence for a direct role of quantitative gene expression deregulation in mantle-cell lymphoma (MCL) pathogenesis. Our aim was to investigate gene expression associations with other pathogenic factors and the significance of gene expression in a multivariate survival analysis. Quantitative expression of 20 genes of potential relevance for MCL prognosis and pathogenesis were analyzed using real-time reverse transcriptase polymerase chain reaction and correlated with clinical and genetic factors, tumor morphology, and Ki-67 index in 65 MCL samples. Genomic losses at the loci of TP53, RB1, and P16 were associated with reduced transcript levels of the respective genes, indicating a gene-dosage effect as the pathomechanism. Analysis of gene expression correlations between the candidate genes revealed a separation into two clusters, one dominated by proliferation activators, another by proliferation inhibitors and regulators of apoptosis. Whereas only weak associations were identified between gene expression and clinical parameters or blastoid morphology, several genes were correlated closely with the Ki-67 index, including the short CCND1 variant (positive correlation) and RB1, ATM, P27, and BMI (negative correlation). In multivariate survival analysis, expression levels of MYC, MDM2, EZH2, and CCND1 were the strongest prognostic factors independently of tumor proliferation and clinical factors. These results indicate a pathogenic contribution of several gene transcript levels to the biology and clinical course of MCL. Genes can be differentiated into factors contributing to proliferation deregulation, either by enhancement or loss of inhibition, and proliferation-independent factors potentially contributing to MCL pathogenesis by apoptosis impairment.

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

DOE PAGES

Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

2015-08-14

Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically,more » the presence of C π...C πinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.« less

Nanoscale analysis of the morphology and surface stability of calcium carbonate polymorphs

PubMed Central

Sekkal, W.; Zaoui, A.

2013-01-01

Under earth surface conditions, in ocean and natural water, calcium carbonate is ubiquitous, forming anhydrous and hydrous minerals. These hydrous phases are of considerable interest for their role as precursors to stable carbonate minerals. Atomistic simulation techniques have been employed here to perform a comprehensive and quantitative study of the structural and energetic stability of dry and hydrous surfaces of calcium carbonate polymorphs using two recently developed forcefields. Results show that the dry forms are prone to ductility; while hydrous phases are found to be brittle. The (001) surface of monohydrocalcite appears to be the most stable (0.99 J/m2) whereas for the ikaite phase, the (001) surface is the most stable. The corresponding value is 0.2 J/m2, i.e. even lower than the surface energy of the Beautiful computed morphology pictures are obtained with Xiao's model and are very similar to the observed SEM images. PMID:23545842

Nanoscale analysis of the morphology and surface stability of calcium carbonate polymorphs.

PubMed

Sekkal, W; Zaoui, A

2013-01-01

Under earth surface conditions, in ocean and natural water, calcium carbonate is ubiquitous, forming anhydrous and hydrous minerals. These hydrous phases are of considerable interest for their role as precursors to stable carbonate minerals. Atomistic simulation techniques have been employed here to perform a comprehensive and quantitative study of the structural and energetic stability of dry and hydrous surfaces of calcium carbonate polymorphs using two recently developed forcefields. Results show that the dry forms are prone to ductility; while hydrous phases are found to be brittle. The (001) surface of monohydrocalcite appears to be the most stable (0.99 J/m(2)) whereas for the ikaite phase, the (001) surface is the most stable. The corresponding value is 0.2 J/m(2), i.e. even lower than the surface energy of the Beautiful computed morphology pictures are obtained with Xiao's model and are very similar to the observed SEM images.