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.

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.

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.

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.

Prospective in (Primate) Dental Analysis through Tooth 3D Topographical Quantification

PubMed Central

Guy, Franck; Gouvard, Florent; Boistel, Renaud; Euriat, Adelaïde; Lazzari, Vincent

2013-01-01

The occlusal morphology of the teeth is mostly determined by the enamel-dentine junction morphology; the enamel-dentine junction plays the role of a primer and conditions the formation of the occlusal enamel reliefs. However, the accretion of the enamel cap yields thickness variations that alter the morphology and the topography of the enamel–dentine junction (i.e., the differential deposition of enamel by the ameloblasts create an external surface that does not necessarily perfectly parallel the enamel–dentine junction). This self-reliant influence of the enamel on tooth morphology is poorly understood and still under-investigated. Studies considering the relationship between enamel and dentine morphologies are rare, and none of them tackled this relationship in a quantitative way. Major limitations arose from: (1) the difficulties to characterize the tooth morphology in its comprehensive tridimensional aspect and (2) practical issues in relating enamel and enamel–dentine junction quantitative traits. We present new aspects of form representation based exclusively on 3D analytical tools and procedures. Our method is applied to a set of 21 unworn upper second molars belonging to eight extant anthropoid genera. Using geometrical analysis of polygonal meshes representatives of the tooth form, we propose a 3D dataset that constitutes a detailed characterization of the enamel and of the enamel–dentine junction morphologies. Also, for the first time, to our knowledge, we intend to establish a quantitative method for comparing enamel and enamel–dentine junction surfaces descriptors (elevation, inclination, orientation, etc.). New indices that allow characterizing the occlusal morphology are proposed and discussed. In this note, we present technical aspects of our method with the example of anthropoid molars. First results show notable individual variations and taxonomic heterogeneities for the selected topographic parameters and for the pattern and strength of association between enamel–dentine junction and enamel, the enamel cap altering in different ways the “transcription” of the enamel–dentine junction morphology. PMID:23826088

A Quantitative Approach to Scar Analysis

PubMed Central

Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

2011-01-01

Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology. PMID:21281794

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...

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.

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.

[The application of stereology in radiology imaging and cell biology fields].

PubMed

Hu, Na; Wang, Yan; Feng, Yuanming; Lin, Wang

2012-08-01

Stereology is an interdisciplinary method for 3D morphological study developed from mathematics and morphology. It is widely used in medical image analysis and cell biology studies. Because of its unbiased, simple, fast, reliable and non-invasive characteristics, stereology has been widely used in biomedical areas for quantitative analysis and statistics, such as histology, pathology and medical imaging. Because the stereological parameters show distinct differences in different pathology, many scholars use stereological methods to do quantitative analysis in their studies in recent years, for example, in the areas of the condition of cancer cells, tumor grade, disease development and the patient's prognosis, etc. This paper describes the stereological concept and estimation methods, also illustrates the applications of stereology in the fields of CT images, MRI images and cell biology, and finally reflects the universality, the superiority and reliability of stereology.

Quantitative Morphology Measures in Galaxies: Ground-Truthing from Simulations

NASA Astrophysics Data System (ADS)

Narayanan, Desika T.; Abruzzo, Matthew W.; Dave, Romeel; Thompson, Robert

2017-01-01

The process of galaxy assembly is a prevalent question in astronomy; there are a variety of potentially important effects, including baryonic accretion from the intergalactic medium, as well as major galaxy mergers. Recent years have ushered in the development of quantitative measures of morphology such as the Gini coefficient (G), the second-order moment of the brightest quintile of a galaxy’s light (M20), and the concentration (C), asymmetry (A), and clumpiness (S) of galaxies. To investigate the efficacy of these observational methods at identifying major mergers, we have run a series of very high resolution cosmological zoom simulations, and coupled these with 3D Monte Carlo dust radiative transfer. Our methodology is powerful in that it allows us to “observe” the simulation as an observer would, while maintaining detailed knowledge of the true merger history of the galaxy. In this presentation, we will present our main results from our analysis of these quantitative morphology measures, with a particular focus on high-redshift (z>2) systems.

Decoupled form and function in disparate herbivorous dinosaur clades

NASA Astrophysics Data System (ADS)

Lautenschlager, Stephan; Brassey, Charlotte A.; Button, David J.; Barrett, Paul M.

2016-05-01

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

Decoupled form and function in disparate herbivorous dinosaur clades.

PubMed

Lautenschlager, Stephan; Brassey, Charlotte A; Button, David J; Barrett, Paul M

2016-05-20

Convergent evolution, the acquisition of morphologically similar traits in unrelated taxa due to similar functional demands or environmental factors, is a common phenomenon in the animal kingdom. Consequently, the occurrence of similar form is used routinely to address fundamental questions in morphofunctional research and to infer function in fossils. However, such qualitative assessments can be misleading and it is essential to test form/function relationships quantitatively. The parallel occurrence of a suite of morphologically convergent craniodental characteristics in three herbivorous, phylogenetically disparate dinosaur clades (Sauropodomorpha, Ornithischia, Theropoda) provides an ideal test case. A combination of computational biomechanical models (Finite Element Analysis, Multibody Dynamics Analysis) demonstrate that despite a high degree of morphological similarity between representative taxa (Plateosaurus engelhardti, Stegosaurus stenops, Erlikosaurus andrewsi) from these clades, their biomechanical behaviours are notably different and difficult to predict on the basis of form alone. These functional differences likely reflect dietary specialisations, demonstrating the value of quantitative biomechanical approaches when evaluating form/function relationships in extinct taxa.

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

PubMed

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

2018-06-18

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

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

Procedures for analysis of debris relative to Space Shuttle systems

NASA Technical Reports Server (NTRS)

Kim, Hae Soo; Cummings, Virginia J.

1993-01-01

Debris samples collected from various Space Shuttle systems have been submitted to the Microchemical Analysis Branch. This investigation was initiated to develop optimal techniques for the analysis of debris. Optical microscopy provides information about the morphology and size of crystallites, particle sizes, amorphous phases, glass phases, and poorly crystallized materials. Scanning electron microscopy with energy dispersive spectrometry is utilized for information on surface morphology and qualitative elemental content of debris. Analytical electron microscopy with wavelength dispersive spectrometry provides information on the quantitative elemental content of debris.

Quantitative 3D Analysis of Nuclear Morphology and Heterochromatin Organization from Whole-Mount Plant Tissue Using NucleusJ.

PubMed

Desset, Sophie; Poulet, Axel; Tatout, Christophe

2018-01-01

Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context. Here, we describe a whole mount tissue preparation procedure coupled to DNA staining using the PicoGreen ® intercalating agent suitable for image analysis of the nucleus in living and fixed tissues. 3D Image analysis is then performed using NucleusJ, an open source ImageJ plugin, which allows for quantifying variations in nuclear morphology such as nuclear volume, sphericity, elongation, and flatness as well as in heterochromatin content and position in respect to the nuclear periphery.

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.

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.

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.

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.

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.

Phenotype classification of single cells using SRS microscopy, RNA sequencing, and microfluidics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Streets, Aaron M.; Cao, Chen; Zhang, Xiannian; Huang, Yanyi

2016-03-01

Phenotype classification of single cells reveals biological variation that is masked in ensemble measurement. This heterogeneity is found in gene and protein expression as well as in cell morphology. Many techniques are available to probe phenotypic heterogeneity at the single cell level, for example quantitative imaging and single-cell RNA sequencing, but it is difficult to perform multiple assays on the same single cell. In order to directly track correlation between morphology and gene expression at the single cell level, we developed a microfluidic platform for quantitative coherent Raman imaging and immediate RNA sequencing (RNA-Seq) of single cells. With this device we actively sort and trap cells for analysis with stimulated Raman scattering microscopy (SRS). The cells are then processed in parallel pipelines for lysis, and preparation of cDNA for high-throughput transcriptome sequencing. SRS microscopy offers three-dimensional imaging with chemical specificity for quantitative analysis of protein and lipid distribution in single cells. Meanwhile, the microfluidic platform facilitates single-cell manipulation, minimizes contamination, and furthermore, provides improved RNA-Seq detection sensitivity and measurement precision, which is necessary for differentiating biological variability from technical noise. By combining coherent Raman microscopy with RNA sequencing, we can better understand the relationship between cellular morphology and gene expression at the single-cell level.

The use of optical coherence tomography to analyze the efficacy of skin care products

NASA Astrophysics Data System (ADS)

Irani, Sarosh; Turani, Zahra; Fotouhi, Audrey; Daveluy, Steven; Mehregan, Darius; Chen, Wei; Gelovani, Juri; Nasiriavanaki, Mohammadreza

2018-02-01

In this study, we assess the applicability of optical coherence tomography (OCT) for non-invasive imaging of skin morphology for the assessment of efficacy of cosmetic skin wrinkle-reduction products in humans. Evaluation of skin care products for reduction of facial wrinkles is largely limited to photographic (non-quantitative) comparison of skin surface texture before and after either single or prolonged application of skin care product. OCT could be a technique for monitoring changes in cross-sectional skin morphology. An optical attenuation coefficient analysis is also carried out to quantitatively study the changes in different layers of the skin.

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.

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, Inc.

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

PubMed

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

2016-04-01

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

Reshaping Plant Biology: Qualitative and Quantitative Descriptors for Plant Morphology

PubMed Central

Balduzzi, Mathilde; Binder, Brad M.; Bucksch, Alexander; Chang, Cynthia; Hong, Lilan; Iyer-Pascuzzi, Anjali S.; Pradal, Christophe; Sparks, Erin E.

2017-01-01

An emerging challenge in plant biology is to develop qualitative and quantitative measures to describe the appearance of plants through the integration of mathematics and biology. A major hurdle in developing these metrics is finding common terminology across fields. In this review, we define approaches for analyzing plant geometry, topology, and shape, and provide examples for how these terms have been and can be applied to plants. In leaf morphological quantifications both geometry and shape have been used to gain insight into leaf function and evolution. For the analysis of cell growth and expansion, we highlight the utility of geometric descriptors for understanding sepal and hypocotyl development. For branched structures, we describe how topology has been applied to quantify root system architecture to lend insight into root function. Lastly, we discuss the importance of using morphological descriptors in ecology to assess how communities interact, function, and respond within different environments. This review aims to provide a basic description of the mathematical principles underlying morphological quantifications. PMID:28217137

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.

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.

Morphometric analysis of a fresh simple crater on the Moon.

NASA Astrophysics Data System (ADS)

Vivaldi, V.; Ninfo, A.; Massironi, M.; Martellato, E.; Cremonese, G.

In this research we are proposing an innovative method to determine and quantify the morphology of a simple fresh impact crater. Linné is a well preserved impact crater of 2.2 km in diameter, located at 27.7oN 11.8oE, near the western edge of Mare Serenitatis on the Moon. The crater was photographed by the Lunar Orbiter and the Apollo space missions. Its particular morphology may place Linné as the most striking example of small fresh simple crater. Morphometric analysis, conducted on recent high resolution DTM from LROC (NASA), quantitatively confirmed the pristine morphology of the crater, revealing a clear inner layering which highlight a sequence of lava emplacement events.

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

PubMed Central

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

2016-01-01

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

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 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

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.

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 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

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).

The gastro-esophageal reflux barrier: biophysical analysis on 3D models of anatomy from magnetic resonance imaging.

PubMed

Roy, S; Fox, M R; Curcic, J; Schwizer, W; Pal, A

2012-07-01

The function and structure of the gastro-esophageal junction (GEJ) determine its efficacy as a reflux barrier. This study presents a novel methodology for the quantitative assessment of GEJ and proximal gastric morphology from magnetic resonance (MR) imaging. Based on this data we propose a new conceptualization of the hypothesis that a flap valve mechanism contributes to reflux protection. 3D models of the GEJ and proximal stomach were reconstructed from MR images in 12 healthy volunteers during respiration and on eating a test meal to maximum satiation. A rotating plane analysis measured the gastro-esophageal insertion angle and span of contact. An ellipsoid fit provided quantitative assessment of gastric shape and orientation relative to a fixed anatomical reference point. Position of the esophageal insertion on the 'gastric ellipse' was noted. An ellipsoid-cylinder model was designed to analyze the relationships among parameters describing the GEJ morphology. The insertion angle became more acute on expiration, but did not change with meal ingestion. In contrast the span of contact did not vary with respiration, but increased with gastric filling. Changes in gastric morphology with distension further augmented the span of gastro-esophageal contact in almost 70% of the studies. Novel MR imaging and biophysical analysis of the GEJ and proximal stomach provide a quantitative description of structures contributing to the reflux barrier. Changes in these parameters during respiration and on eating support the hypothesis that structural components of a functional 'flap valve' like mechanism contribute to reflux protection. © 2012 Blackwell Publishing Ltd.

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

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

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.

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 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.

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.

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).

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

Chuang, Chihpin; Singh, Dileep; Kenesei, Peter

The size and morphology of the graphite particles play a crucial role in determining various mechanical and thermal properties of cast iron. In the present study, we utilized high-energy synchrotron X-ray tomography to perform quantitative 3D-characterization of the distribution of graphite particles in high-strength compacted graphite iron (CGI). The size, shape, and spatial connectivity of graphite were examined. The analysis reveals that the compacted graphite can grow with a coral-tree-like morphology and span several hundred microns in the iron matrix.

Analysis of the variation in low-level laser energy density on the crushed sciatic nerves of rats: a morphological, quantitative, and morphometric study.

PubMed

Ziago, Eduardo Keiske Mastuda; Fazan, Valéria Paula Sassoli; Iyomasa, Mamie Mizusaki; Sousa, Luiz Gustavo; Yamauchi, Paula Yumi; da Silva, Eunice Aparecida; Borie, Eduardo; Fuentes, Ramón; Dias, Fernando José

2017-02-01

The objective of this study was to evaluate three energy densities of low-level laser therapy (LLLT, GaAlAs, 780 nm, 40 mW, 0.04 cm 2 ) for the treatment of lesions to peripheral nerves using the sciatic nerve of rats injured via crushing model (15 kgf, 5.2 MPa). Thirty Wistar rats (♂, 200-250 g) were divided into five groups (n = 6): C-control, not injured, and irradiated; L0-injured nerve without irradiation; L4-injured nerve irradiated with LLLT 4 J/cm 2 (0.16 J); L10-injured nerve irradiated with LLLT 10 J/cm 2 (0.4 J); and L50-injured nerve irradiated with LLLT 50 J/cm 2 (2 J). The animals were sacrificed 2 weeks after the injury via perfusion with glutaraldehyde (2.5%, 0.1 M sodium cacodylate buffer). The nerve tissue was embedded in historesin, cut (3 μm), mounted on slides, and stained (Sudan black and neutral red). The morphological and quantitative analysis (myelin and blood capillary densities) and morphometric parameters (maximum and minimum diameters of nerve fibers, axon diameter, G-ratio, myelin sheath thickness) were assessed using the ImageJ software. ANOVA (parametric) or Kruskal-Wallis (nonparametric) tests were used for the statistical analysis. Groups L0, L4, L10, and L50 exhibited diminished values of all the quantitative and morphometric parameters in comparison to the control group. The morphological, quantitative, and morphometric data revealed improvement after injury in groups L4, L10, and L50 (irradiated groups) compared to the injured-only group (L0); the best results, in general, were observed for the L10 group after 15 days of nerve injury.

'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.

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.

Spermatozoa quality assessment: a combined holographic and Raman microscopy approach

NASA Astrophysics Data System (ADS)

De Angelis, Annalisa; Ferrara, Maria A.; Di Caprio, Giuseppe; Managò, Stefano; Sirleto, Luigi; Coppola, Giuseppe; De Luca, Anna Chiara

2015-05-01

Semen analysis is widely used as diagnostic tool for assessing male fertility, controlling and managing the animal reproduction. The most important parameters measured in a semen analysis are the morphology and biochemical alterations. For obtaining such information, non-invasive, label-free and non-destructive techniques have to be used. Digital Holography (DH) combined with Raman Spectroscopy (RS) could represent the perfect candidate for a rapid, non-destructive and high-sensitive morphological and biochemical sperm cell analysis. In this study, DH-RS combined approach is used for a complete analysis of single bovine spermatozoa. High-resolution images of bovine sperm have been obtained by DH microscopy from the reconstruction of a single acquired hologram, highlighting in some cases morphological alterations. Quantitative 3D reconstructions of sperm head, both normal and anomalous, have been studied and an unexpected structure of the post-acrosomal region of the head has been detected. Such anomalies have been also confirmed by Raman imaging analysis, suggesting the protein vibrations as associated Raman marker of the defect.

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.

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.

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.

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.

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.

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

Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions.

PubMed

Shen, Simon; Syal, Karan; Tao, Nongjian; Wang, Shaopeng

2015-12-01

We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion.

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.

QUANTITATIVE MORPHOLOGY

EPA Science Inventory

Abstract: In toxicology, the role of quantitative assessment of brain morphology can be understood in the context of two types of treatment-related alterations. One type of alteration is specifically associated with treatment and is not observed in control animals. Measurement ...

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Quantitative 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.

First instalment in resolution of the Banksia spinulosa complex (Proteaceae): B. neoanglica, a new species supported by phenetic analysis, ecology and geography

PubMed Central

Stimpson, Margaret L.; Weston, Peter H.; Telford, Ian R.H.; Bruhl, Jeremy J.

2012-01-01

Abstract Taxa in the Banksia spinulosa Sm. complex (Proteaceae) have populations with sympatric, parapatric and allopatric distributions and unclear or disputed boundaries. Our hypothesis is that under biological, phenetic and diagnosable species concepts that each of the currently named taxa within the Banksia spinulosa complex is a separate species. Based on specimens collected as part of this study, and data recorded from specimens in six Australian herbaria, complemented by phenetic analysis (semi–strong multidimensional scaling and UPGMA clustering) and a detailed morphological study, we investigated both morphological variation and geographic distribution in the Banksia spinulosa complex. All specimens used for this study are held at the N.C.W. Beadle Herbarium or the National Herbarium of New South Wales. In total 23 morphological characters (11 quantitative, five binary, and seven multistate characters) were analysed phenetically for 89 specimens. Ordination and cluster analysis resulted in individuals grouping strongly allowing recognition of distinct groups consistent with their recognition as separate species. Additional morphological analysis was completed on all specimens using leaf, floral, fruit and stem morphology, providing clear cut diagnosable groups and strong support for the recognition of Banksia spinulosa var. cunninghamii and Banksia spinulosa var. neoanglica as species. PMID:23170073

Listening to galaxies tuning at z ~ 2.5-3.0: The first strikes of the Hubble fork

NASA Astrophysics Data System (ADS)

Talia, M.; Cimatti, A.; Mignoli, M.; Pozzetti, L.; Renzini, A.; Kurk, J.; Halliday, C.

2014-02-01

Aims: We investigate the morphological properties of 494 galaxies selected from the Galaxy Mass Assembly ultra-deep Spectroscopic Survey (GMASS) at z > 1, primarily in their optical rest frame, using Hubble Space Telescope (HST) infrared images, from the Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS). Methods: The morphological analysis of Wield Field Camera (WFC3) H160 band images was performed using two different methods: a visual classification identifying traditional Hubble types, and a quantitative analysis using parameters that describe structural properties, such as the concentration of light and the rotational asymmetry. The two classifications are compared. We then analysed how apparent morphologies correlate with the physical properties of galaxies. Results: The fractions of both elliptical and disk galaxies decrease between redshifts z ~ 1 to z ~ 3, while at z > 3 the galaxy population is dominated by irregular galaxies. The quantitative morphological analysis shows that, at 1 < z < 3, morphological parameters are not as effective in distinguishing the different morphological Hubble types as they are at low redshift. No significant morphological k-correction was found to be required for the Hubble type classification, with some exceptions. In general, different morphological types occupy the two peaks of the (U - B)rest colour bimodality of galaxies: most irregulars occupy the blue peak, while ellipticals are mainly found in the red peak, though with some level of contamination. Disks are more evenly distributed than either irregulars and ellipticals. We find that the position of a galaxy in a UVJ diagram is related to its morphological type: the "quiescent" region of the plot is mainly occupied by ellipticals and, to a lesser extent, by disks. We find that only ~33% of all morphological ellipticals in our sample are red and passively evolving galaxies, a percentage that is consistent with previous results obtained at z < 1. Blue galaxies morphologically classified as ellipticals show a remarkable structural similarity to red ones. We search for correlations between our morphological and spectroscopic galaxy classifications. Almost all irregulars have a star-forming galaxy spectrum. In addition, the majority of disks show some sign of star-formation activity in their spectra, though in some cases their red continuum is indicative of old stellar populations. Finally, an elliptical morphology may be associated with either passively evolving or strongly star-forming galaxies. Conclusions: We propose that the Hubble sequence of galaxy morphologies takes shape at redshift 2.5 < z < 3. The fractions of both ellipticals and disks decrease with increasing lookback time at z > 1, such that at redshifts z = 2.5-2.7 and above, the Hubble types cannot be identified, and most galaxies are classified as irregular. Appendix A is available in electronic form at http://www.aanda.org

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 analysis.

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.

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.

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

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

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.

An insight into morphometric descriptors of cell shape that pertain to regenerative medicine.

PubMed

Lobo, Joana; See, Eugene Yong-Shun; Biggs, Manus; Pandit, Abhay

2016-07-01

Cellular morphology has recently been indicated as a powerful indicator of cellular function. The analysis of cell shape has evolved from rudimentary forms of microscopic visual inspection to more advanced methodologies that utilize high-resolution microscopy coupled with sophisticated computer hardware and software for data analysis. Despite this progress, there is still a lack of standardization in quantification of morphometric parameters. In addition, uncertainty remains as to which methodologies and parameters of cell morphology will yield meaningful data, which methods should be utilized to categorize cell shape, and the extent of reliability of measurements and the interpretation of the resulting analysis. A large range of descriptors has been employed to objectively assess the cellular morphology in two-dimensional and three-dimensional domains. Intuitively, simple and applicable morphometric descriptors are preferable and standardized protocols for cell shape analysis can be achieved with the help of computerized tools. In this review, cellular morphology is discussed as a descriptor of cellular function and the current morphometric parameters that are used quantitatively in two- and three-dimensional environments are described. Furthermore, the current problems associated with these morphometric measurements are addressed. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

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.

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.

Quantitative assessment of neurite outgrowth in human embryonic stem cell derived hN2 cells using automated high-content image analysis

EPA Science Inventory

Throughout development neurons undergo a number of morphological changes including neurite outgrowth from the cell body. Exposure to neurotoxic chemicals that interfere with this process may result in permanent deficits in nervous system function. Traditionally, rodent primary ne...

Quantitative assessment of neurite outgrowth in human embryonic stem-cell derived neurons using automated high-content image analysis

EPA Science Inventory

During development neurons undergo a number of morphological changes including neurite outgrowth from the cell body. Exposure to neurotoxicants that interfere with this process may cause in permanent deficits in nervous system function. While many studies have used rodent primary...

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.

The application of time series models to cloud field morphology analysis

NASA Technical Reports Server (NTRS)

Chin, Roland T.; Jau, Jack Y. C.; Weinman, James A.

1987-01-01

A modeling method for the quantitative description of remotely sensed cloud field images is presented. A two-dimensional texture modeling scheme based on one-dimensional time series procedures is adopted for this purpose. The time series procedure used is the seasonal autoregressive, moving average (ARMA) process in Box and Jenkins. Cloud field properties such as directionality, clustering and cloud coverage can be retrieved by this method. It has been demonstrated that a cloud field image can be quantitatively defined by a small set of parameters and synthesized surrogates can be reconstructed from these model parameters. This method enables cloud climatology to be studied quantitatively.

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.

Confocal micrographs: automated segmentation and quantitative shape analysis of neuronal cells treated with ostreolysin A/pleurotolysin B pore-forming complex.

PubMed

Kopanja, Lazar; Kovacevic, Zorana; Tadic, Marin; Žužek, Monika Cecilija; Vrecl, Milka; Frangež, Robert

2018-04-23

Detailed shape analysis of cells is important to better understand the physiological mechanisms of toxins and determine their effects on cell morphology. This study aimed to develop a procedure for accurate morphological analysis of cell shape and use it as a tool to estimate toxin activity. With the aim of optimizing the method of cell morphology analysis, we determined the influence of ostreolysin A and pleurotolysin B complex (OlyA/PlyB) on the morphology of murine neuronal NG108-15 cells. A computational method was introduced and successfully applied to quantify morphological attributes of the NG108-15 cell line before and after 30 and 60 min exposure to OlyA/PlyB using confocal microscopy. The modified circularity measure [Formula: see text] for shape analysis was applied, which defines the degree to which the shape of the neuron differs from a perfect circle. It enables better detection of small changes in the shape of cells, making the outcome easily detectable numerically. Additionally, we analyzed the influence of OlyA/PlyB on the cell area, allowing us to detect the cells with blebs. This is important because the formation of plasma membrane protrusions such as blebs often reflects cell injury that leads to necrotic cell death. In summary, we offer a novel analytical method of neuronal cell shape analysis and its correlation with the toxic effects of the pore-forming OlyA/PlyB toxin in situ.

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

PubMed Central

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

2013-01-01

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

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.

[Establishment of cervical vertebral skeletal maturation of female children in Shanghai].

PubMed

Sun, Yan; Chen, Rong-jing; Yu, Quan; Fan, Li; Chen, Wei; Shen, Gang

2009-06-01

To establish a method for quantitatively evaluating skeletal maturation of cervical vertebrae of female children in Shanghai. The samples were selected from lateral cephalometric radiographs of 240 Shanghai girls, aged 8 to 15 years. The parameters were measured to indicate the morphological changes of the third (C3) and fourth (C4) vertebrae in width, height and the depth of the inferior curvature. The independent-sample t test and stepwise multiple regression analysis were used to estimate the growth status and the ratios of C3, C4 cervical vertebrae by SPSS 15.0 software package. The physical and morphological contour of C3, C4 cervical vertebrae increased proportionately with the increment of age. The regression formula for indicating cervical vertebral skeletal age of female children in Shanghai was expressed by the equation Y= -5.696+8.010 AH3/AP3+6.654 AH3/H3+6.045AH4/PH4 (r=0.912). The regression formula resulted from morphological measurements quantitatively indicates the skeletal maturation of cervical vertebrae of female children in Shanghai.

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.

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.

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.

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.

Correlating subjective and objective descriptors of ultra high molecular weight wear particles from total joint prostheses.

PubMed

McMullin, Brian T; Leung, Ming-Ying; Shanbhag, Arun S; McNulty, Donald; Mabrey, Jay D; Agrawal, C Mauli

2006-02-01

A total of 750 images of individual ultra-high molecular weight polyethylene (UHMWPE) particles isolated from periprosthetic failed hip, knee, and shoulder arthroplasties were extracted from archival scanning electron micrographs. Particle size and morphology was subsequently analyzed using computerized image analysis software utilizing five descriptors found in ASTM F1877-98, a standard for quantitative description of wear debris. An online survey application was developed to display particle images, and allowed ten respondents to classify particle morphologies according to commonly used terminology as fibers, flakes, or granules. Particles were categorized based on a simple majority of responses. All descriptors were evaluated using a one-way ANOVA and Tukey-Kramer test for all-pairs comparison among each class of particles. A logistic regression model using half of the particles included in the survey was then used to develop a mathematical scheme to predict whether a given particle should be classified as a fiber, flake, or granule based on its quantitative measurements. The validity of the model was then assessed using the other half of the survey particles and compared with human responses. Comparison of the quantitative measurements of isolated particles showed that the morphologies of each particle type classified by respondents were statistically different from one another (p<0.05). The average agreement between mathematical prediction and human respondents was 83.5% (standard error 0.16%). These data suggest that computerized descriptors can be feasibly correlated with subjective terminology, thus providing a basis for a common vocabulary for particle description which can be translated into quantitative dimensions.

Correlating subjective and objective descriptors of ultra high molecular weight wear particles from total joint prostheses

PubMed Central

McMullin, Brian T.; Leung, Ming-Ying; Shanbhag, Arun S.; McNulty, Donald; Mabrey, Jay D.; Agrawal, C. Mauli

2014-01-01

A total of 750 images of individual ultra-high molecular weight polyethylene (UHMWPE) particles isolated from periprosthetic failed hip, knee, and shoulder arthroplasties were extracted from archival scanning electron micrographs. Particle size and morphology was subsequently analyzed using computerized image analysis software utilizing five descriptors found in ASTM F1877-98, a standard for quantitative description of wear debris. An online survey application was developed to display particle images, and allowed ten respondents to classify particle morphologies according to commonly used terminology as fibers, flakes, or granules. Particles were categorized based on a simple majority of responses. All descriptors were evaluated using a one-way ANOVA and Tukey–Kramer test for all-pairs comparison among each class of particles. A logistic regression model using half of the particles included in the survey was then used to develop a mathematical scheme to predict whether a given particle should be classified as a fiber, flake, or granule based on its quantitative measurements. The validity of the model was then assessed using the other half of the survey particles and compared with human responses. Comparison of the quantitative measurements of isolated particles showed that the morphologies of each particle type classified by respondents were statistically different from one another (po0:05). The average agreement between mathematical prediction and human respondents was 83.5% (standard error 0.16%). These data suggest that computerized descriptors can be feasibly correlated with subjective terminology, thus providing a basis for a common vocabulary for particle description which can be translated into quantitative dimensions. PMID:16112725

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 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.

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.

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.

Aggregation and Disaggregation of Senile Plaques in Alzheimer Disease

NASA Astrophysics Data System (ADS)

Cruz, L.; Urbanc, B.; Buldyrev, S. V.; Christie, R.; Gomez-Isla, T.; Havlin, S.; McNamara, M.; Stanley, H. E.; Hyman, B. T.

1997-07-01

We quantitatively analyzed, using laser scanning confocal microscopy, the three-dimensional structure of individual senile plaques in Alzheimer disease. We carried out the quantitative analysis using statistical methods to gain insights about the processes that govern Aβ peptide deposition. Our results show that plaques are complex porous structures with characteristic pore sizes. We interpret plaque morphology in the context of a new dynamical model based on competing aggregation and disaggregation processes in kinetic steady-state equilibrium with an additional diffusion process allowing Aβ deposits to diffuse over the surface of plaques.

Automated Quantification and Integrative Analysis of 2D and 3D Mitochondrial Shape and Network Properties

PubMed Central

Nikolaisen, Julie; Nilsson, Linn I. H.; Pettersen, Ina K. N.; Willems, Peter H. G. M.; Lorens, James B.; Koopman, Werner J. H.; Tronstad, Karl J.

2014-01-01

Mitochondrial morphology and function are coupled in healthy cells, during pathological conditions and (adaptation to) endogenous and exogenous stress. In this sense mitochondrial shape can range from small globular compartments to complex filamentous networks, even within the same cell. Understanding how mitochondrial morphological changes (i.e. “mitochondrial dynamics”) are linked to cellular (patho) physiology is currently the subject of intense study and requires detailed quantitative information. During the last decade, various computational approaches have been developed for automated 2-dimensional (2D) analysis of mitochondrial morphology and number in microscopy images. Although these strategies are well suited for analysis of adhering cells with a flat morphology they are not applicable for thicker cells, which require a three-dimensional (3D) image acquisition and analysis procedure. Here we developed and validated an automated image analysis algorithm allowing simultaneous 3D quantification of mitochondrial morphology and network properties in human endothelial cells (HUVECs). Cells expressing a mitochondria-targeted green fluorescence protein (mitoGFP) were visualized by 3D confocal microscopy and mitochondrial morphology was quantified using both the established 2D method and the new 3D strategy. We demonstrate that both analyses can be used to characterize and discriminate between various mitochondrial morphologies and network properties. However, the results from 2D and 3D analysis were not equivalent when filamentous mitochondria in normal HUVECs were compared with circular/spherical mitochondria in metabolically stressed HUVECs treated with rotenone (ROT). 2D quantification suggested that metabolic stress induced mitochondrial fragmentation and loss of biomass. In contrast, 3D analysis revealed that the mitochondrial network structure was dissolved without affecting the amount and size of the organelles. Thus, our results demonstrate that 3D imaging and quantification are crucial for proper understanding of mitochondrial shape and topology in non-flat cells. In summary, we here present an integrative method for unbiased 3D quantification of mitochondrial shape and network properties in mammalian cells. PMID:24988307

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.

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.

Modeling aeolian dune and dune field evolution

NASA Astrophysics Data System (ADS)

Diniega, Serina

Aeolian sand dune morphologies and sizes are strongly connected to the environmental context and physical processes active since dune formation. As such, the patterns and measurable features found within dunes and dune fields can be interpreted as records of environmental conditions. Using mathematical models of dune and dune field evolution, it should be possible to quantitatively predict dune field dynamics from current conditions or to determine past field conditions based on present-day observations. In this dissertation, we focus on the construction and quantitative analysis of a continuum dune evolution model. We then apply this model towards interpretation of the formative history of terrestrial and martian dunes and dune fields. Our first aim is to identify the controls for the characteristic lengthscales seen in patterned dune fields. Variations in sand flux, binary dune interactions, and topography are evaluated with respect to evolution of individual dunes. Through the use of both quantitative and qualitative multiscale models, these results are then extended to determine the role such processes may play in (de)stabilization of the dune field. We find that sand flux variations and topography generally destabilize dune fields, while dune collisions can yield more similarly-sized dunes. We construct and apply a phenomenological macroscale dune evolution model to then quantitatively demonstrate how dune collisions cause a dune field to evolve into a set of uniformly-sized dunes. Our second goal is to investigate the influence of reversing winds and polar processes in relation to dune slope and morphology. Using numerical experiments, we investigate possible causes of distinctive morphologies seen in Antarctic and martian polar dunes. Finally, we discuss possible model extensions and needed observations that will enable the inclusion of more realistic physical environments in the dune and dune field evolution models. By elucidating the qualitative and quantitative connections between environmental conditions, physical processes, and resultant dune and dune field morphologies, this research furthers our ability to interpret spacecraft images of dune fields, and to use present-day observations to improve our understanding of past terrestrial and martian environments.

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.

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.

High-definition optical coherence tomography intrinsic skin ageing assessment in women: a pilot study.

PubMed

Boone, M A L M; Suppa, M; Marneffe, A; Miyamoto, M; Jemec, G B E; Del Marmol, V

2015-10-01

Several non-invasive two-dimensional techniques with different lateral resolution and measurable depth range have proved to be useful in assessing and quantifying morphological changes in skin ageing. Among these, only in vivo microscopy techniques permit histometric measurements in vivo. Qualitative and quantitative assessment of chronological (intrinsic) age-related (IAR) morphological changes of epidermis, dermo-epidermal junction (DEJ), papillary dermis (PD), papillary-reticular dermis junction and reticular dermis (RD) have been performed by high-definition optical coherence tomography in real time 3-D. HD-OCT images were taken at the internal site of the right upper arm. Qualitative HD-OCT IAR descriptors were reported at skin surface, at epidermal layer, DEJ, PD and upper RD. Quantitative evaluation of age-related compaction and backscattered intensity or brightness of different skin layers was performed by using the plugin plot z-axis profile of ImageJ(®) software permitting intensity assessment of HD-OCT (DICOM) images (3-D images). Analysis was in blind from all clinical information. Sixty, fair-skinned (Fitzpatrick types I-III) healthy females were analysed retrospectively in this study. The subjects belonged to three age groups: twenty in group I aged 20-39, twenty in group II aged 40-59 and twenty in group III aged 60-79. Only intrinsic ageing in women has been studied. Significant age-related qualitative and quantitative differences could be noticed. IAR changes in dermal matrix fibers morphology/organisation and in microvasculature were observed. The brightness and compaction of the different skin layers increased significantly with intrinsic skin ageing. The depth of visibility of fibers in RD increased significantly in the older age group. In conclusion, HD-OCT allows 3-D in vivo and real time qualitative and quantitative assessment of chronological (intrinsic) age-related morphological skin changes at high resolution from skin surface to a depth of the superficial reticular dermis.

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 equivalent cells. PMID:22046143

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

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.

Mouse spermatozoa with higher fertilization rates have thinner nuclei

PubMed Central

Ikawa, Masahito

2017-01-01

Background Although spermatozoa with normal morphology are assumed to have uniform fertilization ability, recent data show that even normal spermatozoa have considerable variation in their head shape which is associated with differences in fertilization ability. Appropriate quantitative indicators for good sperm morphology, however, remain unidentified. Methods Therefore, in an effort to identify such an indicator, we compared the nuclear contour of normal mouse spermatozoa by quantitative multivariate analysis using elliptic Fourier descriptors combined with principal component analysis. The spermatozoa were obtained from different strains and collection sites which have been shown to be associated with different fertilization abilities. Results We found that the head was 5.7% thinner in spermatozoa from the B6D2F1 (BDF1) strain, known to have a higher fertilization rate, than in those from the C57BL/6N (B6N) strain, which has a lower fertilization rate. Moreover, zona-penetrated spermatozoa in the perivitelline space consistently had 5.4% thinner heads than those isolated from the epididymis before ejaculation. The aspect ratio, which represents the sperm head thinness, uniquely distinguished these sperm populations, confirming its validity as a morphological indicator. Discussion Because aspect ratio has also been shown to characterize human spermatozoa, this unique morphometric indicator might be applicable to compare normal spermatozoa among multiple patients, which will greatly facilitate and enhance current reproductive technologies. PMID:29038763

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

Evaluation of enamel by scanning electron microscopy green LED associated to hydrogen peroxide 35% for dental bleaching

NASA Astrophysics Data System (ADS)

Monteiro, Juliana S. C.; de Oliveira, Susana C. P. S.; Zanin, Fátima A. A.; Santos, Gustavo M. P.; Sampaio, Fernando J. P.; Gomes Júnior, Rafael Araújo; Gesteira, Maria F. M.; Vannier-Santos, Marcos A.; Pinheiro, Antônio Luiz B.

2014-02-01

Dental bleaching is a frequently requested procedure in clinical dental practice. The literature is contradictory regarding the effects of bleaching agents on both morphology and demineralization of enamel after bleaching. The aim of this study was to analyze by SEM the effect of 35% neutral hydrogen peroxide cured by green LED. Buccal surfaces of 15 pre-molars were sectioned and marked with a central groove to allow experimental and control groups on the same specimen. For SEM, 75 electron micrographs were evaluated by tree observers at 43X, 220X and 1000X. Quantitative analysis for the determination of the surface elemental composition of the samples through X-ray microanalysis by SEM was also performed. The protocol tested neither showed significant changes in mineral composition of the samples nor to dental enamel structure when compared to controls. SEM analysis allowed inferring that there were marked morphological differences between the enamel samples highlighting the need for the use of the same tooth in comparative morphological studies. The tested protocol did not cause morphological damage the enamel surface when compared to their respective controls.

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

Investigating Methodological Differences in the Assessment of Dendritic Morphology of Basolateral Amygdala Principal Neurons-A Comparison of Golgi-Cox and Neurobiotin Electroporation Techniques.

PubMed

Klenowski, Paul M; Wright, Sophie E; Mu, Erica W H; Noakes, Peter G; Lavidis, Nickolas A; Bartlett, Selena E; Bellingham, Mark C; Fogarty, Matthew J

2017-12-19

Quantitative assessments of neuronal subtypes in numerous brain regions show large variations in dendritic arbor size. A critical experimental factor is the method used to visualize neurons. We chose to investigate quantitative differences in basolateral amygdala (BLA) principal neuron morphology using two of the most common visualization methods: Golgi-Cox staining and neurobiotin (NB) filling. We show in 8-week-old Wistar rats that NB-filling reveals significantly larger dendritic arbors and different spine densities, compared to Golgi-Cox-stained BLA neurons. Our results demonstrate important differences and provide methodological insights into quantitative disparities of BLA principal neuron morphology reported in the literature.

Remote sensing of the Fram Strait marginal ice zone

USGS Publications Warehouse

Shuchman, R.A.; Burns, B.A.; Johannessen, O.M.; Josberger, E.G.; Campbell, W.J.; Manley, T.O.; Lannelongue, N.

1987-01-01

Sequential remote sensing images of the Fram Strait marginal ice zone played a key role in elucidating the complex interactions of the atmosphere, ocean, and sea ice. Analysis of a subset of these images covering a 1-week period provided quantitative data on the mesoscale ice morphology, including ice edge positions, ice concentrations, floe size distribution, and ice kinematics. The analysis showed that, under light to moderate wind conditions, the morphology of the marginal ice zone reflects the underlying ocean circulation. High-resolution radar observations showed the location and size of ocean eddies near the ice edge. Ice kinematics from sequential radar images revealed an ocean eddy beneath the interior pack ice that was verified by in situ oceanographic measurements.

Induction of a Pregnancy-Like Mammary Gland Differentiation by Docosapentaenoic Omega-3 Fatty Acid

DTIC Science & Technology

2008-09-01

xylenes, and stored in methyl salicylate . Morphological Assessment of Mammary Gland—Whole inguinal mammary glands were removed from virgin control as...respectively, defatted in xylenes, and stored in methyl salicylate . Quantitative RT-PCR analyses RNA was isolated and subjected to real time PCR analysis... methylation , and fatty acid analysis were performed as previously described [28,48]. Briefly, an ali- quot of mammary tissue homogenate in a glass

Practical considerations of image analysis and quantification of signal transduction IHC staining.

PubMed

Grunkin, Michael; Raundahl, Jakob; Foged, Niels T

2011-01-01

The dramatic increase in computer processing power in combination with the availability of high-quality digital cameras during the last 10 years has fertilized the grounds for quantitative microscopy based on digital image analysis. With the present introduction of robust scanners for whole slide imaging in both research and routine, the benefits of automation and objectivity in the analysis of tissue sections will be even more obvious. For in situ studies of signal transduction, the combination of tissue microarrays, immunohistochemistry, digital imaging, and quantitative image analysis will be central operations. However, immunohistochemistry is a multistep procedure including a lot of technical pitfalls leading to intra- and interlaboratory variability of its outcome. The resulting variations in staining intensity and disruption of original morphology are an extra challenge for the image analysis software, which therefore preferably should be dedicated to the detection and quantification of histomorphometrical end points.

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.

[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.

Analysis of airborne LiDAR surveys to quantify the characteristic morphologies of northern forested wetlands

Treesearch

Murray C. Richardson; Carl P. J. Mitchell; Brian A. Branfireun; Randall K. Kolka

2010-01-01

A new technique for quantifying the geomorphic form of northern forested wetlands from airborne LiDAR surveys is introduced, demonstrating the unprecedented ability to characterize the geomorphic form of northern forested wetlands using high-resolution digital topography. Two quantitative indices are presented, including the lagg width index (LWI) which objectively...

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

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.

Label-Free Imaging and Biochemical Characterization of Bovine Sperm Cells

PubMed Central

Ferrara, Maria Antonietta; Di Caprio, Giuseppe; Managò, Stefano; De Angelis, Annalisa; Sirleto, Luigi; Coppola, Giuseppe; De Luca, Anna Chiara

2015-01-01

A full label-free morphological and biochemical characterization is desirable to select spermatozoa during preparation for artificial insemination. In order to study these fundamental parameters, we take advantage of two attractive techniques: digital holography (DH) and Raman spectroscopy (RS). DH presents new opportunities for studying morphological aspect of cells and tissues non-invasively, quantitatively and without the need for staining or tagging, while RS is a very specific technique allowing the biochemical analysis of cellular components with a spatial resolution in the sub-micrometer range. In this paper, morphological and biochemical bovine sperm cell alterations were studied using these techniques. In addition, a complementary DH and RS study was performed to identify X- and Y-chromosome-bearing sperm cells. We demonstrate that the two techniques together are a powerful and highly efficient tool elucidating some important criterions for sperm morphological selection and sex-identification, overcoming many of the limitations associated with existing protocols. PMID:25836358

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.

Advances in the Quantitative Characterization of the Shape of Ash-Sized Pyroclast Populations: Fractal Analyses Coupled to Micro- and Nano-Computed Tomography Techniques

NASA Astrophysics Data System (ADS)

Rausch, J.; Vonlanthen, P.; Grobety, B. H.

2014-12-01

The quantification of shape parameters in pyroclasts is fundamental to infer the dominant type of magma fragmentation (magmatic vs. phreatomagmatic), as well as the behavior of volcanic plumes and clouds in the atmosphere. In a case study aiming at reconstructing the fragmentation mechanisms triggering maar eruptions in two geologically and compositionally distinctive volcanic fields (West and East Eifel, Germany), the shapes of a large number of ash particle contours obtained from SEM images were analyzed by a dilation-based fractal method. Volcanic particle contours are pseudo-fractals showing mostly two distinct slopes in Richardson plots related to the fractal dimensions D1 (small-scale "textural" dimension) and D2 (large-scale "morphological" dimension). The validity of the data obtained from 2D sections was tested by analysing SEM micro-CT slices of one particle cut in different orientations and positions. Results for West Eifel maar particles yield large D1 values (> 1.023), resembling typical values of magmatic particles, which are characterized by a complex shape, especially at small scales. In contrast, the D1 values of ash particles from one East Eifel maar deposit are much smaller, coinciding with the fractal dimensions obtained from phreatomagmatic end-member particles. These quantitative morphological analyses suggest that the studied maar eruptions were triggered by two different fragmentation processes: phreatomagmatic in the East Eifel and magmatic in the West Eifel. The application of fractal analysis to quantitatively characterize the shape of pyroclasts and the linking of fractal dimensions to specific fragmentation processes has turned out to be a very promising tool for studying the fragmentation history of any volcanic eruption. The next step is to extend morphological analysis of volcanic particles to 3 dimensions. SEM micro-CT, already applied in this study, offers the required resolution, but is not suitable for the analysis of a large number of particles. Newly released nano CT-scanners, however, allows the simultaneous analysis of a statistically relevant number of particles (in the hundreds range). Preliminary results of a first trial will be presented.

Monolayer to MTS: using SEM, HIM, TEM and SERS to compare morphology, nanosensor uptake and redox potential in MCF7 cells

NASA Astrophysics Data System (ADS)

Jamieson, L. E.; Bell, A. P.; Harrison, D. J.; Campbell, C. J.

2015-06-01

Cellular redox potential is important for the control and regulation of a vast number of processes occurring in cells. When the fine redox potential balance within cells is disturbed it can have serious consequences such as the initiation or progression of disease. It is thought that a redox gradient develops in cancer tumours where the peripheral regions are well oxygenated and internal regions, further from vascular blood supply, become starved of oxygen and hypoxic. This makes treatment of these areas more challenging as, for example, radiotherapy relies on the presence of oxygen. Currently techniques for quantitative analysis of redox gradients are limited. Surface enhanced Raman scattering (SERS) nanosensors (NS) have been used to detect redox potential in a quantitative manner in monolayer cultured cells with many advantages over other techniques. This technique has considerable potential for use in multicellular tumour spheroids (MTS) - a three dimensional (3D) cell model which better mimics the tumour environment and gradients that develop. MTS are a more realistic model of the in vivo cellular morphology and environment and are becoming an increasingly popular in vitro model, replacing traditional monolayer culture. Imaging techniques such as transmission electron microscopy (TEM), scanning electron microscopy (SEM) and helium ion microscopy (HIM) were used to investigate differences in morphology and NS uptake in monolayer culture compared to MTS. After confirming NS uptake, the first SERS measurements revealing quantitative information on redox potential in MTS were performed.

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

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.

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.

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.

Changes in neocortical and hippocampal microglial cells during hibernation.

PubMed

León-Espinosa, Gonzalo; Regalado-Reyes, Mamen; DeFelipe, Javier; Muñoz, Alberto

2018-05-01

Mammalian hibernation proceeds alongside a wide range of complex brain adaptive changes that appear to protect the brain from extreme hypoxia and hypothermia. Using immunofluorescence, confocal microscopy, quantitative analysis methods and intracellular injections, we have characterized microglia morphological changes that occur in the neocortex and hippocampus of the Syrian hamster during hibernation. In euthermic hamsters, microglial cells showed the typical ramified/resting morphology with multiple long, thin and highly-branched processes homogeneously immunostained for Iba-1. However, during torpor, microglial cell process numbers increase significantly accompanied by a shortening of the Iba-1 immunoreactive processes, which show a fragmented appearance. Adaptative changes of microglial cells during torpor coursed with no expression of microglial cell activation markers. We discuss the possibility that these morphological changes may contribute to neuronal damage prevention during hibernation.

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 nanoscopy: Tackling sampling limitations in (S)TEM imaging of polymers and composites.

PubMed

Gnanasekaran, Karthikeyan; Snel, Roderick; de With, Gijsbertus; Friedrich, Heiner

2016-01-01

Sampling limitations in electron microscopy questions whether the analysis of a bulk material is representative, especially while analyzing hierarchical morphologies that extend over multiple length scales. We tackled this problem by automatically acquiring a large series of partially overlapping (S)TEM images with sufficient resolution, subsequently stitched together to generate a large-area map using an in-house developed acquisition toolbox (TU/e Acquisition ToolBox) and stitching module (TU/e Stitcher). In addition, we show that quantitative image analysis of the large scale maps provides representative information that can be related to the synthesis and process conditions of hierarchical materials, which moves electron microscopy analysis towards becoming a bulk characterization tool. We demonstrate the power of such an analysis by examining two different multi-phase materials that are structured over multiple length scales. Copyright © 2015 Elsevier B.V. All rights reserved.

On the morphometry of terrestrial shield volcanoes

NASA Astrophysics Data System (ADS)

Grosse, Pablo; Kervyn, Matthieu

2016-04-01

Shield volcanoes are described as low angle edifices that have convex up topographic profiles and are built primarily by the accumulation of lava flows. This generic view of shields' morphology is based on a limited number of monogenetic shields from Iceland and Mexico, and a small set of large oceanic islands (Hawaii, Galapagos). Here, the morphometry of over 150 monogenetic and polygenetic shield volcanoes, identified inthe Global Volcanism Network database, are analysed quantitatively from 90-meter resolution DEMs using the MORVOLC algorithm. An additional set of 20 volcanoes identified as stratovolcanoes but having low slopes and being dominantly built up by accumulation of lava flows are documented for comparison. Results show that there is a large variation in shield size (volumes range from 0.1 to >1000 km3), profile shape (height/basal width ratios range from 0.01 to 0.1), flank slope gradients, elongation and summit truncation. Correlation and principal component analysis of the obtained quantitative database enables to identify 4 key morphometric descriptors: size, steepness, plan shape and truncation. Using these descriptors through clustering analysis, a new classification scheme is proposed. It highlights the control of the magma feeding system - either central, along a linear structure, or spatially diffuse - on the resulting shield volcano morphology. Genetic relationships and evolutionary trends between contrasted morphological end-members can be highlighted within this new scheme. Additional findings are that the Galapagos-type morphology with a central deep caldera and steep upper flanks are characteristic of other shields. A series of large oceanic shields have slopes systematically much steeper than the low gradients (<4-8°) generally attributed to large Hawaiian-type shields. Finally, the continuum of morphologies from flat shields to steeper complex volcanic constructs considered as stratovolcanoes calls for a revision of this oversimplified distinction, taking into account the lava/pyroclasts ratio and the spatial distribution of eruptive vents.

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.

Distinct roles of cell wall biogenesis in yeast morphogenesis as revealed by multivariate analysis of high-dimensional morphometric data

PubMed Central

Okada, Hiroki; Ohnuki, Shinsuke; Roncero, Cesar; Konopka, James B.; Ohya, Yoshikazu

2014-01-01

The cell wall of budding yeast is a rigid structure composed of multiple components. To thoroughly understand its involvement in morphogenesis, we used the image analysis software CalMorph to quantitatively analyze cell morphology after treatment with drugs that inhibit different processes during cell wall synthesis. Cells treated with cell wall–affecting drugs exhibited broader necks and increased morphological variation. Tunicamycin, which inhibits the initial step of N-glycosylation of cell wall mannoproteins, induced morphologies similar to those of strains defective in α-mannosylation. The chitin synthase inhibitor nikkomycin Z induced morphological changes similar to those of mutants defective in chitin transglycosylase, possibly due to the critical role of chitin in anchoring the β-glucan network. To define the mode of action of echinocandin B, a 1,3-β-glucan synthase inhibitor, we compared the morphology it induced with mutants of Fks1 that contains the catalytic domain for 1,3-β-glucan synthesis. Echinocandin B exerted morphological effects similar to those observed in some fks1 mutants, with defects in cell polarity and reduced glucan synthesis activity, suggesting that echinocandin B affects not only 1,3-β-glucan synthesis, but also another functional domain. Thus our multivariate analyses reveal discrete functions of cell wall components and increase our understanding of the pharmacology of antifungal drugs. PMID:24258022

Classroom L2 Vocabulary Acquisition: Investigating the Role of Pedagogical Tasks and Form-Focused Instruction

ERIC Educational Resources Information Center

de la Fuente, Maria J.

2006-01-01

Framed under a cognitive approach to task-based L2 learning, this study used a pedagogical approach to investigate the effects of three vocabulary lessons (one traditional and two task-based) on acquisition of basic meanings, forms and morphological aspects of Spanish words. Quantitative analysis performed on the data suggests that the type of…

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...

Morphological and molecular variations induce mitochondrial dysfunction as a possible underlying mechanism of athletic amenorrhea.

PubMed

Xiong, Ruo-Hong; Wen, Shi-Lei; Wang, Qiang; Zhou, Hong-Ying; Feng, Shi

2018-01-01

Female athletes may experience difficulties in achieving pregnancy due to athletic amenorrhea (AA); however, the underlying mechanisms of AA remain unknown. The present study focuses on the mitochondrial alteration and its function in detecting the possible mechanism of AA. An AA rat model was established by excessive swimming. Hematoxylin and eosin staining, and transmission electron microscopic methods were performed to evaluate the morphological changes of the ovary, immunohistochemical examinations and radioimmunoassays were used to detect the reproductive hormones and corresponding receptors. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to test the mtDNA copy number. PCR and western blot analysis were used to test the expression of ND2. The change of morphological features of the rat ovaries revealed evident abnormalities. Particularly, the features of the mitochondria were markedly altered. In addition, reproductive hormones in the serum and tissues of AA rats were also detected to evaluate the function of the ovaries, and the levels of these hormones were significantly decreased. Furthermore, the mitochondrial DNA copy number (mtDNA) and expression of NADH dehydrogenase subunit 2 (ND2) were quantitated by qPCR or western blot analysis. Accordingly, the mtDNA copy number and expression of ND2 expression were markedly reduced in the AA rats. In conclusion, mitochondrial dysfunction in AA may affect the cellular energy supply and, therefore, result in dysfunction of the ovary. Thus, mitochondrial dysfunction may be considered as a possible underlying mechanism for the occurrence of AA.

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 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.

Three-dimensional quadratic modeling and quantitative evaluation of the diaphragm on a volumetric CT scan in patients with chronic obstructive pulmonary disease

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

Chang, Yongjun

Purpose: In patients with chronic obstructive pulmonary disease (COPD), diaphragm function may deteriorate due to reduced muscle fiber length. Quantitative analysis of the morphology of the diaphragm is therefore important. In the authors current study, they propose a diaphragm segmentation method for COPD patients that uses volumetric chest computed tomography (CT) data, and they provide a quantitative analysis of the diaphragmatic dimensions. Methods: Volumetric CT data were obtained from 30 COPD patients and 10 normal control patients using a 16-row multidetector CT scanner (Siemens Sensation 16) with 0.75-mm collimation. Diaphragm segmentation using 3D ray projections on the lower surface ofmore » the lungs was performed to identify the draft diaphragmatic lung surface, which was modeled using quadratic 3D surface fitting and robust regression in order to minimize the effects of segmentation error and parameterize diaphragm morphology. This result was visually evaluated by an expert thoracic radiologist. To take into consideration the shape features of the diaphragm, several quantification parameters—including the shape index on the apex (SIA) (which was computed using gradient set to 0), principal curvatures on the apex on the fitted diaphragm surface (CA), the height between the apex and the base plane (H), the diaphragm lengths along the x-, y-, and z-axes (XL, YL, ZL), quadratic-fitted diaphragm lengths on the z-axis (FZL), average curvature (C), and surface area (SA)—were measured using in-house software and compared with the pulmonary function test (PFT) results. Results: The overall accuracy of the combined segmentation method was 97.22% ± 4.44% while the visual accuracy of the models for the segmented diaphragms was 95.28% ± 2.52% (mean ± SD). The quantitative parameters, including SIA, CA, H, XL, YL, ZL, FZL, C, and SA were 0.85 ± 0.05 (mm{sup −1}), 0.01 ± 0.00 (mm{sup −1}), 17.93 ± 10.78 (mm), 129.80 ± 11.66 (mm), 163.19 ± 13.45 (mm), 71.27 ± 17.52 (mm), 61.59 ± 16.98 (mm), 0.01 ± 0.00 (mm{sup −1}), and 34 380.75 ± 6680.06 (mm{sup 2}), respectively. Several parameters were correlated with the PFT parameters. Conclusions: The authors propose an automatic method for quantitatively evaluating the morphological parameters of the diaphragm on volumetric chest CT in COPD patients. By measuring not only the conventional length and surface area but also the shape features of the diaphragm using quadratic 3D surface modeling, the proposed method is especially useful for quantifying diaphragm characteristics. Their method may be useful for assessing morphological diaphragmatic changes in COPD patients.« less

Quantitative Analysis of TDLUs using Adaptive Morphological Shape Techniques

PubMed Central

Rosebrock, Adrian; Caban, Jesus J.; Figueroa, Jonine; Gierach, Gretchen; Linville, Laura; Hewitt, Stephen; Sherman, Mark

2014-01-01

Within the complex branching system of the breast, terminal duct lobular units (TDLUs) are the anatomical location where most cancer originates. With aging, TDLUs undergo physiological involution, reflected in a loss of structural components (acini) and a reduction in total number. Data suggest that women undergoing benign breast biopsies that do not show age appropriate involution are at increased risk of developing breast cancer. To date, TDLU assessments have generally been made by qualitative visual assessment, rather than by objective quantitative analysis. This paper introduces a technique to automatically estimate a set of quantitative measurements and use those variables to more objectively describe and classify TDLUs. To validate the accuracy of our system, we compared the computer-based morphological properties of 51 TDLUs in breast tissues donated for research by volunteers in the Susan G. Komen Tissue Bank and compared results to those of a pathologist, demonstrating 70% agreement. Secondly, in order to show that our method is applicable to a wider range of datasets, we analyzed 52 TDLUs from biopsies performed for clinical indications in the National Cancer Institute’s Breast Radiology Evaluation and Study of Tissues (BREAST) Stamp Project and obtained 82% correlation with visual assessment. Lastly, we demonstrate the ability to uncover novel measures when researching the structural properties of the acini by applying machine learning and clustering techniques. Through our study we found that while the number of acini per TDLU increases exponentially with the TDLU diameter, the average elongation and roundness remain constant. PMID:25722829

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 considered a birch hybrid zone, harbouring genetic variation which may be advantageous in subarctic regions. PMID:17495985

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.

Investigation of fluvial landforms in the north-eastern Pannonian Basin, using cartographic materials from the XIX-XXI Centuries

NASA Astrophysics Data System (ADS)

Robu, Delia; Niga, Bogdan; Perşoiu, Ioana

2015-04-01

The study area is located in the north-eastern Pannonian Basin, and covers approximately 3700 km2. Using cartographic materials for the last 155 years, we analyzed and defined river network and relict fluvial morphologies created by the rivers Tur, Someş, Homorod and Crasna. Database extraction from each set of historical maps was performed by field verification and validation, associated to GIS techniques. Relict fluvial morphologies on the Someş alluvial cone comprise a wide variety of channel typologies and sizes, drainage directions and their consequent typology, which indicates a complex fluvial evolution. The dominant category of relict fluvial morphology is represented by the meander loop. Following the quantitative analysis on the successive sets of maps we identified and delimited meander loops and meandering paths formed prior to the reference year 1860. Generally, the post-1860 relict fluvial morphologies are secondary morphologies, as the keynote is given by those formed previous to the reference moment 1860. An analysis of the share of the relict fluvial morphologies on the three sets of reference cartographic materials (the second Austro-Hungarian topographic survey, Google Earth and orthophotoplans) highlights that most relict fluvial morphologies were identified on the second Austro-Hungarian topographic survey, followed by those identified in Google Earth and orthophotoplans. The map of fluvial morphologies constructed in this study enables a discussion on drainage directions, based on the observation that a series of abandoned meander loops and segments follow clear directions. We applied several quantitative indices in assessing the relict fluvial morphology (radius of curvature, paleochannel width). Consequently, we identified underfit stream sectors with meander loops larger than the modern ones Someş meanders (on the Racta River), uncharacteristic features such as braided riverbed reaches, a high frequency of meander scrolls present on the right bank of Crasna at its entrance in the plain, or the occurrence of wetlands in an area affected by subsidence (the Ecedeea Plain). Despite the ample human intervention in our study area through sewers, dams, meander cuts, the river network evolution trend remained the same between 1860 and 2005, with evolution and formation of meanders, although the change rate has diminished. "ACKNOWLEDGMENT This paper has been financially supported within the project entitled "SOCERT. Knowledge society, dynamism through research", contract number POSDRU/159/1.5/S/132406. This project is co-financed by European Social Fund through Sectoral Operational Programme for Human Resources Development 2007-2013. Investing in people!"

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

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.

Plant Architecture: A Dynamic, Multilevel and Comprehensive Approach to Plant Form, Structure and Ontogeny

PubMed Central

Barthélémy, Daniel; Caraglio, Yves

2007-01-01

Background and Aims The architecture of a plant depends on the nature and relative arrangement of each of its parts; it is, at any given time, the expression of an equilibrium between endogenous growth processes and exogenous constraints exerted by the environment. The aim of architectural analysis is, by means of observation and sometimes experimentation, to identify and understand these endogenous processes and to separate them from the plasticity of their expression resulting from external influences. Scope Using the identification of several morphological criteria and considering the plant as a whole, from germination to death, architectural analysis is essentially a detailed, multilevel, comprehensive and dynamic approach to plant development. Despite their recent origin, architectural concepts and analysis methods provide a powerful tool for studying plant form and ontogeny. Completed by precise morphological observations and appropriated quantitative methods of analysis, recent researches in this field have greatly increased our understanding of plant structure and development and have led to the establishment of a real conceptual and methodological framework for plant form and structure analysis and representation. This paper is a summarized update of current knowledge on plant architecture and morphology; its implication and possible role in various aspects of modern plant biology is also discussed. PMID:17218346

To 3D or Not to 3D, That Is the Question: Do 3D Surface Analyses Improve the Ecomorphological Power of the Distal Femur in Placental Mammals?

PubMed Central

Gould, Francois D. H.

2014-01-01

Improvements in three-dimensional imaging technologies have renewed interest in the study of functional and ecological morphology. Quantitative approaches to shape analysis are used increasingly to study form-function relationships. These methods are computationally intensive, technically demanding, and time-consuming, which may limit sampling potential. There have been few side-by-side comparisons of the effectiveness of such approaches relative to more traditional analyses using linear measurements and ratios. Morphological variation in the distal femur of mammals has been shown to reflect differences in locomotor modes across clades. Thus I tested whether a geometric morphometric analysis of surface shape was superior to a multivariate analysis of ratios for describing ecomorphological patterns in distal femoral variation. A sample of 164 mammalian specimens from 44 genera was assembled. Each genus was assigned to one of six locomotor categories. The same hypotheses were tested using two methods. Six linear measurements of the distal femur were taken with calipers, from which four ratios were calculated. A 3D model was generated with a laser scanner, and analyzed using three dimensional geometric morphometrics. Locomotor category significantly predicted variation in distal femoral morphology in both analyses. Effect size was larger in the geometric morphometric analysis than in the analysis of ratios. Ordination reveals a similar pattern with arboreal and cursorial taxa as extremes on a continuum of morphologies in both analyses. Discriminant functions calculated from the geometric morphometric analysis were more accurate than those calculated from ratios. Both analysis of ratios and geometric morphometric surface analysis reveal similar, biologically meaningful relationships between distal femoral shape and locomotor mode. The functional signal from the morphology is slightly higher in the geometric morphometric analysis. The practical costs of conducting these sorts of analyses should be weighed against potentially slight increases in power when designing protocols for ecomorphological studies. PMID:24633081

Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis.

PubMed

Luo, Xin; Zang, Xiao; Yang, Lin; Huang, Junzhou; Liang, Faming; Rodriguez-Canales, Jaime; Wistuba, Ignacio I; Gazdar, Adi; Xie, Yang; Xiao, Guanghua

2017-03-01

Pathological examination of histopathological slides is a routine clinical procedure for lung cancer diagnosis and prognosis. Although the classification of lung cancer has been updated to become more specific, only a small subset of the total morphological features are taken into consideration. The vast majority of the detailed morphological features of tumor tissues, particularly tumor cells' surrounding microenvironment, are not fully analyzed. The heterogeneity of tumor cells and close interactions between tumor cells and their microenvironments are closely related to tumor development and progression. The goal of this study is to develop morphological feature-based prediction models for the prognosis of patients with lung cancer. We developed objective and quantitative computational approaches to analyze the morphological features of pathological images for patients with NSCLC. Tissue pathological images were analyzed for 523 patients with adenocarcinoma (ADC) and 511 patients with squamous cell carcinoma (SCC) from The Cancer Genome Atlas lung cancer cohorts. The features extracted from the pathological images were used to develop statistical models that predict patients' survival outcomes in ADC and SCC, respectively. We extracted 943 morphological features from pathological images of hematoxylin and eosin-stained tissue and identified morphological features that are significantly associated with prognosis in ADC and SCC, respectively. Statistical models based on these extracted features stratified NSCLC patients into high-risk and low-risk groups. The models were developed from training sets and validated in independent testing sets: a predicted high-risk group versus a predicted low-risk group (for patients with ADC: hazard ratio = 2.34, 95% confidence interval: 1.12-4.91, p = 0.024; for patients with SCC: hazard ratio = 2.22, 95% confidence interval: 1.15-4.27, p = 0.017) after adjustment for age, sex, smoking status, and pathologic tumor stage. The results suggest that the quantitative morphological features of tumor pathological images predict prognosis in patients with lung cancer. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

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.

Modification of Rat Lung Decellularization Protocol Based on Dynamic Conductometry of Working Solution.

PubMed

Kuevda, E V; Gubareva, E A; Gumenyuk, I S; Sotnichenko, A S; Gilevich, I V; Nakokhov, R Z; Rusinova, T V; Yudina, T G; Red'ko, A N; Alekseenko, S N

2017-03-01

We modified the protocol of obtaining of biological scaffolds of rat lungs based on dynamic recording of specific resistivity of working detergent solution (conductometry) during perfusion decellularization. Termination of sodium deoxycholate exposure after attaining ionic equilibrium plateau did not impair the quality of decellularization and preserved structural matrix components, which was confirmed by morphological analysis and quantitative assay of residual DNA.

The major-effect quantitative trait locus CsARN6.1 encodes an AAA ATPase domain-containing protein that is associated with waterlogging stress tolerance by promoting adventitious root formation

USDA-ARS?s Scientific Manuscript database

In plants, the formation of hypocotyl-derived adventitious roots (AR) is an important morphological acclimation to waterlogging stress, but its genetic basis is largely unknown. In the present study, with combined use of bulked segregant analysis-based high throughput next-gen whole genome sequencin...

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, correlated well with LA voltage. Decreased pulsatility strength in the LA was associated with recurrent AF. LA vortex may have incremental value in predicting the recurrence of AF.

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

Polysaccharides from Ganoderma lucidum attenuate microglia-mediated neuroinflammation and modulate microglial phagocytosis and behavioural response.

PubMed

Cai, Qing; Li, Yuanyuan; Pei, Gang

2017-03-24

Ganoderma lucidum (GL) has been widely used in Asian countries for hundreds of years to promote health and longevity. The pharmacological functions of which had been classified, including the activation of innate immune responses, suppression of tumour and modulation of cell proliferations. Effective fractions of Ganoderma lucidum polysaccharides (GLP) had already been reported to regulate the immune system. Nevertheless, the role of GLP in the microglia-mediated neuroinflammation has not been sufficiently elucidated. Further, GLP effect on microglial behavioural modulations in correlation with the inflammatory responses remains to be unravelled. The aim of this work was to quantitatively analyse the contributions of GLP on microglia. The BV2 microglia and primary mouse microglia were stimulated by lipopolysaccharides (LPS) and amyloid beta 42 (Aβ 42 ) oligomer, respectively. Investigation on the effect of GLP was carried by quantitative determination of the microglial pro- and anti-inflammatory cytokine expressions and behavioural modulations including migration, morphology and phagocytosis. Analysis of microglial morphology and phagocytosis modulations was confirmed in the zebrafish brain. Quantitative results revealed that GLP down-regulates LPS- or Aβ-induced pro-inflammatory cytokines and promotes anti-inflammatory cytokine expressions in BV-2 and primary microglia. In addition, GLP attenuates inflammation-related microglial migration, morphological alterations and phagocytosis probabilities. We also showed that modulations of microglial behavioural responses were associated with MCP-1 and C1q expressions. Overall, our study provides an insight into the GLP regulation of LPS- and Aβ-induced neuroinflammation and serves an implication that the neuroprotective function of GLP might be achieved through modulation of microglial inflammatory and behavioural responses.

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.

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.

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.

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.

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.

Effect of precursor supply on structural and morphological characteristics of fe nanomaterials synthesized via chemical vapor condensation method.

PubMed

Ha, Jong-Keun; Ahn, Hyo-Jun; Kim, Ki-Won; Nam, Tae-Hyun; Cho, Kwon-Koo

2012-01-01

Various physical, chemical and mechanical methods, such as inert gas condensation, chemical vapor condensation, sol-gel, pulsed wire evaporation, evaporation technique, and mechanical alloying, have been used to synthesize nanoparticles. Among them, chemical vapor condensation (CVC) has the benefit of its applicability to almost all materials because a wide range of precursors are available for large-scale production with a non-agglomerated state. In this work, Fe nanoparticles and nanowires were synthesized by chemical vapor condensation method using iron pentacarbonyl (Fe(CO)5) as the precursor. The effect of processing parameters on the microstructure, size and morphology of Fe nanoparticles and nanowires were studied. In particular, we investigated close correlation of size and morphology of Fe nanoparticles and nanowires with atomic quantity of inflow precursor into the electric furnace as the quantitative analysis. The atomic quantity was calculated by Boyle's ideal gas law. The Fe nanoparticles and nanowires with various diameter and morphology have successfully been synthesized by the chemical vapor condensation method.

GUIDOS: tools for the assessment of pattern, connectivity, and fragmentation

NASA Astrophysics Data System (ADS)

Vogt, Peter

2013-04-01

Pattern, connectivity, and fragmentation can be considered as pillars for a quantitative analysis of digital landscape images. The free software toolbox GUIDOS (http://forest.jrc.ec.europa.eu/download/software/guidos) includes a variety of dedicated methodologies for the quantitative assessment of these features. Amongst others, Morphological Spatial Pattern Analysis (MSPA) is used for an intuitive description of image pattern structures and the automatic detection of connectivity pathways. GUIDOS includes tools for the detection and quantitative assessment of key nodes and links as well as to define connectedness in raster images and to setup appropriate input files for an enhanced network analysis using Conefor Sensinode. Finally, fragmentation is usually defined from a species point of view but a generic and quantifiable indicator is needed to measure fragmentation and its changes. Some preliminary results for different conceptual approaches will be shown for a sample dataset. Complemented by pre- and post-processing routines and a complete GIS environment the portable GUIDOS Toolbox may facilitate a holistic assessment in risk assessment studies, landscape planning, and conservation/restoration policies. Alternatively, individual analysis components may contribute to or enhance studies conducted with other software packages in landscape ecology.

Innovative Applications of Laser Scanning and Rapid Prototype Printing to Rock Breakdown Experiments

NASA Technical Reports Server (NTRS)

Bourke, Mary; Viles, Heather; Nicoll, Joe; Lyew-Ayee, Parris; Ghent, Rebecca; Holmlund, James

2008-01-01

We present the novel application of two technologies for use in rock breakdown experiments, i.e. close-range, ground-based 3D triangulation scanning and rapid prototype printing. These techniques aid analyses of form-process interactions across the range of scales relevant to breakdown (micron-m). This is achieved through (a) the creation of DEMs (which permit quantitative description and analysis of rock surface morphology and morphological change) and (b) the production of more realistically-shaped experimental blocks. We illustrate the use of these techniques, alongside appropriate data analysis routines, in experiments designed to investigate the persistence of fluvially-derived features in the face of subsequent wind abrasion and weathering. These techniques have a range of potential applications in experimental field and lab-based geomorphic studies beyond those specifically outlined here.

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.

Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice.

PubMed

Wang, Shuzhen; Chen, Wenyue; Yang, Changdeng; Yao, Jian; Xiao, Wenfei; Xin, Ya; Qiu, Jieren; Hu, Weimin; Yao, Haigen; Ying, Wu; Fu, Yaping; Tong, Jianxin; Chen, Zhongzhong; Ruan, Songlin; Ma, Huasheng

2016-09-13

Polyploidy has pivotal influences on rice (Oryza sativa L.) morphology and physiology, and is very important for understanding rice domestication and improving agricultural traits. Diploid (DP) and triploid (TP) rice shows differences in morphological parameters, such as plant height, leaf length, leaf width and the physiological index of chlorophyll content. However, the underlying mechanisms determining these morphological differences are remain to be defined. To better understand the proteomic changes between DP and TP, tandem mass tags (TMT) mass spectrometry (MS)/MS was used to detect the significant changes to protein expression between DP and TP. Results indicated that both photosynthesis and metabolic pathways were highly significantly associated with proteomic alteration between DP and TP based on biological process and pathway enrichment analysis, and 13 higher abundance chloroplast proteins involving in these two pathways were identified in TP. Quantitative real-time PCR analysis demonstrated that 5 of the 13 chloroplast proteins ATPF, PSAA, PSAB, PSBB and RBL in TP were higher abundance compared with those in DP. This study integrates morphology, physiology and proteomic profiling alteration of DP and TP to address their underlying different molecular mechanisms. Our finding revealed that ATPF, PSAA, PSAB, PSBB and RBL can induce considerable expression changes in TP and may affect the development and growth of rice through photosynthesis and metabolic pathways.

A quantitative framework for flower phenotyping in cultivated carnation (Dianthus caryophyllus L.).

PubMed

Chacón, Borja; Ballester, Roberto; Birlanga, Virginia; Rolland-Lagan, Anne-Gaëlle; Pérez-Pérez, José Manuel

2013-01-01

Most important breeding goals in ornamental crops are plant appearance and flower characteristics where selection is visually performed on direct offspring of crossings. We developed an image analysis toolbox for the acquisition of flower and petal images from cultivated carnation (Dianthus caryophyllus L.) that was validated by a detailed analysis of flower and petal size and shape in 78 commercial cultivars of D. caryophyllus, including 55 standard, 22 spray and 1 pot carnation cultivars. Correlation analyses allowed us to reduce the number of parameters accounting for the observed variation in flower and petal morphology. Convexity was used as a descriptor for the level of serration in flowers and petals. We used a landmark-based approach that allowed us to identify eight main principal components (PCs) accounting for most of the variance observed in petal shape. The effect and the strength of these PCs in standard and spray carnation cultivars are consistent with shared underlying mechanisms involved in the morphological diversification of petals in both subpopulations. Our results also indicate that neighbor-joining trees built with morphological data might infer certain phylogenetic relationships among carnation cultivars. Based on estimated broad-sense heritability values for some flower and petal features, different genetic determinants shall modulate the responses of flower and petal morphology to environmental cues in this species. We believe our image analysis toolbox could allow capturing flower variation in other species of high ornamental value.

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

An Automated Solar Synoptic Analysis Software System

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

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.

Role of citron kinase in dendritic morphogenesis of cortical neurons.

PubMed

Di Cunto, Ferdinando; Ferrara, Luciana; Curtetti, Roberta; Imarisio, Sara; Guazzone, Simona; Broccoli, Vania; Bulfone, Alessandro; Altruda, Fiorella; Vercelli, Alessandro; Silengo, Lorenzo

2003-05-30

Small GTPases of the rho family regulate the extensive rearrangements of the cytoskeleton that characterize neuronal differentiation. Citron kinase is a target molecule for activated rhoA, previously implicated in control of cytokinesis. We have found that, in addition, it could play an important role in modulating the extension of neuronal processes. Using constitutively active and dominant negative mutants, we showed that citron kinase is involved in the morphologic differentiation of N1E-115 neuroblastoma cells induced by serum starvation. More importantly, quantitative analysis of citron kinase knockout cerebral cortex displayed that this molecule may differentially regulate the morphology of the dendritic compartment in corticocollicular versus callosally-projecting pyramidal neurons.

Label-free three-dimensional imaging of cell nucleus using third-harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Lin, Jian; Zheng, Wei; Wang, Zi; Huang, Zhiwei

2014-09-01

We report the implementation of the combined third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) microscopy for label-free three-dimensional (3-D) imaging of cell nucleus morphological changes in liver tissue. THG imaging shows regular spherical shapes of normal hepatocytes nuclei with inner chromatin structures while revealing the condensation of chromatins and nuclear fragmentations in hepatocytes of diseased liver tissue. Colocalized THG and TPEF imaging provides complementary information of cell nuclei and cytoplasm in tissue. This work suggests that 3-D THG microscopy has the potential for quantitative analysis of nuclear morphology in cells at a submicron-resolution without the need for DNA staining.

Label-free three-dimensional imaging of cell nucleus using third-harmonic generation microscopy

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

Lin, Jian; Zheng, Wei; Wang, Zi

2014-09-08

We report the implementation of the combined third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) microscopy for label-free three-dimensional (3-D) imaging of cell nucleus morphological changes in liver tissue. THG imaging shows regular spherical shapes of normal hepatocytes nuclei with inner chromatin structures while revealing the condensation of chromatins and nuclear fragmentations in hepatocytes of diseased liver tissue. Colocalized THG and TPEF imaging provides complementary information of cell nuclei and cytoplasm in tissue. This work suggests that 3-D THG microscopy has the potential for quantitative analysis of nuclear morphology in cells at a submicron-resolution without the need for DNA staining.

Variation of BMP3 Contributes to Dog Breed Skull Diversity

PubMed Central

Schoenebeck, Jeffrey J.; Hutchinson, Sarah A.; Byers, Alexandra; Beale, Holly C.; Carrington, Blake; Faden, Daniel L.; Rimbault, Maud; Decker, Brennan; Kidd, Jeffrey M.; Sood, Raman; Boyko, Adam R.; Fondon, John W.; Wayne, Robert K.; Bustamante, Carlos D.; Ciruna, Brian; Ostrander, Elaine A.

2012-01-01

Since the beginnings of domestication, the craniofacial architecture of the domestic dog has morphed and radiated to human whims. By beginning to define the genetic underpinnings of breed skull shapes, we can elucidate mechanisms of morphological diversification while presenting a framework for understanding human cephalic disorders. Using intrabreed association mapping with museum specimen measurements, we show that skull shape is regulated by at least five quantitative trait loci (QTLs). Our detailed analysis using whole-genome sequencing uncovers a missense mutation in BMP3. Validation studies in zebrafish show that Bmp3 function in cranial development is ancient. Our study reveals the causal variant for a canine QTL contributing to a major morphologic trait. PMID:22876193

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.

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

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.

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

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.

Nanoscale quantification of intracellular element concentration by X-ray fluorescence microscopy combined with X-ray phase contrast nanotomography

NASA Astrophysics Data System (ADS)

Gramaccioni, Chiara; Yang, Yang; Procopio, Alessandra; Pacureanu, Alexandra; Bohic, Sylvain; Malucelli, Emil; Iotti, Stefano; Farruggia, Giovanna; Bukreeva, Inna; Notargiacomo, Andrea; Fratini, Michela; Valenti, Piera; Rosa, Luigi; Berlutti, Francesca; Cloetens, Peter; Lagomarsino, Stefano

2018-01-01

We present here a correlative X-ray microscopy approach for quantitative single cell imaging of molar concentrations. By combining the elemental content provided by X-ray fluorescence microscopy and the morphology information extracted from X-ray phase nanotomography, we determine the intracellular molarity distributions. This correlative method was demonstrated on a freeze-dried human phagocytic cell to obtain the absolute elemental concentration maps of K, P, and Fe. The cell morphology results showed a very good agreement with atomic-force microscopy measurements. This work opens the way for non-destructive single cell chemical analysis down to the sub-cellular level using exclusively synchrotron radiation techniques. It will be of high interest in the case where it is difficult to access the morphology using atomic-force microscopy, for example, on frozen-hydrated cells or tissues.

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.

How cells explore shape space: a quantitative statistical perspective of cellular morphogenesis.

PubMed

Yin, Zheng; Sailem, Heba; Sero, Julia; Ardy, Rico; Wong, Stephen T C; Bakal, Chris

2014-12-01

Through statistical analysis of datasets describing single cell shape following systematic gene depletion, we have found that the morphological landscapes explored by cells are composed of a small number of attractor states. We propose that the topology of these landscapes is in large part determined by cell-intrinsic factors, such as biophysical constraints on cytoskeletal organization, and reflects different stable signaling and/or transcriptional states. Cell-extrinsic factors act to determine how cells explore these landscapes, and the topology of the landscapes themselves. Informational stimuli primarily drive transitions between stable states by engaging signaling networks, while mechanical stimuli tune, or even radically alter, the topology of these landscapes. As environments fluctuate, the topology of morphological landscapes explored by cells dynamically adapts to these fluctuations. Finally we hypothesize how complex cellular and tissue morphologies can be generated from a limited number of simple cell shapes. © 2014 WILEY Periodicals, Inc.

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 identification of fault surfaces through Object Based Image Analysis of a Digital Elevation Model in the submarine area of the North Aegean Basin

NASA Astrophysics Data System (ADS)

Argyropoulou, Evangelia

2015-04-01

The current study was focused on the seafloor morphology of the North Aegean Basin in Greece, through Object Based Image Analysis (OBIA) using a Digital Elevation Model. The goal was the automatic extraction of morphologic and morphotectonic features, resulting into fault surface extraction. An Object Based Image Analysis approach was developed based on the bathymetric data and the extracted features, based on morphological criteria, were compared with the corresponding landforms derived through tectonic analysis. A digital elevation model of 150 meters spatial resolution was used. At first, slope, profile curvature, and percentile were extracted from this bathymetry grid. The OBIA approach was developed within the eCognition environment. Four segmentation levels were created having as a target "level 4". At level 4, the final classes of geomorphological features were classified: discontinuities, fault-like features and fault surfaces. On previous levels, additional landforms were also classified, such as continental platform and continental slope. The results of the developed approach were evaluated by two methods. At first, classification stability measures were computed within eCognition. Then, qualitative and quantitative comparison of the results took place with a reference tectonic map which has been created manually based on the analysis of seismic profiles. The results of this comparison were satisfactory, a fact which determines the correctness of the developed OBIA approach.

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

The neocortex of cetartiodactyls. II. Neuronal morphology of the visual and motor cortices in the giraffe (Giraffa camelopardalis).

PubMed

Jacobs, Bob; Harland, Tessa; Kennedy, Deborah; Schall, Matthew; Wicinski, Bridget; Butti, Camilla; Hof, Patrick R; Sherwood, Chet C; Manger, Paul R

2015-09-01

The present quantitative study extends our investigation of cetartiodactyls by exploring the neuronal morphology in the giraffe (Giraffa camelopardalis) neocortex. Here, we investigate giraffe primary visual and motor cortices from perfusion-fixed brains of three subadults stained with a modified rapid Golgi technique. Neurons (n = 244) were quantified on a computer-assisted microscopy system. Qualitatively, the giraffe neocortex contained an array of complex spiny neurons that included both "typical" pyramidal neuron morphology and "atypical" spiny neurons in terms of morphology and/or orientation. In general, the neocortex exhibited a vertical columnar organization of apical dendrites. Although there was no significant quantitative difference in dendritic complexity for pyramidal neurons between primary visual (n = 78) and motor cortices (n = 65), there was a significant difference in dendritic spine density (motor cortex > visual cortex). The morphology of aspiny neurons in giraffes appeared to be similar to that of other eutherian mammals. For cross-species comparison of neuron morphology, giraffe pyramidal neurons were compared to those quantified with the same methodology in African elephants and some cetaceans (e.g., bottlenose dolphin, minke whale, humpback whale). Across species, the giraffe (and cetaceans) exhibited less widely bifurcating apical dendrites compared to elephants. Quantitative dendritic measures revealed that the elephant and humpback whale had more extensive dendrites than giraffes, whereas the minke whale and bottlenose dolphin had less extensive dendritic arbors. Spine measures were highest in the giraffe, perhaps due to the high quality, perfusion fixation. The neuronal morphology in giraffe neocortex is thus generally consistent with what is known about other cetartiodactyls.

The core contribution of transmission electron microscopy to functional nanomaterials engineering

NASA Astrophysics Data System (ADS)

Carenco, Sophie; Moldovan, Simona; Roiban, Lucian; Florea, Ileana; Portehault, David; Vallé, Karine; Belleville, Philippe; Boissière, Cédric; Rozes, Laurence; Mézailles, Nicolas; Drillon, Marc; Sanchez, Clément; Ersen, Ovidiu

2016-01-01

Research on nanomaterials and nanostructured materials is burgeoning because their numerous and versatile applications contribute to solve societal needs in the domain of medicine, energy, environment and STICs. Optimizing their properties requires in-depth analysis of their structural, morphological and chemical features at the nanoscale. In a transmission electron microscope (TEM), combining tomography with electron energy loss spectroscopy and high-magnification imaging in high-angle annular dark-field mode provides access to all features of the same object. Today, TEM experiments in three dimensions are paramount to solve tough structural problems associated with nanoscale matter. This approach allowed a thorough morphological description of silica fibers. Moreover, quantitative analysis of the mesoporous network of binary metal oxide prepared by template-assisted spray-drying was performed, and the homogeneity of amino functionalized metal-organic frameworks was assessed. Besides, the morphology and internal structure of metal phosphide nanoparticles was deciphered, providing a milestone for understanding phase segregation at the nanoscale. By extrapolating to larger classes of materials, from soft matter to hard metals and/or ceramics, this approach allows probing small volumes and uncovering materials characteristics and properties at two or three dimensions. Altogether, this feature article aims at providing (nano)materials scientists with a representative set of examples that illustrates the capabilities of modern TEM and tomography, which can be transposed to their own research.Research on nanomaterials and nanostructured materials is burgeoning because their numerous and versatile applications contribute to solve societal needs in the domain of medicine, energy, environment and STICs. Optimizing their properties requires in-depth analysis of their structural, morphological and chemical features at the nanoscale. In a transmission electron microscope (TEM), combining tomography with electron energy loss spectroscopy and high-magnification imaging in high-angle annular dark-field mode provides access to all features of the same object. Today, TEM experiments in three dimensions are paramount to solve tough structural problems associated with nanoscale matter. This approach allowed a thorough morphological description of silica fibers. Moreover, quantitative analysis of the mesoporous network of binary metal oxide prepared by template-assisted spray-drying was performed, and the homogeneity of amino functionalized metal-organic frameworks was assessed. Besides, the morphology and internal structure of metal phosphide nanoparticles was deciphered, providing a milestone for understanding phase segregation at the nanoscale. By extrapolating to larger classes of materials, from soft matter to hard metals and/or ceramics, this approach allows probing small volumes and uncovering materials characteristics and properties at two or three dimensions. Altogether, this feature article aims at providing (nano)materials scientists with a representative set of examples that illustrates the capabilities of modern TEM and tomography, which can be transposed to their own research. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05460e

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.

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

Cooper, W. James; Albertson, R Craig; Jacob, Rick E.

Here we present a re-description of Abudefduf luridus and reassign it to the genus Similiparma. We supplement traditional diagnoses and descriptions of this species with quantitative anatomical data collected from a family-wide geometric morphometric analysis of head morphology (44 species representing all 30 damselfish genera) and data from cranial micro-CT scans of fishes in the genus Similiparma. The use of geometric morphometric analyses (and other methods of shape analysis) permits detailed comparisons between the morphology of specific taxa and the anatomical diversity that has arisen in an entire lineage. This provides a particularly useful supplement to traditional description methods andmore » we recommend the use of such techniques by systematists. Similiparma and its close relatives constitute a branch of the damselfish phylogenetic tree that predominantly inhabits rocky reefs in the Atlantic and Eastern Pacific, as opposed to the more commonly studied damselfishes that constitute a large portion of the ichthyofauna on all coral-reef communities.« less

Determine precipitation rates from visible and infrared satellite images of clouds by pattern recognition technique. Progress Report, 1 Jul. 1985 - 31 Mar. 1987 Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Weinman, James A.; Garan, Louis

1987-01-01

A more advanced cloud pattern analysis algorithm was subsequently developed to take the shape and brightness of the various clouds into account in a manner that is more consistent with the human analyst's perception of GOES cloud imagery. The results of that classification scheme were compared with precipitation probabilities observed from ships of opportunity off the U.S. east coast to derive empirical regressions between cloud types and precipitation probability. The cloud morphology was then quantitatively and objectively used to map precipitation probabilities during two winter months during which severe cold air outbreaks were observed over the northwest Atlantic. Precipitation probabilities associated with various cloud types are summarized. Maps of precipitation probability derived from the cloud morphology analysis program for two months and the precipitation probability derived from thirty years of ship observation were observed.

Quantitative evaluation of skeletal muscle defects in second harmonic generation images.

PubMed

Liu, Wenhua; Raben, Nina; Ralston, Evelyn

2013-02-01

Skeletal muscle pathologies cause irregularities in the normally periodic organization of the myofibrils. Objective grading of muscle morphology is necessary to assess muscle health, compare biopsies, and evaluate treatments and the evolution of disease. To facilitate such quantitation, we have developed a fast, sensitive, automatic imaging analysis software. It detects major and minor morphological changes by combining texture features and Fourier transform (FT) techniques. We apply this tool to second harmonic generation (SHG) images of muscle fibers which visualize the repeating myosin bands. Texture features are then calculated by using a Haralick gray-level cooccurrence matrix in MATLAB. Two scores are retrieved from the texture correlation plot by using FT and curve-fitting methods. The sensitivity of the technique was tested on SHG images of human adult and infant muscle biopsies and of mouse muscle samples. The scores are strongly correlated to muscle fiber condition. We named the software MARS (muscle assessment and rating scores). It is executed automatically and is highly sensitive even to subtle defects. We propose MARS as a powerful and unbiased tool to assess muscle health.

Quantitative evaluation of skeletal muscle defects in second harmonic generation images

NASA Astrophysics Data System (ADS)

Liu, Wenhua; Raben, Nina; Ralston, Evelyn

2013-02-01

Skeletal muscle pathologies cause irregularities in the normally periodic organization of the myofibrils. Objective grading of muscle morphology is necessary to assess muscle health, compare biopsies, and evaluate treatments and the evolution of disease. To facilitate such quantitation, we have developed a fast, sensitive, automatic imaging analysis software. It detects major and minor morphological changes by combining texture features and Fourier transform (FT) techniques. We apply this tool to second harmonic generation (SHG) images of muscle fibers which visualize the repeating myosin bands. Texture features are then calculated by using a Haralick gray-level cooccurrence matrix in MATLAB. Two scores are retrieved from the texture correlation plot by using FT and curve-fitting methods. The sensitivity of the technique was tested on SHG images of human adult and infant muscle biopsies and of mouse muscle samples. The scores are strongly correlated to muscle fiber condition. We named the software MARS (muscle assessment and rating scores). It is executed automatically and is highly sensitive even to subtle defects. We propose MARS as a powerful and unbiased tool to assess muscle health.

Proflavine Hemisulfate as a Fluorescent Contrast Agent for Point-of-Care Cytology

PubMed Central

Prieto, Sandra P.; Powless, Amy J.; Boice, Jackson W.; Sharma, Shree G.; Muldoon, Timothy J.

2015-01-01

Proflavine hemisulfate, an acridine-derived fluorescent dye, can be used as a rapid stain for cytologic examination of biological specimens. Proflavine fluorescently stains cell nuclei and cytoplasmic structures, owing to its small amphipathic structure and ability to intercalate DNA. In this manuscript, we demonstrated the use of proflavine as a rapid cytologic dye on a number of specimens, including normal exfoliated oral squamous cells, cultured human oral squamous carcinoma cells, and leukocytes derived from whole blood specimens using a custom-built, portable, LED-illuminated fluorescence microscope. No incubation time was needed after suspending cells in 0.01% (w/v) proflavine diluted in saline. Images of proflavine stained oral cells had clearly visible nuclei as well as granular cytoplasm, while stained leukocytes exhibited bright nuclei, and highlighted the multilobar nature of nuclei in neutrophils. We also demonstrated the utility of quantitative analysis of digital images of proflavine stained cells, which can be used to detect significant morphological differences between different cell types. Proflavine stained oral cells have well-defined nuclei and cell membranes which allowed for quantitative analysis of nuclear to cytoplasmic ratios, as well as image texture analysis to extract quantitative image features. PMID:25962131

Proflavine Hemisulfate as a Fluorescent Contrast Agent for Point-of-Care Cytology.

PubMed

Prieto, Sandra P; Powless, Amy J; Boice, Jackson W; Sharma, Shree G; Muldoon, Timothy J

2015-01-01

Proflavine hemisulfate, an acridine-derived fluorescent dye, can be used as a rapid stain for cytologic examination of biological specimens. Proflavine fluorescently stains cell nuclei and cytoplasmic structures, owing to its small amphipathic structure and ability to intercalate DNA. In this manuscript, we demonstrated the use of proflavine as a rapid cytologic dye on a number of specimens, including normal exfoliated oral squamous cells, cultured human oral squamous carcinoma cells, and leukocytes derived from whole blood specimens using a custom-built, portable, LED-illuminated fluorescence microscope. No incubation time was needed after suspending cells in 0.01% (w/v) proflavine diluted in saline. Images of proflavine stained oral cells had clearly visible nuclei as well as granular cytoplasm, while stained leukocytes exhibited bright nuclei, and highlighted the multilobar nature of nuclei in neutrophils. We also demonstrated the utility of quantitative analysis of digital images of proflavine stained cells, which can be used to detect significant morphological differences between different cell types. Proflavine stained oral cells have well-defined nuclei and cell membranes which allowed for quantitative analysis of nuclear to cytoplasmic ratios, as well as image texture analysis to extract quantitative image features.

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

A Histopathological Scheme for the Quantitative Scoring of Intervertebral Disc Degeneration and the Therapeutic Utility of Adult Mesenchymal Stem Cells for Intervertebral Disc Regeneration

PubMed Central

Shu, Cindy C.; Smith, Margaret M.; Smith, Susan M.; Dart, Andrew J.; Little, Christopher B.; Melrose, James

2017-01-01

The purpose of this study was to develop a quantitative histopathological scoring scheme to evaluate disc degeneration and regeneration using an ovine annular lesion model of experimental disc degeneration. Toluidine blue and Haematoxylin and Eosin (H&E) staining were used to evaluate cellular morphology: (i) disc structure/lesion morphology; (ii) proteoglycan depletion; (iii) cellular morphology; (iv) blood vessel in-growth; (v) cell influx into lesion; and (vi) cystic degeneration/chondroid metaplasia. Three study groups were examined: 5 × 5 mm lesion; 6 × 20 mm lesion; and 6 × 20 mm lesion plus mesenchymal stem cell (MSC) treatment. Lumbar intervertebral discs (IVDs) were scored under categories (i–vi) to provide a cumulative score, which underwent statistical analysis using STATA software. Focal proteoglycan depletion was associated with 5 × 5 mm annular rim lesions, bifurcations, annular delamellation, concentric and radial annular tears and an early influx of blood vessels and cells around remodeling lesions but the inner lesion did not heal. Similar features in 6 × 20 mm lesions occurred over a 3–6-month post operative period. MSCs induced a strong recovery in discal pathology with a reduction in cumulative histopathology degeneracy score from 15.2 to 2.7 (p = 0.001) over a three-month recovery period but no recovery in carrier injected discs. PMID:28498326

A Histopathological Scheme for the Quantitative Scoring of Intervertebral Disc Degeneration and the Therapeutic Utility of Adult Mesenchymal Stem Cells for Intervertebral Disc Regeneration.

PubMed

Shu, Cindy C; Smith, Margaret M; Smith, Susan M; Dart, Andrew J; Little, Christopher B; Melrose, James

2017-05-12

The purpose of this study was to develop a quantitative histopathological scoring scheme to evaluate disc degeneration and regeneration using an ovine annular lesion model of experimental disc degeneration. Toluidine blue and Haematoxylin and Eosin (H&E) staining were used to evaluate cellular morphology: (i) disc structure/lesion morphology; (ii) proteoglycan depletion; (iii) cellular morphology; (iv) blood vessel in-growth; (v) cell influx into lesion; and (vi) cystic degeneration/chondroid metaplasia. Three study groups were examined: 5 × 5 mm lesion; 6 × 20 mm lesion; and 6 × 20 mm lesion plus mesenchymal stem cell (MSC) treatment. Lumbar intervertebral discs (IVDs) were scored under categories (i-vi) to provide a cumulative score, which underwent statistical analysis using STATA software. Focal proteoglycan depletion was associated with 5 × 5 mm annular rim lesions, bifurcations, annular delamellation, concentric and radial annular tears and an early influx of blood vessels and cells around remodeling lesions but the inner lesion did not heal. Similar features in 6 × 20 mm lesions occurred over a 3-6-month post operative period. MSCs induced a strong recovery in discal pathology with a reduction in cumulative histopathology degeneracy score from 15.2 to 2.7 ( p = 0.001) over a three-month recovery period but no recovery in carrier injected discs.

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 encourage the use of this method in future investigations, particularly for longitudinal studies. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Quantitative morphometrical characterization of human pronuclear zygotes.

PubMed

Beuchat, A; Thévenaz, P; Unser, M; Ebner, T; Senn, A; Urner, F; Germond, M; Sorzano, C O S

2008-09-01

Identification of embryos with high implantation potential remains a challenge in in vitro fertilization (IVF). Subjective pronuclear (PN) zygote scoring systems have been developed for that purpose. The aim of this work was to provide a software tool that enables objective measuring of morphological characteristics of the human PN zygote. A computer program was created to analyse zygote images semi-automatically, providing precise morphological measurements. The accuracy of this approach was first validated by comparing zygotes from two different IVF centres with computer-assisted measurements or subjective scoring. Computer-assisted measurement and subjective scoring were then compared for their ability to classify zygotes with high and low implantation probability by using a linear discriminant analysis. Zygote images coming from the two IVF centres were analysed with the software, resulting in a series of precise measurements of 24 variables. Using subjective scoring, the cytoplasmic halo was the only feature which was significantly different between the two IVF centres. Computer-assisted measurements revealed significant differences between centres in PN centring, PN proximity, cytoplasmic halo and features related to nucleolar precursor bodies distribution. The zygote classification error achieved with the computer-assisted measurements (0.363) was slightly inferior to that of the subjective ones (0.393). A precise and objective characterization of the morphology of human PN zygotes can be achieved by the use of an advanced image analysis tool. This computer-assisted analysis allows for a better morphological characterization of human zygotes and can be used for classification.

A Quantitative Framework for Flower Phenotyping in Cultivated Carnation (Dianthus caryophyllus L.)

PubMed Central

Chacón, Borja; Ballester, Roberto; Birlanga, Virginia; Rolland-Lagan, Anne-Gaëlle; Pérez-Pérez, José Manuel

2013-01-01

Most important breeding goals in ornamental crops are plant appearance and flower characteristics where selection is visually performed on direct offspring of crossings. We developed an image analysis toolbox for the acquisition of flower and petal images from cultivated carnation (Dianthus caryophyllus L.) that was validated by a detailed analysis of flower and petal size and shape in 78 commercial cultivars of D. caryophyllus, including 55 standard, 22 spray and 1 pot carnation cultivars. Correlation analyses allowed us to reduce the number of parameters accounting for the observed variation in flower and petal morphology. Convexity was used as a descriptor for the level of serration in flowers and petals. We used a landmark-based approach that allowed us to identify eight main principal components (PCs) accounting for most of the variance observed in petal shape. The effect and the strength of these PCs in standard and spray carnation cultivars are consistent with shared underlying mechanisms involved in the morphological diversification of petals in both subpopulations. Our results also indicate that neighbor-joining trees built with morphological data might infer certain phylogenetic relationships among carnation cultivars. Based on estimated broad-sense heritability values for some flower and petal features, different genetic determinants shall modulate the responses of flower and petal morphology to environmental cues in this species. We believe our image analysis toolbox could allow capturing flower variation in other species of high ornamental value. PMID:24349209

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

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.

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.

Chemical Characterization and Determination of the Anti-Oxidant Capacity of Two Brown Algae with Respect to Sampling Season and Morphological Structures Using Infrared Spectroscopy and Multivariate Analyses.

PubMed

Beratto, Angelo; Agurto, Cristian; Freer, Juanita; Peña-Farfal, Carlos; Troncoso, Nicolás; Agurto, Andrés; Castillo, Rosario Del P

2017-10-01

Brown algae biomass has been shown to be a highly important industrial source for the production of alginates and different nutraceutical products. The characterization of this biomass is necessary in order to allocate its use to specific applications according to the chemical and biological characteristics of this highly variable resource. The methods commonly used for algae characterization require a long time for the analysis and rigorous pretreatments of samples. In this work, nondestructive and fast analyses of different morphological structures from Lessonia spicata and Macrocystis pyrifera, which were collected during different seasons, were performed using Fourier transform infrared (FT-IR) techniques in combination with chemometric methods. Mid-infrared (IR) and near-infrared (NIR) spectral ranges were tested to evaluate the spectral differences between the species, seasons, and morphological structures of algae using a principal component analysis (PCA). Quantitative analyses of the polyphenol and alginate contents and the anti-oxidant capacity of the samples were performed using partial least squares (PLS) with both spectral ranges in order to build a predictive model for the rapid quantification of these parameters with industrial purposes. The PCA mainly showed differences in the samples based on seasonal sampling, where changes were observed in the bands corresponding to polysaccharides, proteins, and lipids. The obtained PLS models had high correlation coefficients (r) for the polyphenol content and anti-oxidant capacity (r > 0.9) and lower values for the alginate determination (0.7 < r < 0.8). Fourier transform infrared-based techniques were suitable tools for the rapid characterization of algae biomass, in which high variability in the samples was incorporated for the qualitative and quantitative analyses, and have the potential to be used on an industrial scale.

Musical representation of dendritic spine distribution: a new exploratory tool.

PubMed

Toharia, Pablo; Morales, Juan; de Juan, Octavio; Fernaud, Isabel; Rodríguez, Angel; DeFelipe, Javier

2014-04-01

Dendritic spines are small protrusions along the dendrites of many types of neurons in the central nervous system and represent the major target of excitatory synapses. For this reason, numerous anatomical, physiological and computational studies have focused on these structures. In the cerebral cortex the most abundant and characteristic neuronal type are pyramidal cells (about 85 % of all neurons) and their dendritic spines are the main postsynaptic target of excitatory glutamatergic synapses. Thus, our understanding of the synaptic organization of the cerebral cortex largely depends on the knowledge regarding synaptic inputs to dendritic spines of pyramidal cells. Much of the structural data on dendritic spines produced by modern neuroscience involves the quantitative analysis of image stacks from light and electron microscopy, using standard statistical and mathematical tools and software developed to this end. Here, we present a new method with musical feedback for exploring dendritic spine morphology and distribution patterns in pyramidal neurons. We demonstrate that audio analysis of spiny dendrites with apparently similar morphology may "sound" quite different, revealing anatomical substrates that are not apparent from simple visual inspection. These morphological/music translations may serve as a guide for further mathematical analysis of the design of the pyramidal neurons and of spiny dendrites in general.

Morphological Characters and Transcriptome Profiles Associated with Black Skin and Red Skin in Crimson Snapper (Lutjanus erythropterus)

PubMed Central

Zhang, Yan-Ping; Wang, Zhong-Duo; Guo, Yu-Song; Liu, Li; Yu, Juan; Zhang, Shun; Liu, Shao-Jun; Liu, Chu-Wu

2015-01-01

In this study, morphology observation and illumina sequencing were performed on two different coloration skins of crimson snapper (Lutjanus erythropterus), the black zone and the red zone. Three types of chromatophores, melanophores, iridophores and xanthophores, were organized in the skins. The main differences between the two colorations were in the amount and distribution of the three chromatophores. After comparing the two transcriptomes, 9200 unigenes with significantly different expressions (ratio change ≥ 2 and q-value ≤ 0.05) were found, of which 5972 were up-regulated in black skin and 3228 were up-regulated in red skin. Through the function annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the differentially transcribed genes, we excavated a number of uncharacterized candidate pigment genes as well as found the conserved genes affecting pigmentation in crimson snapper. The patterns of expression of 14 pigment genes were confirmed by the Quantitative real-time PCR analysis between the two color skins. Overall, this study shows a global survey of the morphological characters and transcriptome analysis of the different coloration skins in crimson snapper, and provides valuable cellular and genetic information to uncover the mechanism of the formation of pigment patterns in snappers. PMID:26569232

Morphological Characters and Transcriptome Profiles Associated with Black Skin and Red Skin in Crimson Snapper (Lutjanus erythropterus).

PubMed

Zhang, Yan-Ping; Wang, Zhong-Duo; Guo, Yu-Song; Liu, Li; Yu, Juan; Zhang, Shun; Liu, Shao-Jun; Liu, Chu-Wu

2015-11-12

In this study, morphology observation and illumina sequencing were performed on two different coloration skins of crimson snapper (Lutjanus erythropterus), the black zone and the red zone. Three types of chromatophores, melanophores, iridophores and xanthophores, were organized in the skins. The main differences between the two colorations were in the amount and distribution of the three chromatophores. After comparing the two transcriptomes, 9200 unigenes with significantly different expressions (ratio change ≥ 2 and q-value ≤ 0.05) were found, of which 5972 were up-regulated in black skin and 3228 were up-regulated in red skin. Through the function annotation, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the differentially transcribed genes, we excavated a number of uncharacterized candidate pigment genes as well as found the conserved genes affecting pigmentation in crimson snapper. The patterns of expression of 14 pigment genes were confirmed by the Quantitative real-time PCR analysis between the two color skins. Overall, this study shows a global survey of the morphological characters and transcriptome analysis of the different coloration skins in crimson snapper, and provides valuable cellular and genetic information to uncover the mechanism of the formation of pigment patterns in snappers.

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.

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 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.

Quantitative evaluation of bone resorption activity of osteoclast-like cells by measuring calcium phosphate resorbing area using incubator-facilitated and video-enhanced microscopy.

PubMed

Morimoto, Yoshitaka; Hoshino, Hironobu; Sakurai, Takashi; Terakawa, Susumu; Nagano, Akira

2009-04-01

Quantitative evaluation of the ability of bone resorption activity in live osteoclast-like cells (OCLs) has not yet been reported on. In this study, we observed the sequential morphological change of OCLs and measured the resorbing calcium phosphate (CP) area made by OCLs alone and with the addition of elcatonin utilizing incubator facilitated video-enhanced microscopy. OCLs, which were obtained from a coculture of ddy-mouse osteoblastic cells and bone marrow cells, were cultured on CP-coated quartz cover slips. The CP-free area increased constantly in the OCLs alone, whereas it did not increase after the addition of elcatonin. This study showed that analysis of the resorbed areas under the OCL body using this method enables the sequential quantitative evaluation of the bone resorption activity and the effect of several therapeutic agents on bone resorption in vitro.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

PubMed

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

Clathrin-independent carriers form a high capacity endocytic sorting system at the leading edge of migrating cells

PubMed Central

Howes, Mark T.; Kirkham, Matthew; Riches, James; Cortese, Katia; Walser, Piers J.; Simpson, Fiona; Hill, Michelle M.; Jones, Alun; Lundmark, Richard; Lindsay, Margaret R.; Hernandez-Deviez, Delia J.; Hadzic, Gordana; McCluskey, Adam; Bashir, Rumasia; Liu, Libin; Pilch, Paul; McMahon, Harvey; Robinson, Phillip J.; Hancock, John F.; Mayor, Satyajit

2010-01-01

Although the importance of clathrin- and caveolin-independent endocytic pathways has recently emerged, key aspects of these routes remain unknown. Using quantitative ultrastructural approaches, we show that clathrin-independent carriers (CLICs) account for approximately three times the volume internalized by the clathrin-mediated endocytic pathway, forming the major pathway involved in uptake of fluid and bulk membrane in fibroblasts. Electron tomographic analysis of the 3D morphology of the earliest carriers shows that they are multidomain organelles that form a complex sorting station as they mature. Proteomic analysis provides direct links between CLICs, cellular adhesion turnover, and migration. Consistent with this, CLIC-mediated endocytosis of key cargo proteins, CD44 and Thy-1, is polarized at the leading edge of migrating fibroblasts, while transient ablation of CLICs impairs their ability to migrate. These studies provide the first quantitative ultrastructural analysis and molecular characterization of the major endocytic pathway in fibroblasts, a pathway that provides rapid membrane turnover at the leading edge of migrating cells. PMID:20713605

Changes of the elemental distributions in marine diatoms as a reporter of sample preparation artefacts. A nuclear microscopy application

NASA Astrophysics Data System (ADS)

Godinho, R. M.; Cabrita, M. T.; Alves, L. C.; Pinheiro, T.

2015-04-01

Studies of the elemental composition of whole marine diatoms cells have high interest as they constitute a direct measurement of environmental changes, and allow anticipating consequences of anthropogenic alterations to organisms, ecosystems and global marine geochemical cycles. Nuclear microscopy is a powerful tool allowing direct measurement of whole cells giving qualitative imaging of distribution, and quantitative determination of intracellular concentration. Major obstacles to the analysis of marine microalgae are high medium salinity and the recurrent presence of extracellular exudates produced by algae to maintain colonies in natural media and in vitro. The objective of this paper was to optimize the methodology of sample preparation of marine unicellular algae for elemental analysis with nuclear microscopy, allowing further studies on cellular response to metals. Primary cultures of Coscinodiscus wailesii maintained in vitro were used to optimize protocols for elemental analysis with nuclear microscopy techniques. Adequate cell preparation procedures to isolate the cells from media components and exudates were established. The use of chemical agents proved to be inappropriate for elemental determination and for intracellular morphological analysis. The assessment of morphology and elemental partitioning in cell compartments obtained with nuclear microscopy techniques enabled to infer their function in natural environment and imbalances in exposure condition. Exposure to metal affected C. wailesii morphology and internal elemental distribution.

Systematic analysis of Ca2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles

PubMed Central

Ghanegolmohammadi, Farzan; Yoshida, Mitsunori; Ohnuki, Shinsuke; Sukegawa, Yuko; Okada, Hiroki; Obara, Keisuke; Kihara, Akio; Suzuki, Kuninori; Kojima, Tetsuya; Yachie, Nozomu; Hirata, Dai; Ohya, Yoshikazu

2017-01-01

We investigated the global landscape of Ca2+ homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca2+-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca2+. After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca2+–cls interactions. We found that high-dimensional, morphological Ca2+–cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca2+–cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca2+–cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca2+-sensitive phenotypes triggered by inactivation of calcineurin, a Ca2+-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca2+ homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca2+ homeostasis. PMID:28566553

New software for cervical vertebral geometry assessment and its relationship to skeletal maturation—a pilot study

PubMed Central

Cunha, A R; Júnior, G C; Fernandes, N; Campos, M J S; Costa, L F M; Vitral, R W F; Bolognese, A M

2014-01-01

Objectives: In the present study, we developed new software for quantitative analysis of cervical vertebrae maturation, and we evaluated its applicability through a multinomial logistic regression model (MLRM). Methods: Digitized images of the bodies of the second (C2), third (C3) and fourth (C4) cervical vertebrae were analysed in cephalometric radiographs of 236 subjects (116 boys and 120 girls) by using a software developed for digitized vertebrae analysis. The sample was initially distributed into 11 categories according to the Fishman's skeletal maturity indicators and were then grouped into four stages for quantitative cervical maturational changes (QCMC) analysis (QCMC I, II, III and IV). Seven variables of interest were measured and analysed to identify morphologic alterations of the vertebral bodies in each QCMC category. Results: Statistically significant differences (p < 0.05) were observed among all QCMC categories for the variables analysed. The MLRM used to calculate the probability that an individual belonged to each of the four cervical vertebrae maturation categories was constructed by taking into account gender, chronological age and four variables determined by digitized vertebrae analysis (Ang_C3, MP_C3, MP_C4 and SP_C4). The MLRM presented a predictability of 81.4%. The weighted κ test showed almost perfect agreement (κ = 0.832) between the categories defined initially by the method of Fishman and those allocated by the MLRM. Conclusions: Significant alterations in the morphologies of the C2, C3 and C4 vertebral bodies that were analysed through the digitized vertebrae analysis software occur during the different stages of skeletal maturation. The model that combines the four parameters measured on the vertebral bodies, the age and the gender showed an excellent prediction. PMID:24319125

New software for cervical vertebral geometry assessment and its relationship to skeletal maturation--a pilot study.

PubMed

Santiago, R C; Cunha, A R; Júnior, G C; Fernandes, N; Campos, M J S; Costa, L F M; Vitral, R W F; Bolognese, A M

2014-01-01

In the present study, we developed new software for quantitative analysis of cervical vertebrae maturation, and we evaluated its applicability through a multinomial logistic regression model (MLRM). Digitized images of the bodies of the second (C2), third (C3) and fourth (C4) cervical vertebrae were analysed in cephalometric radiographs of 236 subjects (116 boys and 120 girls) by using a software developed for digitized vertebrae analysis. The sample was initially distributed into 11 categories according to the Fishman's skeletal maturity indicators and were then grouped into four stages for quantitative cervical maturational changes (QCMC) analysis (QCMC I, II, III and IV). Seven variables of interest were measured and analysed to identify morphologic alterations of the vertebral bodies in each QCMC category. Statistically significant differences (p < 0.05) were observed among all QCMC categories for the variables analysed. The MLRM used to calculate the probability that an individual belonged to each of the four cervical vertebrae maturation categories was constructed by taking into account gender, chronological age and four variables determined by digitized vertebrae analysis (Ang_C3, MP_C3, MP_C4 and SP_C4). The MLRM presented a predictability of 81.4%. The weighted κ test showed almost perfect agreement (κ = 0.832) between the categories defined initially by the method of Fishman and those allocated by the MLRM. Significant alterations in the morphologies of the C2, C3 and C4 vertebral bodies that were analysed through the digitized vertebrae analysis software occur during the different stages of skeletal maturation. The model that combines the four parameters measured on the vertebral bodies, the age and the gender showed an excellent prediction.

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.

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.

Structural development and kinetic analysis of PbTiO3 powders processed at low-temperature via new sol-gel approach

NASA Astrophysics Data System (ADS)

Bel-Hadj-Tahar, Radhouane; Abboud, Mohamed

2018-04-01

The synthesis of crystalline lead titanate powder by a generic low-temperature sol-gel approach is developed. Acetoin was added as ligand, instead of the commonly used alkanolamines, to ensure total dissolution of the precursor compounds. The feasibility of the acetoin-Ti isopropoxide complex as a new precursor of PbTiO3 perovskite particles via sol-gel method has been demonstrated. No excess lead has been introduced. Nanometric PbTiO3 crystallites have been formed at 400 °C under atmospheric pressure from titanium isopropoxide and lead acetate in alcoholic solution by remarkably low activation energy of crystallization process of 90 kJ mol-1. The powders show tetragonal lattice and dendritic morphology. In addition to the effect of heat-treatment temperature, time, and atmosphere, the sol chemistry particularly influenced the phase composition, particle size, and particle morphology. The use of different ligands significantly modified powder morphology. The extent of the crystallization was quantitatively evaluated by differential thermal analysis and analyzed by Johnson-Mehl-Avrami approach. The crystallization followed two rate regimes depending on the interval of the crystallized fraction.

A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

PubMed Central

Li, Feng; Kitashiba, Hiroyasu; Inaba, Kiyofumi; Nishio, Takeshi

2009-01-01

For identification of genes responsible for varietal differences in flowering time and leaf morphological traits, we constructed a linkage map of Brassica rapa DNA markers including 170 EST-based markers, 12 SSR markers, and 59 BAC sequence-based markers, of which 151 are single nucleotide polymorphism (SNP) markers. By BLASTN, 223 markers were shown to have homologous regions in Arabidopsis thaliana, and these homologous loci covered nearly the whole genome of A. thaliana. Synteny analysis between B. rapa and A. thaliana revealed 33 large syntenic regions. Three quantitative trait loci (QTLs) for flowering time were detected. BrFLC1 and BrFLC2 were linked to the QTLs for bolting time, budding time, and flowering time. Three SNPs in the promoter, which may be the cause of low expression of BrFLC2 in the early-flowering parental line, were identified. For leaf lobe depth and leaf hairiness, one major QTL corresponding to a syntenic region containing GIBBERELLIN 20 OXIDASE 3 and one major QTL containing BrGL1, respectively, were detected. Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits. PMID:19884167

Doxorubicin-loaded Zein in situ gel for interstitial chemotherapy.

PubMed

Cao, Xiaoying; Geng, Jianning; Su, Suwen; Zhang, Linan; Xu, Qian; Zhang, Li; Xie, Yinghua; Wu, Shaomei; Sun, Yongjun; Gao, Zibin

2012-01-01

A novel drug delivery system of doxorubicin (DOX)-loaded Zein in situ gel for interstitial chemotherapy was investigated in this study. The possible mechanisms of drug release were described according to morphological analysis by optical microscopy and scanning electronic microscope (SEM). In vitro and in vivo anti-tumor activity studies showed that DOX-loaded Zein in situ gel was superior to DOX solution. Local pharmacokinetics in tumor tissue was studied by quantitative analysis with confocal laser scanning microscopy (CLSM) combined with microdialysis technology. A pharmacokinetics mathematical model of DOX-loaded Zein in situ gel in tumors was then built.

Lunar terrain mapping and relative-roughness analysis

NASA Technical Reports Server (NTRS)

Rowan, L. C.; Mccauley, J. F.; Holm, E. A.

1971-01-01

Terrain maps of the equatorial zone were prepared at scales of 1:2,000,000 and 1:1,000,000 to classify lunar terrain with respect to roughness and to provide a basis for selecting sites for Surveyor and Apollo landings, as well as for Ranger and Lunar Orbiter photographs. Lunar terrain was described by qualitative and quantitative methods and divided into four fundamental classes: maria, terrae, craters, and linear features. Some 35 subdivisions were defined and mapped throughout the equatorial zone, and, in addition, most of the map units were illustrated by photographs. The terrain types were analyzed quantitatively to characterize and order their relative roughness characteristics. For some morphologically homogeneous mare areas, relative roughness can be extrapolated to the large scales from measurements at small scales.

Automated method for the identification and analysis of vascular tree structures in retinal vessel network

NASA Astrophysics Data System (ADS)

Joshi, Vinayak S.; Garvin, Mona K.; Reinhardt, Joseph M.; Abramoff, Michael D.

2011-03-01

Structural analysis of retinal vessel network has so far served in the diagnosis of retinopathies and systemic diseases. The retinopathies are known to affect the morphologic properties of retinal vessels such as course, shape, caliber, and tortuosity. Whether the arteries and the veins respond to these changes together or in tandem has always been a topic of discussion. However the diseases such as diabetic retinopathy and retinopathy of prematurity have been diagnosed with the morphologic changes specific either to arteries or to veins. Thus a method describing the separation of retinal vessel trees imaged in a two dimensional color fundus image may assist in artery-vein classification and quantitative assessment of morphologic changes particular to arteries or veins. We propose a method based on mathematical morphology and graph search to identify and label the retinal vessel trees, which provides a structural mapping of vessel network in terms of each individual primary vessel, its branches and spatial positions of branching and cross-over points. The method was evaluated on a dataset of 15 fundus images resulting into an accuracy of 92.87 % correctly assigned vessel pixels when compared with the manual labeling of separated vessel trees. Accordingly, the structural mapping method performs well and we are currently investigating its potential in evaluating the characteristic properties specific to arteries or veins.

Wave energy and swimming performance shape coral reef fish assemblages

PubMed Central

Fulton, C.J; Bellwood, D.R; Wainwright, P.C

2005-01-01

Physical factors often have an overriding influence on the distribution patterns of organisms, and can ultimately shape the long-term structure of communities. Although distribution patterns in sessile marine organisms have frequently been attributed to functional characteristics interacting with wave-induced water motion, similar evidence for mobile organisms is lacking. Links between fin morphology and swimming performance were examined in three diverse coral reef fish families from two major evolutionary lineages. Among-habitat variation in morphology and performance was directly compared with quantitative values of wave-induced water motion from seven coral reef habitats of different depth and wave exposure on the Great Barrier Reef. Fin morphology was strongly correlated with both field and experimental swimming speeds in all three families. The range of observed swimming speeds coincided closely with the magnitude of water velocities commonly found on coral reefs. Distribution patterns in all three families displayed highly congruent relationships between fin morphology and wave-induced water motion. Our findings indicate a general functional relationship between fin morphology and swimming performance in labriform-swimming fishes, and provide quantitative evidence that wave energy may directly influence the assemblage structure of coral reef fishes through interactions with morphology and swimming performance. PMID:15888415

Novel method for edge detection of retinal vessels based on the model of the retinal vascular network and mathematical morphology

NASA Astrophysics Data System (ADS)

Xu, Lei; Zheng, Xiaoxiang; Zhang, Hengyi; Yu, Yajun

1998-09-01

Accurate edge detection of retinal vessels is a prerequisite for quantitative analysis of subtle morphological changes of retinal vessels under different pathological conditions. A novel method for edge detection of retinal vessels is presented in this paper. Methods: (1) Wavelet-based image preprocessing. (2) The signed edge detection algorithm and mathematical morphological operation are applied to get the approximate regions that contain retinal vessels. (3) By convolving the preprocessed image with a LoG operator only on the detected approximate regions of retinal vessels, followed by edges refining, clear edge maps of the retinal vessels are fast obtained. Results: A detailed performance evaluation together with the existing techniques is given to demonstrate the strong features of our method. Conclusions: True edge locations of retinal vessels can be fast detected with continuous structures of retinal vessels, less non- vessel segments left and insensitivity to noise. The method is also suitable for other application fields such as road edge detection.

Differentiation of malignant and benign breast lesions: Added value of the qualitative analysis of breast lesions on diffusion-weighted imaging (DWI) using readout-segmented echo-planar imaging at 3.0 T.

PubMed

An, Yeong Yi; Kim, Sung Hun; Kang, Bong Joo

2017-01-01

To determine the added value of qualitative analysis as an adjunct to quantitative analysis for the discrimination of benign and malignant lesions in patients with breast cancer using diffusion-weighted imaging (DWI) with readout-segmented echo-planar imaging (rs-EPI). A total of 99 patients with 144 lesions were reviewed from our prospectively collected database. DWI data were obtained using rs-EPI acquired at 3.0 T. The diagnostic performances of DWI in the qualitative, quantitative, and combination analyses were compared with that of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). Additionally, the effect of lesion size on the diagnostic performance of the DWI combination analysis was evaluated. The strongest indicators of malignancy on DWI were a heterogeneous pattern (P = 0.005) and an apparent diffusion coefficient (ADC) value <1.0 × 10-3 mm2/sec (P = 0.002). The area under the curve (AUC) values for the qualitative analysis, quantitative analysis, and combination analysis on DWI were 0.732 (95% CI, 0.651-0.803), 0.780 (95% CI, 0.703-0.846), and 0.826 (95% CI, 0.754-0.885), respectively (P<0.0001). The AUC for the combination analysis on DWI was superior to that for DCE-MRI alone (0.651, P = 0.003) but inferior to that for DCE-MRI plus the ADC value (0.883, P = 0.03). For the DWI combination analysis, the sensitivity was significantly lower in the size ≤1 cm group than in the size >1 cm group (80% vs. 95.6%, P = 0.034). Qualitative analysis of tumor morphology was diagnostically applicable on DWI using rs-EPI. This qualitative analysis adds value to quantitative analyses for lesion characterization in patients with breast cancer.

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.

Dietary Ecology of Murinae (Muridae, Rodentia): A Geometric Morphometric Approach

PubMed Central

Gómez Cano, Ana Rosa; Hernández Fernández, Manuel; Álvarez-Sierra, M. Ángeles

2013-01-01

Murine rodents represent a highly diverse group, which displays great ecological versatility. In the present paper we analyse the relationship between dental morphology, on one hand, using geometric morphometrics based upon the outline of first upper molar and the dietary preference of extant murine genera, on the other. This ecomorphological study of extant murine rodents demonstrates that dietary groups can be distinguished with the use of a quantitative geometric morphometric approach based on first upper molar outline. A discriminant analysis of the geometric morphometric variables of the first upper molars enables us to infer the dietary preferences of extinct murine genera from the Iberian Peninsula. Most of the extinct genera were omnivore; only Stephanomys showed a pattern of dental morphology alike that of the herbivore genera. PMID:24236090

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.

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.

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 species for both minor and major castes, information on geographic distribution and biology, taxonomic discussions, and descriptions of intraspecific variation. Traditional taxonomy and multivariate morphometric analysis are independent sources of information which, in combination, allow more precise species delimitation. Moreover, quantitative characters included in identification keys improve accuracy of determination in difficult cases.

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 species for both minor and major castes, information on geographic distribution and biology, taxonomic discussions, and descriptions of intraspecific variation. Traditional taxonomy and multivariate morphometric analysis are independent sources of information which, in combination, allow more precise species delimitation. Moreover, quantitative characters included in identification keys improve accuracy of determination in difficult cases. PMID:28050160

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.

New insights on ion track morphology in pyrochlores by aberration corrected scanning transmission electron microscopy

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

Sachan, Ritesh; Zhang, Yanwen; Ou, Xin

Here we demonstrate the enhanced imaging capabilities of an aberration corrected scanning transmission electron microscope to advance the understanding of ion track structure in pyrochlore structured materials (i.e., Gd 2Ti 2O 7 and Gd 2TiZrO 7). Track formation occurs due to the inelastic transfer of energy from incident ions to electrons, and atomic-level details of track morphology as a function of energy-loss are revealed in the present work. A comparison of imaging details obtained by varying collection angles of detectors is discussed in the present work. A quantitative analysis of phase identification using high-angle annular dark field imaging is performedmore » on the ion tracks. Finally, a novel 3-dimensional track reconstruction method is provided that is based on depth dependent imaging of the ion tracks. The technique is used in extracting the atomic-level details of nanoscale features, such as the disordered ion tracks, which are embedded in relatively thicker matrix. Another relevance of the method is shown by measuring the tilt of the ion tracks relative to the electron beam incidence that helps in knowing the structure and geometry of ion tracks quantitatively.« less

New insights on ion track morphology in pyrochlores by aberration corrected scanning transmission electron microscopy

DOE PAGES

Sachan, Ritesh; Zhang, Yanwen; Ou, Xin; ...

2016-12-13

Here we demonstrate the enhanced imaging capabilities of an aberration corrected scanning transmission electron microscope to advance the understanding of ion track structure in pyrochlore structured materials (i.e., Gd 2Ti 2O 7 and Gd 2TiZrO 7). Track formation occurs due to the inelastic transfer of energy from incident ions to electrons, and atomic-level details of track morphology as a function of energy-loss are revealed in the present work. A comparison of imaging details obtained by varying collection angles of detectors is discussed in the present work. A quantitative analysis of phase identification using high-angle annular dark field imaging is performedmore » on the ion tracks. Finally, a novel 3-dimensional track reconstruction method is provided that is based on depth dependent imaging of the ion tracks. The technique is used in extracting the atomic-level details of nanoscale features, such as the disordered ion tracks, which are embedded in relatively thicker matrix. Another relevance of the method is shown by measuring the tilt of the ion tracks relative to the electron beam incidence that helps in knowing the structure and geometry of ion tracks quantitatively.« less

Non-Linear Optical Microscopy Sheds Light on Cardiovascular Disease

PubMed Central

Caorsi, Valentina; Toepfer, Christopher; Sikkel, Markus B.; Lyon, Alexander R.; MacLeod, Ken; Ferenczi, Mike A.

2013-01-01

Many cardiac diseases have been associated with increased fibrosis and changes in the organization of fibrillar collagen. The degree of fibrosis is routinely analyzed with invasive histological and immunohistochemical methods, giving a limited and qualitative understanding of the tissue's morphological adaptation to disease. Our aim is to quantitatively evaluate the increase in fibrosis by three-dimensional imaging of the collagen network in the myocardium using the non-linear optical microscopy techniques Two-Photon Excitation microscopy (TPE) and Second Harmonic signal Generation (SHG). No sample staining is needed because numerous endogenous fluorophores are excited by a two-photon mechanism and highly non-centrosymmetric structures such as collagen generate strong second harmonic signals. We propose for the first time a 3D quantitative analysis to carefully evaluate the increased fibrosis in tissue from a rat model of heart failure post myocardial infarction. We show how to measure changes in fibrosis from the backward SHG (BSHG) alone, as only backward-propagating SHG is accessible for true in vivo applications. A 5-fold increase in collagen I fibrosis is detected in the remote surviving myocardium measured 20 weeks after infarction. The spatial distribution is also shown to change markedly, providing insight into the morphology of disease progression. PMID:23409139

Longitudinal study of arteriogenesis with swept source optical coherence tomography and hyperspectral imaging

NASA Astrophysics Data System (ADS)

Poole, Kristin M.; Patil, Chetan A.; Nelson, Christopher E.; McCormack, Devin R.; Madonna, Megan C.; Duvall, Craig L.; Skala, Melissa C.

2014-03-01

Peripheral arterial disease (PAD) is an atherosclerotic disease of the extremities that leads to high rates of myocardial infarction and stroke, increased mortality, and reduced quality of life. PAD is especially prevalent in diabetic patients, and is commonly modeled by hind limb ischemia in mice to study collateral vessel development and test novel therapies. Current techniques used to assess recovery cannot obtain quantitative, physiological data non-invasively. Here, we have applied hyperspectral imaging and swept source optical coherence tomography (OCT) to study longitudinal changes in blood oxygenation and vascular morphology, respectively, intravitally in the diabetic mouse hind limb ischemia model. Additionally, recommended ranges for controlling physiological variability in blood oxygenation with respect to respiration rate and body core temperature were determined from a control animal experiment. In the longitudinal study with diabetic mice, hyperspectral imaging data revealed the dynamics of blood oxygenation recovery distally in the ischemic footpad. In diabetic mice, there is an early increase in oxygenation that is not sustained in the long term. Quantitative analysis of vascular morphology obtained from Hessian-filtered speckle variance OCT volumes revealed temporal dynamics in vascular density, total vessel length, and vessel diameter distribution in the adductor muscle of the ischemic limb. The combination of hyperspectral imaging and speckle variance OCT enabled acquisition of novel functional and morphological endpoints from individual animals, and provides a more robust platform for future preclinical evaluations of novel therapies for PAD.

Distinguishing between natural and hatchery Snake River fall Chinook salmon subyearlings in the field using body morphology

USGS Publications Warehouse

Tiffan, K.F.; Connor, W.P.

2011-01-01

We used body morphology to distinguish between natural- and hatchery-origin subyearling fall Chinook salmon Oncorhynchus tshawytscha in rearing areas of the Snake River and at a downstream dam during seaward migration. Using subjective eye and body shape characteristics, field personnel correctly classified 88.9–100% of natural subyearlings (N = 626) and 90.0–100% of hatchery subyearlings (N = 867) in rearing areas from 2001 to 2008. The morphological characteristics used by these personnel proved to have a quantitative basis, as was shown by digital photography and principal components analysis. Natural subyearlings had smaller eyes and pupils, smaller heads, deeper bodies, and shorter caudal peduncles than their hatchery counterparts during rearing and at the dam. A discriminant function fitted from this set of morphological characteristics classified the origin of fish during rearing and at the dam with over 97% accuracy. We hypothesize that these morphological differences were primarily due to environmental influences during incubation and rearing because it is highly probable that a large portion of the natural juveniles we studied were the offspring of hatchery × hatchery mating in the wild. The findings in this paper might provide guidance for others seeking to differentiate between natural and hatchery fish.

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.

NeuronMetrics: Software for Semi-Automated Processing of Cultured-Neuron Images

PubMed Central

Narro, Martha L.; Yang, Fan; Kraft, Robert; Wenk, Carola; Efrat, Alon; Restifo, Linda L.

2007-01-01

Using primary cell culture to screen for changes in neuronal morphology requires specialized analysis software. We developed NeuronMetrics™ for semi-automated, quantitative analysis of two-dimensional (2D) images of fluorescently labeled cultured neurons. It skeletonizes the neuron image using two complementary image-processing techniques, capturing fine terminal neurites with high fidelity. An algorithm was devised to span wide gaps in the skeleton. NeuronMetrics uses a novel strategy based on geometric features called faces to extract a branch-number estimate from complex arbors with numerous neurite-to-neurite contacts, without creating a precise, contact-free representation of the neurite arbor. It estimates total neurite length, branch number, primary neurite number, territory (the area of the convex polygon bounding the skeleton and cell body), and Polarity Index (a measure of neuronal polarity). These parameters provide fundamental information about the size and shape of neurite arbors, which are critical factors for neuronal function. NeuronMetrics streamlines optional manual tasks such as removing noise, isolating the largest primary neurite, and correcting length for self-fasciculating neurites. Numeric data are output in a single text file, readily imported into other applications for further analysis. Written as modules for ImageJ, NeuronMetrics provides practical analysis tools that are easy to use and support batch processing. Depending on the need for manual intervention, processing time for a batch of ~60 2D images is 1.0–2.5 hours, from a folder of images to a table of numeric data. NeuronMetrics’ output accelerates the quantitative detection of mutations and chemical compounds that alter neurite morphology in vitro, and will contribute to the use of cultured neurons for drug discovery. PMID:17270152

NeuronMetrics: software for semi-automated processing of cultured neuron images.

PubMed

Narro, Martha L; Yang, Fan; Kraft, Robert; Wenk, Carola; Efrat, Alon; Restifo, Linda L

2007-03-23

Using primary cell culture to screen for changes in neuronal morphology requires specialized analysis software. We developed NeuronMetrics for semi-automated, quantitative analysis of two-dimensional (2D) images of fluorescently labeled cultured neurons. It skeletonizes the neuron image using two complementary image-processing techniques, capturing fine terminal neurites with high fidelity. An algorithm was devised to span wide gaps in the skeleton. NeuronMetrics uses a novel strategy based on geometric features called faces to extract a branch number estimate from complex arbors with numerous neurite-to-neurite contacts, without creating a precise, contact-free representation of the neurite arbor. It estimates total neurite length, branch number, primary neurite number, territory (the area of the convex polygon bounding the skeleton and cell body), and Polarity Index (a measure of neuronal polarity). These parameters provide fundamental information about the size and shape of neurite arbors, which are critical factors for neuronal function. NeuronMetrics streamlines optional manual tasks such as removing noise, isolating the largest primary neurite, and correcting length for self-fasciculating neurites. Numeric data are output in a single text file, readily imported into other applications for further analysis. Written as modules for ImageJ, NeuronMetrics provides practical analysis tools that are easy to use and support batch processing. Depending on the need for manual intervention, processing time for a batch of approximately 60 2D images is 1.0-2.5 h, from a folder of images to a table of numeric data. NeuronMetrics' output accelerates the quantitative detection of mutations and chemical compounds that alter neurite morphology in vitro, and will contribute to the use of cultured neurons for drug discovery.

Mitochondrial and Morphologic Alterations in Native Human Corneal Endothelial Cells Associated With Diabetes Mellitus.

PubMed

Aldrich, Benjamin T; Schlötzer-Schrehardt, Ursula; Skeie, Jessica M; Burckart, Kimberlee A; Schmidt, Gregory A; Reed, Cynthia R; Zimmerman, M Bridget; Kruse, Friedrich E; Greiner, Mark A

2017-04-01

To characterize changes in the energy-producing metabolic activity and morphologic ultrastructure of corneal endothelial cells associated with diabetes mellitus. Transplant suitable corneoscleral tissue was obtained from donors aged 50 to 75 years. We assayed 3-mm punches of endothelium-Descemet membrane for mitochondrial respiration and glycolysis activity using extracellular flux analysis of oxygen and pH, respectively. Transmission electron microscopy was used to assess qualitative and quantitative ultrastructural changes in corneal endothelial cells and associated Descemet membrane. For purposes of analysis, samples were divided into four groups based on a medical history of diabetes regardless of type: (1) nondiabetic, (2) noninsulin-dependent diabetic, (3) insulin-dependent diabetic, and (4) insulin-dependent diabetic with specified complications due to diabetes (advanced diabetic). In total, 229 corneas from 159 donors were analyzed. Insulin-dependent diabetic samples with complications due to diabetes displayed the lowest spare respiratory values compared to all other groups (P ≤ 0.002). The remaining mitochondrial respiration and glycolysis metrics did not differ significantly among groups. Compared to nondiabetic controls, the endothelium from advanced diabetic samples had alterations in mitochondrial morphology, pronounced Golgi bodies associated with abundant vesicles, accumulation of lysosomal bodies/autophagosomes, and focal production of abnormal long-spacing collagen. Extracellular flux analysis suggests that corneal endothelial cells of donors with advanced diabetes have impaired mitochondrial function. Metabolic findings are supported by observed differences in mitochondrial morphology of advanced diabetic samples but not controls. Additional studies are needed to determine the precise mechanism(s) by which mitochondria become impaired in diabetic corneal endothelial cells.

Dielectric and electric modulus study of PPy/TiO2/CNT/SLS composite with temperature

NASA Astrophysics Data System (ADS)

Tiwari, D. C.; Atri, Priyanka; Sharma, Rishi

2013-02-01

Here we report the preparation and electrical characterization of nanocomposite of PPy/TiO2/CNT/SLS synthesized by in situ oxidative polymerization of pyrrole in the presence of TiO2 nanofibers, CNT and surfactant sodium lauryl sulfate. The surface morphology and elemental analysis is studied by SEM and EDAX. Dielectric and modulas studies were carried out in frequency range of 1 KHz to 2 MHz which provides quantitative description of grain and grain boundary effect in nanocomposite material.

Scientific and Technological Principles of Development of New Cold-Resistant Arc-Steels (Steels for Arctic Applications)

NASA Astrophysics Data System (ADS)

Sych, O. V.; Khlusova, E. I.; Yashin, E. A.

2017-12-01

The paper presents the results of quantitative analysis of C, Mn, Ni and Cu content on strength and cold-resistance of rolled plates. Relations between the ferritic-bainitic structure morphology and anisotropy and steel performance characteristics have been established. Influence of thermal and deformation rolling patterns on steel structure has been studied. The steel chemical composition has been improved and precision thermomechanical processing conditions for production of cold-resistant Arc-steel plates have been developed.

Surface colour photometry of galaxies with Schmidt telescopes.

NASA Technical Reports Server (NTRS)

Wray, J. D.

1972-01-01

A method is described which owes its practicality to the capability of Schmidt telescopes to record a number of galaxy images on a single plate and to the existence of high speed computer controlled area-scanning precision microdensitometers such as the Photometric Data Systems model 1010. The method of analysis results in quantitative color-index information which is displayed in a manner that allows any user to effectively study the morphological properties of the distribution of color-index in galaxies.

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 quantitative evaluation of the fibrocartilaginous condylar component. PMID:24092237

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.

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 [

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.

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 .

Linking hydrology, morphodynamics and ecology to assess the restoration potential of the heavily regulated Sarca River, NE Italy

NASA Astrophysics Data System (ADS)

Carolli, Mauro; Zolezzi, Guido; Pellegrini, Stefano; Gelmini, Francesca; Deriu, Micaela

2017-04-01

We develop an integrated eco-hydro-morphological quantitative investigation of the upper course of the Alpine Sarca River (NE Italy), for the purpose of assessing its potential in terms of environmental restoration. The Sarca River has been subject to heavy exploitation for hydropower production since the 1950s through a complex infrastructural system. As for many regulated Alpine rivers, increasing local interest has recently been developing to design and implement river restoration measures to improve the environmental conditions and ecosystem services that the river can provide. The aim of the work is to develop and apply a quantitative approach for a preliminary assessment of the successful potential of different river restoration options in the light of the recent eco-hydro-morphological dynamics of the Sarca river system at the catchment scale. The proposed analysis consists of three main steps: (1) detection of the main drivers of flow and sediment supply regimes alteration and characterization of such alteration; (2) a quantification of the effects of those alterations on geomorphic processes and fish habitat conditions; (3) the analysis of the restoration potential in the light of the results of the previous assessment. The analysis is tailored to the existing data availability, which is relatively high as for most river systems of comparable size in Europe, but not as much as in the case of a targeted research project, thus providing a representative case for many other regulated river catchments. Hydrological alteration is quantified by comparing recent (20 years) streamflow time series with a reconstructed series of analogous length, using a hydrological model that has been run excluding any man-made water abstraction, release and artificial reservoirs. upstream and downstream a large dam in the middle course of the river. By choosing the adult marble trout as target (endemic) fish species, effects of the alterations on the temporal and spatial habitat suitability have been assessed by applying a hydraulic-habitat method combined with the streamflow time series. Geomorphological trajectories of the last decades have been reconstructed through the analysis of aerial photos, and the geomorphic effects of flow regime alteration have been assessed in terms of the changes in frequency and duration of gravel-transporting flood events. Results indicate hydropower as one of the drivers of hydro-morphological alteration, with widespread torrent control works in the catchment playing a relevant role in reducing sediment supply. Recent changes in flow management related to the imposition of a Minimum Environmental Flow correspond to significant increase in the continuous duration of suitable habitat events, despite representing only a first step towards a dynamic ecological flow regime. While floods able to drive morphological changes still occurred after regulation, their frequency and duration have dramatically decreased, contributing to channel narrowing and morphological simplification. Overall, the analysis suggests that: (i) morphological river restoration aimed at restoring self-formed morphodynamics can only be effective if designed together with a dynamic geomorphic flow regime, and (ii) dynamic ecological flows should designed with a twofold objective of improving habitat and spawning sites conditions together with recreational uses of the river.

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.

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 development of the pharate adult. © 2017 The Authors Journal of Morphology Published by Wiley Periodicals, Inc.

Adrenergic nerve fibres and mast cells: correlation in rat thymus.

PubMed

Artico, Marco; Cavallotti, Carlo; Cavallotti, Daniela

2002-10-21

The interactions between adrenergic nerve fibres and mast cells (MCs) were studied in the thymus of adult and old rats by morphological methods and by quantitative analysis of images (QAIs). The whole thymus was drawn in adult (12 months old) rats: normal, sympathectomized or electrostimulated. Thymuses from the above-mentioned animals were weighed, measured and dissected. Thymic slices were stained with eosin orange for detection of microanatomical details and with Bodian's method for identification of the whole nerve fibres. Thymic MCs were stained with Astrablau. Histofluorescence microscopy was used for staining of adrenergic nerve fibres. Finally, all morphological results were submitted to the QAIs and statistical analysis of data. Our results suggest that after surgical sympathectomy, the greater part of adrenergic nerve fibres disappear while related MCs appear to show less evident fluorescence and few granules. On the contrary, electrostimulation of the cervical superior ganglion induced an increase in the fluorescence of adrenergic nerve fibres and of related MCs.

Whole-organ cell shape analysis reveals the developmental basis of ascidian notochord taper.

PubMed

Veeman, Michael T; Smith, William C

2013-01-15

Here we use in toto imaging together with computational segmentation and analysis methods to quantify the shape of every cell at multiple stages in the development of a simple organ: the notochord of the ascidian Ciona savignyi. We find that cell shape in the intercalated notochord depends strongly on anterior-posterior (AP) position, with cells in the middle of the notochord consistently wider than cells at the anterior or posterior. This morphological feature of having a tapered notochord is present in many chordates. We find that ascidian notochord taper involves three main mechanisms: Planar Cell Polarity (PCP) pathway-independent sibling cell volume asymmetries that precede notochord cell intercalation; the developmental timing of intercalation, which proceeds from the anterior and posterior towards the middle; and the differential rates of notochord cell narrowing after intercalation. A quantitative model shows how the morphology of an entire developing organ can be controlled by this small set of cellular mechanisms. Copyright © 2012 Elsevier Inc. All rights reserved.

Whole-organ cell shape analysis reveals the developmental basis of ascidian notochord taper

PubMed Central

Veeman, Michael T.; Smith, William C.

2012-01-01

Here we use in toto imaging together with computational segmentation and analysis methods to quantify the shape of every cell at multiple stages in the development of a simple organ: the notochord of the ascidian Ciona savignyi. We find that cell shape in the intercalated notochord depends strongly on anterior-posterior (AP) position, with cells in the middle of the notochord consistently wider than cells at the anterior or posterior. This morphological feature of having a tapered notochord is present in many chordates. We find that ascidian notochord taper involves three main mechanisms: Planar Cell Polarity (PCP) pathway-independent sibling cell volume asymmetries that precede notochord cell intercalation; the developmental timing of intercalation, which proceeds from the anterior and posterior towards the middle; and the differential rates of notochord cell narrowing after intercalation. A quantitative model shows how the morphology of an entire developing organ can be controlled by this small set of cellular mechanisms. PMID:23165294

Nanoscale nuclear architecture for cancer diagnosis beyond pathology via spatial-domain low-coherence quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Wang, Pin; Bista, Rajan K.; Khalbuss, Walid E.; Qiu, Wei; Uttam, Shikhar; Staton, Kevin; Zhang, Lin; Brentnall, Teresa A.; Brand, Randall E.; Liu, Yang

2010-11-01

Definitive diagnosis of malignancy is often challenging due to limited availability of human cell or tissue samples and morphological similarity with certain benign conditions. Our recently developed novel technology-spatial-domain low-coherence quantitative phase microscopy (SL-QPM)-overcomes the technical difficulties and enables us to obtain quantitative information about cell nuclear architectural characteristics with nanoscale sensitivity. We explore its ability to improve the identification of malignancy, especially in cytopathologically non-cancerous-appearing cells. We perform proof-of-concept experiments with an animal model of colorectal carcinogenesis-APCMin mouse model and human cytology specimens of colorectal cancer. We show the ability of in situ nanoscale nuclear architectural characteristics in identifying cancerous cells, especially in those labeled as ``indeterminate or normal'' by expert cytopathologists. Our approach is based on the quantitative analysis of the cell nucleus on the original cytology slides without additional processing, which can be readily applied in a conventional clinical setting. Our simple and practical optical microscopy technique may lead to the development of novel methods for early detection of cancer.

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 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.

Evolution of Quantitative Measures in NMR: Quantum Mechanical qHNMR Advances Chemical Standardization of a Red Clover (Trifolium pratense) Extract

PubMed Central

2017-01-01

Chemical standardization, along with morphological and DNA analysis ensures the authenticity and advances the integrity evaluation of botanical preparations. Achievement of a more comprehensive, metabolomic standardization requires simultaneous quantitation of multiple marker compounds. Employing quantitative 1H NMR (qHNMR), this study determined the total isoflavone content (TIfCo; 34.5–36.5% w/w) via multimarker standardization and assessed the stability of a 10-year-old isoflavone-enriched red clover extract (RCE). Eleven markers (nine isoflavones, two flavonols) were targeted simultaneously, and outcomes were compared with LC-based standardization. Two advanced quantitative measures in qHNMR were applied to derive quantities from complex and/or overlapping resonances: a quantum mechanical (QM) method (QM-qHNMR) that employs 1H iterative full spin analysis, and a non-QM method that uses linear peak fitting algorithms (PF-qHNMR). A 10 min UHPLC-UV method provided auxiliary orthogonal quantitation. This is the first systematic evaluation of QM and non-QM deconvolution as qHNMR quantitation measures. It demonstrates that QM-qHNMR can account successfully for the complexity of 1H NMR spectra of individual analytes and how QM-qHNMR can be built for mixtures such as botanical extracts. The contents of the main bioactive markers were in good agreement with earlier HPLC-UV results, demonstrating the chemical stability of the RCE. QM-qHNMR advances chemical standardization by its inherent QM accuracy and the use of universal calibrants, avoiding the impractical need for identical reference materials. PMID:28067513

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.

A feasible high spatiotemporal resolution breast DCE-MRI protocol for clinical settings.

PubMed

Tudorica, Luminita A; Oh, Karen Y; Roy, Nicole; Kettler, Mark D; Chen, Yiyi; Hemmingson, Stephanie L; Afzal, Aneela; Grinstead, John W; Laub, Gerhard; Li, Xin; Huang, Wei

2012-11-01

Three dimensional bilateral imaging is the standard for most clinical breast dynamic contrast-enhanced (DCE) MRI protocols. Because of high spatial resolution (sRes) requirement, the typical 1-2 min temporal resolution (tRes) afforded by a conventional full-k-space-sampling gradient echo (GRE) sequence precludes meaningful and accurate pharmacokinetic analysis of DCE time-course data. The commercially available, GRE-based, k-space undersampling and data sharing TWIST (time-resolved angiography with stochastic trajectories) sequence was used in this study to perform DCE-MRI exams on thirty one patients (with 36 suspicious breast lesions) before their biopsies. The TWIST DCE-MRI was immediately followed by a single-frame conventional GRE acquisition. Blinded from each other, three radiologist readers assessed agreements in multiple lesion morphology categories between the last set of TWIST DCE images and the conventional GRE images. Fleiss' κ test was used to evaluate inter-reader agreement. The TWIST DCE time-course data were subjected to quantitative pharmacokinetic analyses. With a four-channel phased-array breast coil, the TWIST sequence produced DCE images with 20 s or less tRes and ~ 1.0×1.0×1.4 mm(3) sRes. There were no significant differences in signal-to-noise (P=.45) and contrast-to-noise (P=.51) ratios between the TWIST and conventional GRE images. The agreements in morphology evaluations between the two image sets were excellent with the intra-reader agreement ranging from 79% for mass margin to 100% for mammographic density and the inter-reader κ value ranging from 0.54 (P<.0001) for lesion size to 1.00 (P<.0001) for background parenchymal enhancement. Quantitative analyses of the DCE time-course data provided higher breast cancer diagnostic accuracy (91% specificity at 100% sensitivity) than the current clinical practice of morphology and qualitative kinetics assessments. The TWIST sequence may be used in clinical settings to acquire high spatiotemporal resolution breast DCE-MRI images for both precise lesion morphology characterization and accurate pharmacokinetic analysis. Copyright © 2012 Elsevier Inc. All rights reserved.

Variation in brain anatomy in frogs and its possible bearing on their locomotor ecology.

PubMed

Manzano, Adriana S; Herrel, Anthony; Fabre, Anne-Claire; Abdala, Virginia

2017-07-01

Despite the long-standing interest in the evolution of the brain, relatively little is known about variation in brain anatomy in frogs. Yet, frogs are ecologically diverse and, as such, variation in brain anatomy linked to differences in lifestyle or locomotor behavior can be expected. Here we present a comparative morphological study focusing on the macro- and micro-anatomy of the six regions of the brain and its choroid plexus: the olfactory bulbs, the telencephalon, the diencephalon, the mesencephalon, the rhombencephalon, and the cerebellum. We also report on the comparative anatomy of the plexus brachialis responsible for the innervation of the forelimbs. It is commonly thought that amphibians have a simplified brain organization, associated with their supposedly limited behavioral complexity and reduced motor skills. We compare frogs with different ecologies that also use their limbs in different contexts and for other functions. Our results show that brain morphology is more complex and more variable than typically assumed. Moreover, variation in brain morphology among species appears related to locomotor behavior as suggested by our quantitative analyses. Thus we propose that brain morphology may be related to the locomotor mode, at least in the frogs included in our analysis. © 2017 Anatomical Society.

Morphology and Structure of Ultraluminous Infrared Galaxies at z ≈ 2 in the EGS Field

NASA Astrophysics Data System (ADS)

Fang, G. W.; Ma, Z. Y.; Chen, Y.; Kong, X.

2014-11-01

Using high-resolution HST WFC3 (Hubble Space Telescope Wide Field Camera 3) F160W imaging from the CANDELS-EGS (Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey-Extended Groth Strip) field, we present the morphology analysis of 9 ultraluminous infrared galaxies (ULIRGs) at z≈2. We find a wide range of morphological diversities for these ULIRGs, from spheroid to multiple bright nuclei or diffuse structures, e.g., double nuclei, bridges, dual asymmetries, irregular, or elliptical structures. In quantitative, these sources show a lower Gini coefficient (G) and a higher moment (M_{20}) in the rest-frame optical morphology, compared to the lower redshift counterparts, indicating less concentrated and symmetric spatial distribution of the stellar mass of ULIRGs at z≈2. Moreover, we derive accurate effective radii of these ULIRGs through 2-D profile fitting, which range from 2.4 to 5.8 kpc, with a mean value of (3.9±1.1) kpc. We find that the sizes of these ULIRGs at z≈2 are on average one to two times smaller than those of the local star-forming galaxies with analogous stellar mass. Our results are consistent with those studies at similar redshift and infrared luminosity.

Insights on landscape evolution and climatic forcing on Titan

NASA Astrophysics Data System (ADS)

Lucas, A.; Daudon, C.; Rodriguez, S.; Cornet, T.; Perron, J. T.

2017-12-01

The landscapes of Titan were observed for nearly 13 years by the Cassini spacecraft and Huygens probe. With dunes, mountains, seas, lakes, rivers..., the great morphological variety observed testifies to the geological richness that Titan shares with the Earth. In this study, we combine analysis of radar and hyperspectral data provided by the Cassini-Huygens mission, with models of valley and river network evolution to better understand the processes at work that sculpt these familiar landscapes. We develop quantitative criteria for comparing 3D morphologies obtained by numerical simulation with those derived for Titan by photogrammetry. These criteria are validated on Earth's landscapes. We simulate morphologies similar to those observed and show that landscapes at the equator and poles are mainly controlled by river incision and mass wasting such as landslides for which we quantify their respective contribution. Subsequently, we relate modeling to precipitation rates of methane and show values that are to be compared with general circulation model predictions (GCM). Our results also show a very young age of formation of the observed morphologies, less than a few million years. Finally, we provide new constraints on current amplitude of the tidal effects and organic precipitation rates from atmosphere chemistry.

Quantitative determination of low-Z elements in single atmospheric particles on boron substrates by automated scanning electron microscopy-energy-dispersive X-ray spectrometry.

PubMed

Choël, Marie; Deboudt, Karine; Osán, János; Flament, Pascal; Van Grieken, René

2005-09-01

Atmospheric aerosols consist of a complex heterogeneous mixture of particles. Single-particle analysis techniques are known to provide unique information on the size-resolved chemical composition of aerosols. A scanning electron microscope (SEM) combined with a thin-window energy-dispersive X-ray (EDX) detector enables the morphological and elemental analysis of single particles down to 0.1 microm with a detection limit of 1-10 wt %, low-Z elements included. To obtain data statistically representative of the air masses sampled, a computer-controlled procedure can be implemented in order to run hundreds of single-particle analyses (typically 1000-2000) automatically in a relatively short period of time (generally 4-8 h, depending on the setup and on the particle loading). However, automated particle analysis by SEM-EDX raises two practical challenges: the accuracy of the particle recognition and the reliability of the quantitative analysis, especially for micrometer-sized particles with low atomic number contents. Since low-Z analysis is hampered by the use of traditional polycarbonate membranes, an alternate choice of substrate is a prerequisite. In this work, boron is being studied as a promising material for particle microanalysis. As EDX is generally said to probe a volume of approximately 1 microm3, geometry effects arise from the finite size of microparticles. These particle geometry effects must be corrected by means of a robust concentration calculation procedure. Conventional quantitative methods developed for bulk samples generate elemental concentrations considerably in error when applied to microparticles. A new methodology for particle microanalysis, combining the use of boron as the substrate material and a reverse Monte Carlo quantitative program, was tested on standard particles ranging from 0.25 to 10 microm. We demonstrate that the quantitative determination of low-Z elements in microparticles is achievable and that highly accurate results can be obtained using the automatic data processing described here compared to conventional methods.

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.

[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.

MIH supplementation strategies: prospective clinical and laboratory trial.

PubMed

Baroni, C; Marchionni, S

2011-03-01

The use of calcium-phosphate casein on hypomineralized molars (molar incisor hypomineralization, MIH) has been proposed but not clinically investigated. Qualitative and quantitative effects of supplementation with a calcium-phosphate casein product on MIH molars were monitored over a period of three years. Molar replicas, minimally invasive biopsies and their SEM microphotographs, plus ESEM/EDX semi-quantitative peaks of elements present in affected enamel were evaluated. Mineralization, morphology, and porosity appeared markedly improved, with calcium and phosphate levels reaching almost normal levels at three years' follow-up. The hypothesis tested was rejected, since calcium-phosphate casein improved enamel morphology in vivo.

Bilateral cartilage T2 mapping 9 years after Mega-OATS implantation at the knee: a quantitative 3T MRI study.

PubMed

Jungmann, P M; Brucker, P U; Baum, T; Link, T M; Foerschner, F; Minzlaff, P; Banke, I J; Saier, T; Imhoff, A B; Rummeny, E J; Bauer, J S

2015-12-01

To evaluate morphological and quantitative MR findings 9 years after autograft transfer of the posterior femoral condyle (Mega-OATS) and to correlate these findings with clinical outcomes. Quantitative MR measurements were also obtained of the contralateral knee and the utility as reference standard was investigated. Both knees of 20 patients with Mega-OATS osteochondral repair at the medial femoral condyle (MFC) were studied using 3T MRI 9 years after the procedure. MR-sequences included morphological sequences and a 2D multislice multiecho (MSME) spin echo (SE) sequence for quantitative cartilage T2 mapping. Cartilage segmentation was performed at the cartilage repair site and six additional knee compartments. Semi-quantitative MR observation of cartilage repair tissue (MOCART) scores and clinical Lysholm scores were obtained. Paired t-tests and Spearman correlations were used for statistical analysis. Global T2-values were significantly higher at ipsilateral knees compared to contralateral knees (42.1 ± 3.0 ms vs 40.4 ± 2.6 ms, P = 0.018). T2-values of the Mega-OATS site correlated significantly with MOCART scores (R = -0.64, P = 0.006). The correlations between MOCART and Lysholm scores and between absolute T2-values and Lysholm scores were not significant (P > 0.05). However, higher T2 side-to-side differences at the femoral condyles correlated significantly with more severe clinical symptoms (medial, R = -0.53, P = 0.030; lateral, R = -0.51, P = 0.038). Despite long-term survival, 9 years after Mega-OATS procedures, T2-values of the grafts were increased compared to contralateral knees. Clinical scores correlated best with T2 side-to-side differences of the femoral condyles, indicating that intraindividual adjustment may be beneficial for outcome evaluation. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Tibial coverage, meniscus position, size and damage in knees discordant for joint space narrowing – data from the Osteoarthritis Initiative

PubMed Central

Bloecker, K.; Guermazi, A.; Wirth, W.; Benichou, O.; Kwoh, C.K.; Hunter, D.J.; Englund, M.; Resch, H.; Eckstein, F.

2013-01-01

SUMMARY Introduction Meniscal extrusion is thought to be associated with less meniscus coverage of the tibial surface, but the association of radiographic disease stage with quantitative measures of tibial plateau coverage is unknown. We therefore compared quantitative and semi-quantitative measures of meniscus position and morphology in individuals with bilateral painful knees discordant on medial joint space narrowing (mJSN). Methods A sample of 60 participants from the first half (2,678 cases) of the Osteoarthritis Initiative cohort fulfilled the inclusion criteria: bilateral frequent pain, Osteoarthritis Research Society International (OARSI) mJSN grades 1–3 in one, no-JSN in the contra-lateral (CL), and no lateral JSN in either knee (43 unilateral mJSN1; 17 mJSN2/3; 22 men, 38 women, body mass index (BMI) 31.3 ± 3.9 kg/m2). Segmentation and three-dimensional quantitative analysis of the tibial plateau and meniscus, and semi-quantitative evaluation of meniscus damage (magnetic resonance imaging (MRI) osteoarthritis knee score – MOAKS) was performed using coronal 3T MR images (MPR DESSwe and intermediate-weighted turbo spin echo (IW-TSE) images). CL knees were compared using paired t-tests (between-knee, within-person design). Results Medial tibial plateau coverage was 36 ± 9% in mJSN1 vs 45 ± 8% in CL no-JSN knees, and was 31 ± 9% in mJSN2/3 vs 46 ± 6% in no-JSN knees (both P < 0.001). mJSN knees showed greater meniscus extrusion and damage (MOAKS), but no significant difference in meniscus volume. No significant differences in lateral tibial coverage, lateral meniscus morphology or position were observed. Conclusions Knees with medial JSN showed substantially less medial tibial plateau coverage by the meniscus. We suggest that the less meniscal coverage, i.e., less mechanical protection may be a reason for greater rates of cartilage loss observed in JSN knees. PMID:23220556

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.

Quantitative tracking of tumor cells in phase-contrast microscopy exploiting halo artifact pattern

NASA Astrophysics Data System (ADS)

Kang, Mi-Sun; Song, Soo-Min; Lee, Hana; Kim, Myoung-Hee

2012-03-01

Tumor cell morphology is closely related to its invasiveness characteristics and migratory behaviors. An invasive tumor cell has a highly irregular shape, whereas a spherical cell is non-metastatic. Thus, quantitative analysis of cell features is crucial to determine tumor malignancy or to test the efficacy of anticancer treatment. We use phase-contrast microscopy to analyze single cell morphology and to monitor its change because it enables observation of long-term activity of living cells without photobleaching and phototoxicity, which is common in other fluorescence-labeled microscopy. Despite this advantage, there are image-level drawbacks to phase-contrast microscopy, such as local light effect and contrast interference ring, among others. Thus, we first applied a local filter to compensate for non-uniform illumination. Then, we used intensity distribution information to detect the cell boundary. In phase-contrast microscopy images, the cell normally appears as a dark region surrounded by a bright halo. As the halo artifact around the cell body is minimal and has an asymmetric diffusion pattern, we calculated the cross-sectional plane that intersected the center of each cell and was orthogonal to the first principal axis. Then, we extracted the dark cell region by level set. However, a dense population of cultured cells still rendered single-cell analysis difficult. Finally, we measured roundness and size to classify tumor cells into malignant and benign groups. We validated segmentation accuracy by comparing our findings with manually obtained results.

Quantitative Proteomic Analysis Reveals Populus cathayana Females Are More Sensitive and Respond More Sophisticatedly to Iron Deficiency than Males.

PubMed

Zhang, Sheng; Zhang, Yunxiang; Cao, Yanchun; Lei, Yanbao; Jiang, Hao

2016-03-04

Previous studies have shown that there are significant sexual differences in the morphological and physiological responses of Populus cathayana Rehder to nitrogen and phosphorus deficiencies, but little is known about the sex-specific differences in responses to iron deficiency. In this study, the effects of iron deficiency on the morphology, physiology, and proteome of P. cathayana males and females were investigated. The results showed that iron deficiency (25 days) significantly decreased height growth, photosynthetic rate, chlorophyll content, and tissue iron concentration in both sexes. A comparison between the sexes indicated that iron-deficient males had less height inhibition and photosynthesis system II or chloroplast ultrastructural damage than iron-deficient females. iTRAQ-based quantitative proteomic analysis revealed that 144 and 68 proteins were decreased in abundance (e.g., proteins involved in photosynthesis, carbohydrate and energy metabolism, and gene expression regulation) and 78 and 39 proteins were increased in abundance (e.g., proteins involved in amino acid metabolism and stress response) according to the criterion of ratio ≥1.5 in females and males, respectively. A comparison between the sexes indicated that iron-deficient females exhibited a greater change in the proteins involved in photosynthesis, carbon and energy metabolism, the redox system, and stress responsive proteins. This study reveals females are more sensitive and have a more sophisticated response to iron deficiency compared with males and provides new insights into differential sexual responses to nutrient deficiency.

Comparative neuronal morphology of the cerebellar cortex in afrotherians, carnivores, cetartiodactyls, and primates

PubMed Central

Jacobs, Bob; Johnson, Nicholas L.; Wahl, Devin; Schall, Matthew; Maseko, Busisiwe C.; Lewandowski, Albert; Raghanti, Mary A.; Wicinski, Bridget; Butti, Camilla; Hopkins, William D.; Bertelsen, Mads F.; Walsh, Timothy; Roberts, John R.; Reep, Roger L.; Hof, Patrick R.; Sherwood, Chet C.; Manger, Paul R.

2014-01-01

Although the basic morphological characteristics of neurons in the cerebellar cortex have been documented in several species, virtually nothing is known about the quantitative morphological characteristics of these neurons across different taxa. To that end, the present study investigated cerebellar neuronal morphology among eight different, large-brained mammalian species comprising a broad phylogenetic range: afrotherians (African elephant, Florida manatee), carnivores (Siberian tiger, clouded leopard), cetartiodactyls (humpback whale, giraffe) and primates (human, common chimpanzee). Specifically, several neuron types (e.g., stellate, basket, Lugaro, Golgi, and granule neurons; N = 317) of the cerebellar cortex were stained with a modified rapid Golgi technique and quantified on a computer-assisted microscopy system. There was a 64-fold variation in brain mass across species in our sample (from clouded leopard to the elephant) and a 103-fold variation in cerebellar volume. Most dendritic measures tended to increase with cerebellar volume. The cerebellar cortex in these species exhibited the trilaminate pattern common to all mammals. Morphologically, neuron types in the cerebellar cortex were generally consistent with those described in primates (Fox et al., 1967) and rodents (Palay and Chan-Palay, 1974), although there was substantial quantitative variation across species. In particular, Lugaro neurons in the elephant appeared to be disproportionately larger than those in other species. To explore potential quantitative differences in dendritic measures across species, MARSplines analyses were used to evaluate whether species could be differentiated from each other based on dendritic characteristics alone. Results of these analyses indicated that there were significant differences among all species in dendritic measures. PMID:24795574

Multichannel series piezoelectric quartz crystal cell sensor for real time and quantitative monitoring of the living cell and assessment of cytotoxicity.

PubMed

Tong, Feifei; Lian, Yan; Zhou, Huang; Shi, Xiaohong; He, Fengjiao

2014-10-21

A new multichannel series piezoelectric quartz crystal (MSPQC) cell sensor for real time monitoring of living cells in vitro was reported in this paper. The constructed sensor was used successfully to monitor adhesion, spreading, proliferation, and apoptosis of MG63 osteosarcoma cells and investigate the effects of different concentrations of cobalt chloride on MG63 cells. Quantitative real time and dynamic cell analyses data were conducted using the MSPQC cell sensor. Compared with methods such as fluorescence staining and morphology observation by microscopy, the MSPQC cell sensor is noninvasive, label free, simple, cheap, and capable of online monitoring. It can automatically record the growth status of cells and quantitatively evaluate cell proliferation and the apoptotic response to drugs. It will be a valuable detection and analysis tool for the acquisition of cellular level information and is anticipated to have application in the field of cell biology research or cytotoxicity testing in the future.

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.

Exploration of the Genetic Organization of Morphological Modularity on the Mouse Mandible Using a Set of Interspecific Recombinant Congenic Strains Between C57BL/6 and Mice of the Mus spretus Species

PubMed Central

Burgio, Gaëtan; Baylac, Michel; Heyer, Evelyne; Montagutelli, Xavier

2012-01-01

Morphological integration and modularity within semi-autonomous modules are essential mechanisms for the evolution of morphological traits. However, the genetic makeup responsible for the control of variational modularity is still relatively unknown. In our study, we tested the hypothesis that the genetic variation for mandible shape clustered into two morphogenetic components: the alveolar group and the ascending ramus. We used the mouse as a model system to investigate genetics determinants of mandible shape. To do this, we used a combination of geometric morphometric tools and a set of 18 interspecific recombinant congenic strains (IRCS) derived from the distantly related species, Mus spretus SEG/Pas and Mus musculus C57BL/6. Quantitative trait loci (QTL) analysis comparing mandible morphometry between the C57BL/6 and the IRCSs identified 42 putative SEG/Pas segments responsible for the genetic variation. The magnitude of the QTL effects was dependent on the proportion of SEG/Pas genome inherited. Using a multivariate correlation coefficient adapted for modularity assessment and a two-block partial least squares analysis to explore the morphological integration, we found that these QTL clustered into two well-integrated morphogenetic groups, corresponding to the ascending ramus and the alveolar region. Together, these results provide evidence that the mouse mandible is subjected to genetic coordination in a modular manner. PMID:23050236

Current perspectives of CASA applications in diverse mammalian spermatozoa.

PubMed

van der Horst, Gerhard; Maree, Liana; du Plessis, Stefan S

2018-03-26

Since the advent of computer-aided sperm analysis (CASA) some four decades ago, advances in computer technology and software algorithms have helped establish it as a research and diagnostic instrument for the analysis of spermatozoa. Despite mammalian spermatozoa being the most diverse cell type known, CASA is a great tool that has the capacity to provide rapid, reliable and objective quantitative assessment of sperm quality. This paper provides contemporary research findings illustrating the scientific and commercial applications of CASA and its ability to evaluate diverse mammalian spermatozoa (human, primates, rodents, domestic mammals, wildlife species) at both structural and functional levels. The potential of CASA to quantitatively measure essential aspects related to sperm subpopulations, hyperactivation, morphology and morphometry is also demonstrated. Furthermore, applications of CASA are provided for improved mammalian sperm quality assessment, evaluation of sperm functionality and the effect of different chemical substances or pathologies on sperm fertilising ability. It is clear that CASA has evolved significantly and is currently superior to many manual techniques in the research and clinical setting.

Stem cell behavior on tailored porous oxide surface coatings.

PubMed

Lavenus, Sandrine; Poxson, David J; Ogievetsky, Nika; Dordick, Jonathan S; Siegel, Richard W

2015-07-01

Nanoscale surface topographies are known to have a profound influence on cell behavior, including cell guidance, migration, morphology, proliferation, and differentiation. In this study, we have observed the behavior of human mesenchymal stem cells cultured on a range of tailored porous SiO2 and TiO2 nanostructured surface coatings fabricated via glancing angle electron-beam deposition. By controlling the physical vapor deposition angle during fabrication, we could control systematically the deposited coating porosity, along with associated topographic features. Immunocytochemistry and image analysis quantitatively revealed the number of adherent cells, as well as their basic cellular morphology, on these surfaces. Signaling pathway studies showed that even with subtle changes in nanoscale surface structures, the behavior of mesenchymal stem cells was strongly influenced by the precise surface structures of these porous coatings. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantitative microlocalization of diffusible ions in normal and galactose cataractous rat lens by secondary ion mass spectrometry.

PubMed

Burns, M S; File, D M

1986-11-01

Secondary ion mass spectrometry (SIMS) is a surface analytical technique with high sensitivity for elemental detection and microlocalization capabilities within the micrometre range. Quantitative analysis of epoxy resins and gelatin have been reported (Burns-Bellhorn & File, 1979). We report here the first application of this technique to quantitative microlocalization in the context of a physiological problem--analyses of sodium, potassium and calcium in normal and galactose-induced cataract in rat lens. It is known that during the development of galactose-induced cataract the whole lens content of potassium is decreased, sodium is increased and, in late stages, calcium concentration increases. Whether these alterations in diffusible ions occur homogeneously or heterogeneously is not known. Standard curves were generated from epoxy resins containing known concentrations of sodium, potassium or calcium organometallic compounds using the Cameca IMS 300 Secondary Ion Mass Spectrometer. Normal and cataractous lenses were prepared by freezing in isopentane in a liquid nitrogen bath followed by freeze-drying at -30 degrees C. After dry embedding in epoxy resin, 10 microns thick sections of lens were pressure mounted on silicon wafers, overcoated with gold, and ion emission measured under the same instrumental conditions used to obtain the standard curves. Quantitative analysis of an area 27 microns in diameter, or a total analysed volume of 1.1 microns3, was performed by using a mechanical aperture in the ion optical system. Ion images provided qualitative microanalysis with a lateral resolution of 1 micron. Control rat lenses gave values for sodium and potassium content with a precision of +/- 17% or less. These values were compared to flame photometry and atomic absorption measurements of normal lenses and were accurate within 25%. Analysis of serum and blood also gave accurate and precise measurements of these elements. Normal rat lenses had a gradient of sodium, and, to a lesser degree, of potassium from the cortex to the nucleus. Development of galactose-induced cataract was heterogeneous by morphological criteria, beginning at the lens equator and spreading from the cortex into the nucleus. However, the loss of potassium and increase in sodium concentration occurred at early stages in both the cortex and nucleus cells, possibly because these cells are interconnected by gap junctions. There is a local alteration in elemental content prior to morphologically demonstrable cataract formation.(ABSTRACT TRUNCATED AT 400 WORDS)

A new transform for the analysis of complex fractionated atrial electrograms

PubMed Central

2011-01-01

Background Representation of independent biophysical sources using Fourier analysis can be inefficient because the basis is sinusoidal and general. When complex fractionated atrial electrograms (CFAE) are acquired during atrial fibrillation (AF), the electrogram morphology depends on the mix of distinct nonsinusoidal generators. Identification of these generators using efficient methods of representation and comparison would be useful for targeting catheter ablation sites to prevent arrhythmia reinduction. Method A data-driven basis and transform is described which utilizes the ensemble average of signal segments to identify and distinguish CFAE morphologic components and frequencies. Calculation of the dominant frequency (DF) of actual CFAE, and identification of simulated independent generator frequencies and morphologies embedded in CFAE, is done using a total of 216 recordings from 10 paroxysmal and 10 persistent AF patients. The transform is tested versus Fourier analysis to detect spectral components in the presence of phase noise and interference. Correspondence is shown between ensemble basis vectors of highest power and corresponding synthetic drivers embedded in CFAE. Results The ensemble basis is orthogonal, and efficient for representation of CFAE components as compared with Fourier analysis (p ≤ 0.002). When three synthetic drivers with additive phase noise and interference were decomposed, the top three peaks in the ensemble power spectrum corresponded to the driver frequencies more closely as compared with top Fourier power spectrum peaks (p ≤ 0.005). The synthesized drivers with phase noise and interference were extractable from their corresponding ensemble basis with a mean error of less than 10%. Conclusions The new transform is able to efficiently identify CFAE features using DF calculation and by discerning morphologic differences. Unlike the Fourier transform method, it does not distort CFAE signals prior to analysis, and is relatively robust to jitter in periodic events. Thus the ensemble method can provide a useful alternative for quantitative characterization of CFAE during clinical study. PMID:21569421

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.

Automated high resolution full-field spatial coherence tomography for quantitative phase imaging of human red blood cells

NASA Astrophysics Data System (ADS)

Singla, Neeru; Dubey, Kavita; Srivastava, Vishal; Ahmad, Azeem; Mehta, D. S.

2018-02-01

We developed an automated high-resolution full-field spatial coherence tomography (FF-SCT) microscope for quantitative phase imaging that is based on the spatial, rather than the temporal, coherence gating. The Red and Green color laser light was used for finding the quantitative phase images of unstained human red blood cells (RBCs). This study uses morphological parameters of unstained RBCs phase images to distinguish between normal and infected cells. We recorded the single interferogram by a FF-SCT microscope for red and green color wavelength and average the two phase images to further reduced the noise artifacts. In order to characterize anemia infected from normal cells different morphological features were extracted and these features were used to train machine learning ensemble model to classify RBCs with high accuracy.

SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells.

PubMed

Stylianidou, Stella; Brennan, Connor; Nissen, Silas B; Kuwada, Nathan J; Wiggins, Paul A

2016-11-01

Many quantitative cell biology questions require fast yet reliable automated image segmentation to identify and link cells from frame-to-frame, and characterize the cell morphology and fluorescence. We present SuperSegger, an automated MATLAB-based image processing package well-suited to quantitative analysis of high-throughput live-cell fluorescence microscopy of bacterial cells. SuperSegger incorporates machine-learning algorithms to optimize cellular boundaries and automated error resolution to reliably link cells from frame-to-frame. Unlike existing packages, it can reliably segment microcolonies with many cells, facilitating the analysis of cell-cycle dynamics in bacteria as well as cell-contact mediated phenomena. This package has a range of built-in capabilities for characterizing bacterial cells, including the identification of cell division events, mother, daughter and neighbouring cells, and computing statistics on cellular fluorescence, the location and intensity of fluorescent foci. SuperSegger provides a variety of postprocessing data visualization tools for single cell and population level analysis, such as histograms, kymographs, frame mosaics, movies and consensus images. Finally, we demonstrate the power of the package by analyzing lag phase growth with single cell resolution. © 2016 John Wiley & Sons Ltd.

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.

Contrasting patterns of structural host specificity of two species of Heligmosomoides nematodes in sympatric rodents.

PubMed

Clough, Dagmar; Råberg, Lars

2014-12-01

Host specificity is a fundamental property of parasites. Whereas most studies focus on measures of specificity on host range, only few studies have considered quantitative aspects such as infection intensity or prevalence. The relative importance of these quantitative aspects is still unclear, mainly because of methodological constraints, yet central to a precise assessment of host specificity. Here, we assessed simultaneously two quantitative measures of host specificity of Heligmosomoides glareoli and Heligmosomoides polygyrus polygyrus infections in sympatric rodent hosts. We used standard morphological techniques as well as real-time quantitative PCR and sequencing of the rDNA ITS2 fragment to analyse parasite infection via faecal sample remains. Although both parasite species are thought to be strictly species-specific, we found morphologically and molecularly validated co- and cross-infections. We also detected contrasting patterns within and between host species with regard to specificity for prevalence and intensity of infection. H. glareoli intensities were twofold higher in bank voles than in yellow-necked mice, but prevalence did not differ significantly between species (33 vs. 18%). We found the opposite pattern in H. polygyrus infections with similar intensity levels between host species but significantly higher prevalence in mouse hosts (56 vs. 10%). Detection rates were higher with molecular tools than morphological methods. Our results emphasize the necessity to consider quantitative aspects of specificity for a full view of a parasites' capacity to replicate and transmit in hosts and present a worked example of how modern molecular tools help to advance our understanding of selective forces in host-parasite ecology and evolution.

Prospects and challenges of quantitative phase imaging in tumor cell biology

NASA Astrophysics Data System (ADS)

Kemper, Björn; Götte, Martin; Greve, Burkhard; Ketelhut, Steffi

2016-03-01

Quantitative phase imaging (QPI) techniques provide high resolution label-free quantitative live cell imaging. Here, prospects and challenges of QPI in tumor cell biology are presented, using the example of digital holographic microscopy (DHM). It is shown that the evaluation of quantitative DHM phase images allows the retrieval of different parameter sets for quantification of cellular motion changes in migration and motility assays that are caused by genetic modifications. Furthermore, we demonstrate simultaneously label-free imaging of cell growth and morphology properties.

[Image processing applying in analysis of motion features of cultured cardiac myocyte in rat].

PubMed

Teng, Qizhi; He, Xiaohai; Luo, Daisheng; Wang, Zhengrong; Zhou, Beiyi; Yuan, Zhirun; Tao, Dachang

2007-02-01

Study of mechanism of medicine actions, by quantitative analysis of cultured cardiac myocyte, is one of the cutting edge researches in myocyte dynamics and molecular biology. The characteristics of cardiac myocyte auto-beating without external stimulation make the research sense. Research of the morphology and cardiac myocyte motion using image analysis can reveal the fundamental mechanism of medical actions, increase the accuracy of medicine filtering, and design the optimal formula of medicine for best medical treatments. A system of hardware and software has been built with complete sets of functions including living cardiac myocyte image acquisition, image processing, motion image analysis, and image recognition. In this paper, theories and approaches are introduced for analysis of living cardiac myocyte motion images and implementing quantitative analysis of cardiac myocyte features. A motion estimation algorithm is used for motion vector detection of particular points and amplitude and frequency detection of a cardiac myocyte. Beatings of cardiac myocytes are sometimes very small. In such case, it is difficult to detect the motion vectors from the particular points in a time sequence of images. For this reason, an image correlation theory is employed to detect the beating frequencies. Active contour algorithm in terms of energy function is proposed to approximate the boundary and detect the changes of edge of myocyte.

Intra- and inter-observer reliability of quantitative analysis of the infra-patellar fat pad and comparison between fat- and non-fat-suppressed imaging--Data from the osteoarthritis initiative.

PubMed

Steidle-Kloc, E; Wirth, W; Ruhdorfer, A; Dannhauer, T; Eckstein, F

2016-03-01

The infra-patellar fat pad (IPFP), as intra-articular adipose tissue represents a potential source of pro-inflammatory cytokines and its size has been suggested to be associated with osteoarthritis (OA) of the knee. This study examines inter- and intra-observer reliability of fat-suppressed (fs) and non-fat-suppressed (nfs) MR imaging for determination of IPFP morphological measurements as novel biomarkers. The IPFP of nine right knees of healthy Osteoarthritis Initiative participants was segmented by five readers, using fs and nfs baseline sagittal MRIs. The intra-observer reliability was determined from baseline and 1-year follow-up images. All segmentations were quality controlled (QC) by an expert reader. Reliability was expressed as root mean square coefficient of variation (RMS CV%). After QC, the inter-observer reliability for fs (nfs) imaging was 2.0% (1.1%) for IPFP volume, 2.1%/2.5% (1.6%/1.8%) for anterior/posterior surface areas, 1.8% (1.8%) for depth, and 2.1% (2.4%) for maximum sagittal area. The intra-observer reliability was 3.1% (5.0%) for volume, 2.3%/2.8% (2.5%/2.9%) for anterior/posterior surfaces, 1.9% (3.5%) for depth, and 3.3% (4.5%) for maximum sagittal area. IPFP volume from nfs images was systematically greater (+7.3%) than from fs images, but highly correlated (r=0.98). The results suggest that quantitative measurements of IPFP morphology can be performed with satisfactory reliability when expert QC is implemented. The IPFP is more clearly depicted in nfs images, and there is a small systematic off-set versus analysis from fs images. However, the high linear relationship between fs and nfs imaging suggests that fs images can be used to analyze IPFP morphology, when nfs images are not available. Copyright © 2015 Elsevier GmbH. All rights reserved.

Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy?

PubMed Central

2015-01-01

Nematodes inhabiting benthic deep-sea ecosystems account for >90% of the total metazoan abundances and they have been hypothesised to be hyper-diverse, but their biodiversity is still largely unknown. Metabarcoding could facilitate the census of biodiversity, especially for those tiny metazoans for which morphological identification is difficult. We compared, for the first time, different DNA extraction procedures based on the use of two commercial kits and a previously published laboratory protocol and tested their suitability for sequencing analyses of 18S rDNA of marine nematodes. We also investigated the reliability of Roche 454 sequencing analyses for assessing the biodiversity of deep-sea nematode assemblages previously morphologically identified. Finally, intra-genomic variation in 18S rRNA gene repeats was investigated by Illumina MiSeq in different deep-sea nematode morphospecies to assess the influence of polymorphisms on nematode biodiversity estimates. Our results indicate that the two commercial kits should be preferred for the molecular analysis of biodiversity of deep-sea nematodes since they consistently provide amplifiable DNA suitable for sequencing. We report that the morphological identification of deep-sea nematodes matches the results obtained by metabarcoding analysis only at the order-family level and that a large portion of Operational Clustered Taxonomic Units (OCTUs) was not assigned. We also show that independently from the cut-off criteria and bioinformatic pipelines used, the number of OCTUs largely exceeds the number of individuals and that 18S rRNA gene of different morpho-species of nematodes displayed intra-genomic polymorphisms. Our results indicate that metabarcoding is an important tool to explore the diversity of deep-sea nematodes, but still fails in identifying most of the species due to limited number of sequences deposited in the public databases, and in providing quantitative data on the species encountered. These aspects should be carefully taken into account before using metabarcoding in quantitative ecological research and monitoring programmes of marine biodiversity. PMID:26701112

Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy?

PubMed

Dell'Anno, Antonio; Carugati, Laura; Corinaldesi, Cinzia; Riccioni, Giulia; Danovaro, Roberto

2015-01-01

Nematodes inhabiting benthic deep-sea ecosystems account for >90% of the total metazoan abundances and they have been hypothesised to be hyper-diverse, but their biodiversity is still largely unknown. Metabarcoding could facilitate the census of biodiversity, especially for those tiny metazoans for which morphological identification is difficult. We compared, for the first time, different DNA extraction procedures based on the use of two commercial kits and a previously published laboratory protocol and tested their suitability for sequencing analyses of 18S rDNA of marine nematodes. We also investigated the reliability of Roche 454 sequencing analyses for assessing the biodiversity of deep-sea nematode assemblages previously morphologically identified. Finally, intra-genomic variation in 18S rRNA gene repeats was investigated by Illumina MiSeq in different deep-sea nematode morphospecies to assess the influence of polymorphisms on nematode biodiversity estimates. Our results indicate that the two commercial kits should be preferred for the molecular analysis of biodiversity of deep-sea nematodes since they consistently provide amplifiable DNA suitable for sequencing. We report that the morphological identification of deep-sea nematodes matches the results obtained by metabarcoding analysis only at the order-family level and that a large portion of Operational Clustered Taxonomic Units (OCTUs) was not assigned. We also show that independently from the cut-off criteria and bioinformatic pipelines used, the number of OCTUs largely exceeds the number of individuals and that 18S rRNA gene of different morpho-species of nematodes displayed intra-genomic polymorphisms. Our results indicate that metabarcoding is an important tool to explore the diversity of deep-sea nematodes, but still fails in identifying most of the species due to limited number of sequences deposited in the public databases, and in providing quantitative data on the species encountered. These aspects should be carefully taken into account before using metabarcoding in quantitative ecological research and monitoring programmes of marine biodiversity.

Intra- and inter-observer reliability of quantitative analysis of the infra-patellar fat pad and comparison between fat- and non-fat-suppressed imaging—Data from the osteoarthritis initiative

PubMed Central

Steidle-Kloc, E.; Wirth, W.; Ruhdorfer, A.; Dannhauer, T.; Eckstein, F.

2015-01-01

The infra-patellar fat pad (IPFP), as intra-articular adipose tissue represents a potential source of pro-inflammatory cytokines and its size has been suggested to be associated with osteoarthritis (OA) of the knee. This study examines inter- and intra-observer reliability of fat-suppressed (fs) and non-fat-suppressed (nfs) MR imaging for determination of IPFP morphological measurements as novel biomarkers. The IPFP of nine right knees of healthy Osteoarthritis Initiative participants was segmented by five readers, using fs and nfs baseline sagittal MRIs. The intra-observer reliability was determined from baseline and 1-year follow-up images. All segmentations were quality controlled (QC) by an expert reader. Reliability was expressed as root mean square coefficient of variation (RMS CV%). After QC, the inter-observer reliability for fs (nfs) imaging was 2.0% (1.1%) for IPFP volume, 2.1%/2.5% (1.6%/1.8%) for anterior/posterior surface areas, 1.8% (1.8%) for depth, and 2.1% (2.4%) for maximum sagittal area. The intra-observer reliability was 3.1% (5.0%) for volume, 2.3%/2.8% (2.5%/2.9%) for anterior/posterior surfaces, 1.9% (3.5%) for depth, and 3.3% (4.5%) for maximum sagittal area. IPFP volume from nfs images was systematically greater (+7.3%) than from fs images, but highly correlated (r = 0.98). The results suggest that quantitative measurements of IPFP morphology can be performed with satisfactory reliability when expert QC is implemented. The IPFP is more clearly depicted in nfs images, and there is a small systematic off-set versus analysis from fs images. However, the high linear relationship between fs and nfs imaging suggests that fs images can be used to analyze IPFP morphology, when nfs images are not available. PMID:26569532

A New Species of Haplophyllum A. Juss. (Rutaceae) from the Iberian Peninsula: Evidence from Morphological, Karyological and Molecular Analyses

PubMed Central

NAVARRO, F. B.; SUÁREZ-SANTIAGO, V. N.; BLANCA, G.

2004-01-01

• Background and Aims The discovery of a new species, Haplophyllum bastetanum F.B. Navarro, V.N. Suárez-Santiago & Blanca sp. nov., in the south-east of Spain has prompted the comparative study of species of the Iberian Peninsula, and others related, through morphological, cytogenetic, molecular, distributional and ecological characterization. • Methods The morphological study involved a quantitative analysis of the species present in the Iberian Peninsula and a comparative analysis of the morphological characteristics between H. bastetanum and other related species. Mitotic analyses were made with root meristems taken from germinating seeds. Phylogenetic analyses of the internal transcribed spacer sequences of nuclear ribosomal DNA were performed using neighbour-joining (NJ) and maximum-parsimony methods. • Key Results Haplophyllum bastetanum is a diploid species (2n = 18) distinguished primarily for its non-trifoliate glabrous leaves, lanceolate sepals, dark-green petals with a dorsal band of hairs, and a highly hairy ovary with round-apex locules. The other two Iberian species (H. linifolium and H. rosmarinifolium) are tetraploid (2n = 36) and have yellow petals. Both phylogenetic methods generated a well-supported clade grouping H. linifolium with H. rosmarinifolium. In the NJ tree, the H. linifolium–H. rosmarinifolium clade is a sister group to H. bastetanum, while in the parsimony analysis this occurred only when the gaps were coded as a fifth base and the characters were reweighted according to the rescaled consistency index. This latter group is supported by the sequence divergence among taxa. • Conclusions The phylogenies established from DNA sequences together with morphological and cytogenetic analyses support the separation of H. bastetanum as a new species. The results suggest that the change in the number of chromosomes may be the key mechanism of speciation of the genus Haplophyllum in the Iberian Peninsula. An evolutionary scheme for them is propounded. PMID:15306560

Image Analysis of DNA Fiber and Nucleus in Plants.

PubMed

Ohmido, Nobuko; Wako, Toshiyuki; Kato, Seiji; Fukui, Kiichi

2016-01-01

Advances in cytology have led to the application of a wide range of visualization methods in plant genome studies. Image analysis methods are indispensable tools where morphology, density, and color play important roles in the biological systems. Visualization and image analysis methods are useful techniques in the analyses of the detailed structure and function of extended DNA fibers (EDFs) and interphase nuclei. The EDF is the highest in the spatial resolving power to reveal genome structure and it can be used for physical mapping, especially for closely located genes and tandemly repeated sequences. One the other hand, analyzing nuclear DNA and proteins would reveal nuclear structure and functions. In this chapter, we describe the image analysis protocol for quantitatively analyzing different types of plant genome, EDFs and interphase nuclei.

Quantifying Morphological Parameters of the Terminal Branching Units in a Mouse Lung by Phase Contrast Synchrotron Radiation Computed Tomography

PubMed Central

Hwang, Jeongeun; Kim, Miju; Kim, Seunghwan; Lee, Jinwon

2013-01-01

An effective technique of phase contrast synchrotron radiation computed tomography was established for the quantitative analysis of the microstructures in the respiratory zone of a mouse lung. Heitzman’s method was adopted for the whole-lung sample preparation, and Canny’s edge detector was used for locating the air-tissue boundaries. This technique revealed detailed morphology of the respiratory zone components, including terminal bronchioles and alveolar sacs, with sufficiently high resolution of 1.74 µm isotropic voxel size. The technique enabled visual inspection of the respiratory zone components and comprehension of their relative positions in three dimensions. To check the method’s feasibility for quantitative imaging, morphological parameters such as diameter, surface area and volume were measured and analyzed for sixteen randomly selected terminal branching units, each consisting of a terminal bronchiole and a pair of succeeding alveolar sacs. The four types of asymmetry ratios concerning alveolar sac mouth diameter, alveolar sac surface area, and alveolar sac volume are measured. This is the first ever finding of the asymmetry ratio for the terminal bronchioles and alveolar sacs, and it is noteworthy that an appreciable degree of branching asymmetry was observed among the alveolar sacs at the terminal end of the airway tree, despite the number of samples was small yet. The series of efficient techniques developed and confirmed in this study, from sample preparation to quantification, is expected to contribute to a wider and exacter application of phase contrast synchrotron radiation computed tomography to a variety of studies. PMID:23704918

Abnormal aortic arch morphology in Turner syndrome patients is a risk factor for hypertension.

PubMed

De Groote, Katya; Devos, Daniël; Van Herck, Koen; Demulier, Laurent; Buysse, Wesley; De Schepper, Jean; De Wolf, Daniël

2015-09-01

Hypertension in Turner syndrome (TS) is a multifactorial, highly prevalent and significant problem that warrants timely diagnosis and rigorous treatment. The objective of this study was to investigate the association between abnormal aortic arch morphology and hypertension in adult TS patients. This was a single centre retrospective study in 74 adult TS patients (age 29.41 ± 8.91 years) who underwent a routine cardiac MRI. Patients were assigned to the hypertensive group (N = 31) if blood pressure exceeded 140/90 mmHg and/or if they were treated with antihypertensive medication. Aortic arch morphology was evaluated on MRI images and initially assigned as normal (N = 54) or abnormal (N = 20), based on the curve of the transverse arch and the distance between the left common carotid-left subclavian artery. We additionally used a new more objective method to describe aortic arch abnormality in TS by determination of the relative position of the highest point of the transverse arch (AoHP). Logistic regression analysis showed that hypertension is significantly and independently associated with age, BMI and abnormal arch morphology, with a larger effect size for the new AoHP method than for the classical method. TS patients with hypertension and abnormal arch morphology more often had dilatation of the ascending aorta. There is a significant association between abnormal arch morphology and hypertension in TS patients, independent of age and BMI, and not related to other structural heart disease. We suggest that aortic arch morphology should be included in the risk stratification for hypertension in TS and propose a new quantitative method to express aortic arch morphology.

Loss of the integral nuclear envelope protein SUN1 induces alteration of nucleoli

PubMed Central

Matsumoto, Ayaka; Sakamoto, Chiyomi; Matsumori, Haruka; Katahira, Jun; Yasuda, Yoko; Yoshidome, Katsuhide; Tsujimoto, Masahiko; Goldberg, Ilya G; Matsuura, Nariaki; Nakao, Mitsuyoshi; Saitoh, Noriko; Hieda, Miki

2016-01-01

ABSTRACT A supervised machine learning algorithm, which is qualified for image classification and analyzing similarities, is based on multiple discriminative morphological features that are automatically assembled during the learning processes. The algorithm is suitable for population-based analysis of images of biological materials that are generally complex and heterogeneous. Here we used the algorithm wndchrm to quantify the effects on nucleolar morphology of the loss of the components of nuclear envelope in a human mammary epithelial cell line. The linker of nucleoskeleton and cytoskeleton (LINC) complex, an assembly of nuclear envelope proteins comprising mainly members of the SUN and nesprin families, connects the nuclear lamina and cytoskeletal filaments. The components of the LINC complex are markedly deficient in breast cancer tissues. We found that a reduction in the levels of SUN1, SUN2, and lamin A/C led to significant changes in morphologies that were computationally classified using wndchrm with approximately 100% accuracy. In particular, depletion of SUN1 caused nucleolar hypertrophy and reduced rRNA synthesis. Further, wndchrm revealed a consistent negative correlation between SUN1 expression and the size of nucleoli in human breast cancer tissues. Our unbiased morphological quantitation strategies using wndchrm revealed an unexpected link between the components of the LINC complex and the morphologies of nucleoli that serves as an indicator of the malignant phenotype of breast cancer cells. PMID:26962703

Loss of the integral nuclear envelope protein SUN1 induces alteration of nucleoli.

PubMed

Matsumoto, Ayaka; Sakamoto, Chiyomi; Matsumori, Haruka; Katahira, Jun; Yasuda, Yoko; Yoshidome, Katsuhide; Tsujimoto, Masahiko; Goldberg, Ilya G; Matsuura, Nariaki; Nakao, Mitsuyoshi; Saitoh, Noriko; Hieda, Miki

2016-01-01

A supervised machine learning algorithm, which is qualified for image classification and analyzing similarities, is based on multiple discriminative morphological features that are automatically assembled during the learning processes. The algorithm is suitable for population-based analysis of images of biological materials that are generally complex and heterogeneous. Here we used the algorithm wndchrm to quantify the effects on nucleolar morphology of the loss of the components of nuclear envelope in a human mammary epithelial cell line. The linker of nucleoskeleton and cytoskeleton (LINC) complex, an assembly of nuclear envelope proteins comprising mainly members of the SUN and nesprin families, connects the nuclear lamina and cytoskeletal filaments. The components of the LINC complex are markedly deficient in breast cancer tissues. We found that a reduction in the levels of SUN1, SUN2, and lamin A/C led to significant changes in morphologies that were computationally classified using wndchrm with approximately 100% accuracy. In particular, depletion of SUN1 caused nucleolar hypertrophy and reduced rRNA synthesis. Further, wndchrm revealed a consistent negative correlation between SUN1 expression and the size of nucleoli in human breast cancer tissues. Our unbiased morphological quantitation strategies using wndchrm revealed an unexpected link between the components of the LINC complex and the morphologies of nucleoli that serves as an indicator of the malignant phenotype of breast cancer cells.

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.

A novel mesh processing based technique for 3D plant analysis

PubMed Central

2012-01-01

Background In recent years, imaging based, automated, non-invasive, and non-destructive high-throughput plant phenotyping platforms have become popular tools for plant biology, underpinning the field of plant phenomics. Such platforms acquire and record large amounts of raw data that must be accurately and robustly calibrated, reconstructed, and analysed, requiring the development of sophisticated image understanding and quantification algorithms. The raw data can be processed in different ways, and the past few years have seen the emergence of two main approaches: 2D image processing and 3D mesh processing algorithms. Direct image quantification methods (usually 2D) dominate the current literature due to comparative simplicity. However, 3D mesh analysis provides the tremendous potential to accurately estimate specific morphological features cross-sectionally and monitor them over-time. Result In this paper, we present a novel 3D mesh based technique developed for temporal high-throughput plant phenomics and perform initial tests for the analysis of Gossypium hirsutum vegetative growth. Based on plant meshes previously reconstructed from multi-view images, the methodology involves several stages, including morphological mesh segmentation, phenotypic parameters estimation, and plant organs tracking over time. The initial study focuses on presenting and validating the accuracy of the methodology on dicotyledons such as cotton but we believe the approach will be more broadly applicable. This study involved applying our technique to a set of six Gossypium hirsutum (cotton) plants studied over four time-points. Manual measurements, performed for each plant at every time-point, were used to assess the accuracy of our pipeline and quantify the error on the morphological parameters estimated. Conclusion By directly comparing our automated mesh based quantitative data with manual measurements of individual stem height, leaf width and leaf length, we obtained the mean absolute errors of 9.34%, 5.75%, 8.78%, and correlation coefficients 0.88, 0.96, and 0.95 respectively. The temporal matching of leaves was accurate in 95% of the cases and the average execution time required to analyse a plant over four time-points was 4.9 minutes. The mesh processing based methodology is thus considered suitable for quantitative 4D monitoring of plant phenotypic features. PMID:22553969

Segmentation-free image processing and analysis of precipitate shapes in 2D and 3D

NASA Astrophysics Data System (ADS)

Bales, Ben; Pollock, Tresa; Petzold, Linda

2017-06-01

Segmentation based image analysis techniques are routinely employed for quantitative analysis of complex microstructures containing two or more phases. The primary advantage of these approaches is that spatial information on the distribution of phases is retained, enabling subjective judgements of the quality of the segmentation and subsequent analysis process. The downside is that computing micrograph segmentations with data from morphologically complex microstructures gathered with error-prone detectors is challenging and, if no special care is taken, the artifacts of the segmentation will make any subsequent analysis and conclusions uncertain. In this paper we demonstrate, using a two phase nickel-base superalloy microstructure as a model system, a new methodology for analysis of precipitate shapes using a segmentation-free approach based on the histogram of oriented gradients feature descriptor, a classic tool in image analysis. The benefits of this methodology for analysis of microstructure in two and three-dimensions are demonstrated.

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.

HeLa cells response to photodynamic treatment with Radachlorin at various irradiation parameters

NASA Astrophysics Data System (ADS)

Belashov, A. V.; Zhikhoreva, A. A.; Belyaeva, T. N.; Kornilova, E. S.; Petrov, N. V.; Salova, A. V.; Semenova, I. V.; Vasyutinskii, O. S.

2017-07-01

Measurements of average phase shifts introduced by living HeLa cells to probe wave front were carried out. Variations of this value were monitored in the course of morphological changes caused by photodynamic treatment at various irradiation doses. Observations of changes in living cells were also performed by means of far field optical microscopy and confocal fluorescent microscopy. Quantitative analysis of the data obtained shows that average phase shift introduced by the cells may either increase or decrease depending upon major parameters of the treatment.

Comparison of Quantitative Antifungal Testing Methods for Textile Fabrics.

PubMed

Imoto, Yasuo; Seino, Satoshi; Nakagawa, Takashi; Yamamoto, Takao A

2017-01-01

　Quantitative antifungal testing methods for textile fabrics under growth-supportive conditions were studied. Fungal growth activities on unfinished textile fabrics and textile fabrics modified with Ag nanoparticles were investigated using the colony counting method and the luminescence method. Morphological changes of the fungi during incubation were investigated by microscopic observation. Comparison of the results indicated that the fungal growth activity values obtained with the colony counting method depended on the morphological state of the fungi on textile fabrics, whereas those obtained with the luminescence method did not. Our findings indicated that unique characteristics of each testing method must be taken into account for the proper evaluation of antifungal activity.

Bayesian species delimitation in Pleophylla chafers (Coleoptera) - the importance of prior choice and morphology.

PubMed

Eberle, Jonas; Warnock, Rachel C M; Ahrens, Dirk

2016-05-05

Defining species units can be challenging, especially during the earliest stages of speciation, when phylogenetic inference and delimitation methods may be compromised by incomplete lineage sorting (ILS) or secondary gene flow. Integrative approaches to taxonomy, which combine molecular and morphological evidence, have the potential to be valuable in such cases. In this study we investigated the South African scarab beetle genus Pleophylla using data collected from 110 individuals of eight putative morphospecies. The dataset included four molecular markers (cox1, 16S, rrnL, ITS1) and morphometric data based on male genital morphology. We applied a suite of molecular and morphological approaches to species delimitation, and implemented a novel Bayesian approach in the software iBPP, which enables continuous morphological trait and molecular data to be combined. Traditional morphology-based species assignments were supported quantitatively by morphometric analyses of the male genitalia (eigenshape analysis, CVA, LDA). While the ITS1-based delineation was also broadly congruent with the morphospecies, the cox1 data resulted in over-splitting (GMYC modelling, haplotype networks, PTP, ABGD). In the most extreme case morphospecies shared identical haplotypes, which may be attributable to ILS based on statistical tests performed using the software JML. We found the strongest support for putative morphospecies based on phylogenetic evidence using the combined approach implemented in iBPP. However, support for putative species was sensitive to the use of alternative guide trees and alternative combinations of priors on the population size (θ) and rootage (τ 0 ) parameters, especially when the analysis was based on molecular or morphological data alone. We demonstrate that continuous morphological trait data can be extremely valuable in assessing competing hypotheses to species delimitation. In particular, we show that the inclusion of morphological data in an integrative Bayesian framework can improve the resolution of inferred species units. However, we also demonstrate that this approach is extremely sensitive to guide tree and prior parameter choice. These parameters should be chosen with caution - if possible - based on independent empirical evidence, or careful sensitivity analyses should be performed to assess the robustness of results. Young species provide exemplars for investigating the mechanisms of speciation and for assessing the performance of tools used to delimit species on the basis of molecular and/or morphological evidence.

[Sex differentiation in plants. Terms and notions].

PubMed

Godin, V N

2007-01-01

There are two methodological approaches to the study of sex in plants: the descriptive and morphological approach and the quantitative approach. The former is based exclusively on external morphological peculiarities of the generative organs of the flower, the latter is based on the functioning of individuals as parents of the coming generation. It has been suggested to recognize three flower types: staminate, pistillate, and complete. Depending on the distribution pattern of the flowers of different sex type, there are monomorphic populations (all individuals form flowers of the same type) and heteromorphic populations (individuals have flowers of different types). Monomorphic populations include monoclinous, monoecious, gynomonoecious, andromonoecious, and polygamomonoecious ones. Among heteromorphic populations, dioecious, polygamodioecious, subdioecious, paradioecious, and trioecious ones are recognized. It is desirable to give up the usage of such terms as "bisexual", "polygamous", "functionally female", and "functionally male" flowers, "temporary dioecy" and some others. The notion "gender" has been established in English-language works for describing the sex quantitavely; two additional terms have been proposed: "phenotypic gender" and "functional gender". The recently developed quantitative approach is at present in the process of accumulating material, and in need of the further elaborating the methodological base for research. Analysis of the principal notions shows the necessity to form their integrated structure and to correct the usage of the existing and new terms.

Mapping morphological shape as a high-dimensional functional curve

PubMed Central

Fu, Guifang; Huang, Mian; Bo, Wenhao; Hao, Han; Wu, Rongling

2018-01-01

Abstract Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000–4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of ‘function’ instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do. PMID:28062411

Pathological Gleason prediction through gland ring morphometry in immunofluorescent prostate cancer images

NASA Astrophysics Data System (ADS)

Scott, Richard; Khan, Faisal M.; Zeineh, Jack; Donovan, Michael; Fernandez, Gerardo

2016-03-01

The Gleason score is the most common architectural and morphological assessment of prostate cancer severity and prognosis. There have been numerous quantitative techniques developed to approximate and duplicate the Gleason scoring system. Most of these approaches have been developed in standard H and E brightfield microscopy. Immunofluorescence (IF) image analysis of tissue pathology has recently been proven to be extremely valuable and robust in developing prognostic assessments of disease, particularly in prostate cancer. There have been significant advances in the literature in quantitative biomarker expression as well as characterization of glandular architectures in discrete gland rings. In this work we leverage a new method of segmenting gland rings in IF images for predicting the pathological Gleason; both the clinical and the image specific grade, which may not necessarily be the same. We combine these measures with nuclear specific characteristics as assessed by the MST algorithm. Our individual features correlate well univariately with the Gleason grades, and in a multivariate setting have an accuracy of 85% in predicting the Gleason grade. Additionally, these features correlate strongly with clinical progression outcomes (CI of 0.89), significantly outperforming the clinical Gleason grades (CI of 0.78). This work presents the first assessment of morphological gland unit features from IF images for predicting the Gleason grade.

Effects of spacer orientations on the cake formation during membrane fouling: Quantitative analysis based on 3D OCT imaging.

PubMed

Liu, Xin; Li, Weiyi; Chong, Tzyy Haur; Fane, Anthony G

2017-03-01

Spacer design plays an important role in improving the performance of membrane processes for water/wastewater treatment. This work focused on a fundamental issue of spacer design, i.e., investigating the effects of spacer orientations on the fouling behavior during a membrane process. A series of fouling experiments with different spacer orientation were carried out to in situ characterize the formation of a cake layer in a spacer unit cell via 3D optical coherence tomography (OCT) imaging. The cake layers formed at different times were digitalized for quantitatively analyzing the variation in the cake morphology as a function of time. In particular, the local deposition rates were evaluated to determine the active regions where the instantaneous changes in deposit thickness were significant. The characterization results indicate that varying the spacer orientation could substantially change the evolution of membrane fouling by particulate foulants and thereby result in a cake layer with various morphologies; the competition between growth and erosion at different locations would instantaneously respond to the micro-hydrodynamic environment that might change with time. This work confirms that the OCT-based characterization method is a powerful tool for exploring novel spacer design. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2010-01-01

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

Texture analysis applied to second harmonic generation image data for ovarian cancer classification

NASA Astrophysics Data System (ADS)

Wen, Bruce L.; Brewer, Molly A.; Nadiarnykh, Oleg; Hocker, James; Singh, Vikas; Mackie, Thomas R.; Campagnola, Paul J.

2014-09-01

Remodeling of the extracellular matrix has been implicated in ovarian cancer. To quantitate the remodeling, we implement a form of texture analysis to delineate the collagen fibrillar morphology observed in second harmonic generation microscopy images of human normal and high grade malignant ovarian tissues. In the learning stage, a dictionary of "textons"-frequently occurring texture features that are identified by measuring the image response to a filter bank of various shapes, sizes, and orientations-is created. By calculating a representative model based on the texton distribution for each tissue type using a training set of respective second harmonic generation images, we then perform classification between images of normal and high grade malignant ovarian tissues. By optimizing the number of textons and nearest neighbors, we achieved classification accuracy up to 97% based on the area under receiver operating characteristic curves (true positives versus false positives). The local analysis algorithm is a more general method to probe rapidly changing fibrillar morphologies than global analyses such as FFT. It is also more versatile than other texture approaches as the filter bank can be highly tailored to specific applications (e.g., different disease states) by creating customized libraries based on common image features.

The Use of Multidimensional Image-Based Analysis to Accurately Monitor Cell Growth in 3D Bioreactor Culture

PubMed Central

Baradez, Marc-Olivier; Marshall, Damian

2011-01-01

The transition from traditional culture methods towards bioreactor based bioprocessing to produce cells in commercially viable quantities for cell therapy applications requires the development of robust methods to ensure the quality of the cells produced. Standard methods for measuring cell quality parameters such as viability provide only limited information making process monitoring and optimisation difficult. Here we describe a 3D image-based approach to develop cell distribution maps which can be used to simultaneously measure the number, confluency and morphology of cells attached to microcarriers in a stirred tank bioreactor. The accuracy of the cell distribution measurements is validated using in silico modelling of synthetic image datasets and is shown to have an accuracy >90%. Using the cell distribution mapping process and principal component analysis we show how cell growth can be quantitatively monitored over a 13 day bioreactor culture period and how changes to manufacture processes such as initial cell seeding density can significantly influence cell morphology and the rate at which cells are produced. Taken together, these results demonstrate how image-based analysis can be incorporated in cell quality control processes facilitating the transition towards bioreactor based manufacture for clinical grade cells. PMID:22028809

The use of multidimensional image-based analysis to accurately monitor cell growth in 3D bioreactor culture.

PubMed

Baradez, Marc-Olivier; Marshall, Damian

2011-01-01

The transition from traditional culture methods towards bioreactor based bioprocessing to produce cells in commercially viable quantities for cell therapy applications requires the development of robust methods to ensure the quality of the cells produced. Standard methods for measuring cell quality parameters such as viability provide only limited information making process monitoring and optimisation difficult. Here we describe a 3D image-based approach to develop cell distribution maps which can be used to simultaneously measure the number, confluency and morphology of cells attached to microcarriers in a stirred tank bioreactor. The accuracy of the cell distribution measurements is validated using in silico modelling of synthetic image datasets and is shown to have an accuracy >90%. Using the cell distribution mapping process and principal component analysis we show how cell growth can be quantitatively monitored over a 13 day bioreactor culture period and how changes to manufacture processes such as initial cell seeding density can significantly influence cell morphology and the rate at which cells are produced. Taken together, these results demonstrate how image-based analysis can be incorporated in cell quality control processes facilitating the transition towards bioreactor based manufacture for clinical grade cells.

Superolateral Hoffa's fat pad (SHFP) oedema and patellar cartilage volume loss: quantitative analysis using longitudinal data from the Foundation for the National Institute of Health (FNIH) Osteoarthritis Biomarkers Consortium.

PubMed

Haj-Mirzaian, Arya; Guermazi, Ali; Hafezi-Nejad, Nima; Sereni, Christopher; Hakky, Michael; Hunter, David J; Zikria, Bashir; Roemer, Frank W; Demehri, Shadpour

2018-04-12

To determine the association of superolateral Hoffa's fat pad (SHFP) oedema and patellofemoral joint structural damage in participants of Foundation for the National Institute of Health Osteoarthritis Biomarkers Consortium study. Baseline and 24-month MRIs of 600 subjects were assessed. The presence of SHFP oedema (using 0-3 grading scale) and patellar morphology metrics were determined using baseline MRI. Quantitative patellar cartilage volume and semi-quantitative MRI osteoarthritis knee score (MOAKS) variables were extracted. The associations between SHFP oedema and patellar cartilage damage, bone marrow lesion (BML), osteophyte and morphology were evaluated in cross-sectional model. In longitudinal analysis, the associations between oedema and cartilage volume loss (defined using reliable change index) and MOAKS worsening were evaluated. In cross-sectional evaluations, the presence of SHFP oedema was associated with simultaneous lateral patellar cartilage/BML defects and inferior-medial patellar osteophyte size. A significant positive correlation between the degree of patella alta and SHFP oedema was detected (r = 0.259, p < 0.001). The presence of oedema was associated with 24-month cartilage volume loss (odds ratio (OR) 2.11, 95% confidence interval 1.46-3.06) and medial patellar BML size (OR 1.92 (1.15-3.21)) and number (OR 2.50 (1.29-4.88)) worsening. The optimal cut-off value for the grade of baseline SHFP oedema regarding both presence and worsening of patellar structural damage was ≥ 1 (presence of any SHFP hyperintensity). The presence of SHFP oedema could be considered as a predictor of future patellar cartilage loss and BML worsening, and an indicator of simultaneous cartilage, BML and osteophyte defects. • SHFP oedema was associated with simultaneous lateral patellar OA-related structural damage. • SHFP oedema was associated with longitudinal patellar cartilage loss over 24 months. • SHFP oedema could be considered as indicator and predictor of patellar OA.

Zebrafish Caudal Fin Angiogenesis Assay—Advanced Quantitative Assessment Including 3-Way Correlative Microscopy

PubMed Central

Correa Shokiche, Carlos; Schaad, Laura; Triet, Ramona; Jazwinska, Anna; Tschanz, Stefan A.; Djonov, Valentin

2016-01-01

Background Researchers evaluating angiomodulating compounds as a part of scientific projects or pre-clinical studies are often confronted with limitations of applied animal models. The rough and insufficient early-stage compound assessment without reliable quantification of the vascular response counts, at least partially, to the low transition rate to clinics. Objective To establish an advanced, rapid and cost-effective angiogenesis assay for the precise and sensitive assessment of angiomodulating compounds using zebrafish caudal fin regeneration. It should provide information regarding the angiogenic mechanisms involved and should include qualitative and quantitative data of drug effects in a non-biased and time-efficient way. Approach & Results Basic vascular parameters (total regenerated area, vascular projection area, contour length, vessel area density) were extracted from in vivo fluorescence microscopy images using a stereological approach. Skeletonization of the vasculature by our custom-made software Skelios provided additional parameters including “graph energy” and “distance to farthest node”. The latter gave important insights into the complexity, connectivity and maturation status of the regenerating vascular network. The employment of a reference point (vascular parameters prior amputation) is unique for the model and crucial for a proper assessment. Additionally, the assay provides exceptional possibilities for correlative microscopy by combining in vivo-imaging and morphological investigation of the area of interest. The 3-way correlative microscopy links the dynamic changes in vivo with their structural substrate at the subcellular level. Conclusions The improved zebrafish fin regeneration model with advanced quantitative analysis and optional 3-way correlative morphology is a promising in vivo angiogenesis assay, well-suitable for basic research and preclinical investigations. PMID:26950851

Quantitative phase imaging characterization of tumor-associated blood vessel formation on a chip

NASA Astrophysics Data System (ADS)

Guo, Peng; Huang, Jing; Moses, Marsha A.

2018-02-01

Angiogenesis, the formation of new blood vessels from existing ones, is a biological process that has an essential role in solid tumor growth, development, and progression. Recent advances in Lab-on-a-Chip technology has created an opportunity for scientists to observe endothelial cell (EC) behaviors during the dynamic process of angiogenesis using a simple and economical in vitro platform that recapitulates in vivo blood vessel formation. Here, we use quantitative phase imaging (QPI) microscopy to continuously and non-invasively characterize the dynamic process of tumor cell-induced angiogenic sprout formation on a microfluidic chip. The live tumor cell-induced angiogenic sprouts are generated by multicellular endothelial sprouting into 3 dimensional (3D) Matrigel using human umbilical vein endothelial cells (HUVECs). By using QPI, we quantitatively measure a panel of cellular morphological and behavioral parameters of each individual EC participating in this sprouting. In this proof-of-principle study, we demonstrate that QPI is a powerful tool that can provide real-time quantitative analysis of biological processes in in vitro 3D biomimetic devices, which, in turn, can improve our understanding of the biology underlying functional tissue engineering.

Application of different analytical methods for the characterization of non-spherical micro- and nanoparticles.

PubMed

Mathaes, Roman; Winter, Gerhard; Engert, Julia; Besheer, Ahmed

2013-09-10

Non-spherical micro- and nanoparticles have recently gained considerable attention due to their surprisingly different interaction with biological systems compared to their spherical counterparts, opening new opportunities for drug delivery and vaccination. Up till now, electron microscopy is the only method to quantitatively identify the critical quality attributes (CQAs) of non-spherical particles produced by film-stretching; namely size, morphology and the quality of non-spherical particles (degree of contamination with spherical ones). However, electron microscopy requires expensive instrumentation, demanding sample preparation and non-trivial image analysis. To circumvent these drawbacks, the ability of different particle analysis methods to quantitatively identify the CQA of spherical and non-spherical poly(1-phenylethene-1,2-diyl (polystyrene) particles over a wide size range (40 nm, 2 μm and 10 μm) was investigated. To this end, light obscuration, image-based analysis methods (Microflow imaging, MFI, and Vi-Cell XR Coulter Counter) and flow cytometry were used to study particles in the micron range, while asymmetric flow field fractionation (AF4) coupled to multi-angle laser scattering (MALS) and quasi elastic light scattering (QELS) was used for particles in the nanometer range, and all measurements were benchmarked against electron microscopy. Results show that MFI can reliably identify particle size and aspect ratios of the 10 μm particles, but not the 2 μm ones. Meanwhile, flow cytometry was able to differentiate between spherical and non-spherical 10 or 2 μm particles, and determine the amount of impurities in the sample. As for the nanoparticles, AF4 coupled to MALS and QELS allowed the measurement of the geometric (rg) and hydrodynamic (rh) radii of the particles, as well as their shape factors (rg/rh), confirming their morphology. While this study shows the utility of MFI, flow cytometry and AF4 for quantitative evaluation of the CQA of non-spherical particles over a wide size range, the limitations of the methods are discussed. The use of orthogonal characterization methods can provide a complete picture about the CQA of non-spherical particles over a wide size range. Copyright © 2013 Elsevier B.V. All rights reserved.

Small lunar craters at the Apollo 16 and 17 landing sites - morphology and degradation

NASA Astrophysics Data System (ADS)

Mahanti, P.; Robinson, M. S.; Thompson, T. J.; Henriksen, M. R.

2018-01-01

New analysis and modeling approaches are applied to high-resolution images and topography of the Apollo 16 and 17 landing sites to investigate the morphology and estimate degradation of small lunar craters (SLCs; 35 to 250 m diameter). We find SLCs at the two sites are mostly degraded with an average depth-diameter ratio (d/D) < 0.1 , resulting in a landscape dominated by shallow, inverted cone-shaped craters. An improved standardized morphological classification and a novel set of quantitative shape indicators are defined and used to compare SLCs between the two sites. Our classification methodology allows morphological class populations to be designated with minimal (and measurable) ambiguity simplifying the study of SLC degradation at different target regions. SLC shape indicators are computationally obtained from topography, further facilitating a quantitative and repeatable comparison across study areas. Our results indicate that the interior slopes of SLCs evolve faster and through different processes relative to larger craters ( > 500 m). Assuming SLCs are formed with large initial depth-to-diameter ratio (d/D ≥ 0.2), our observation that even the fresher SLCs are relatively shallow imply that a faster mass wasting process post-formation stabilizes the crater walls and eventually slows down degradation. We also found that the Apollo 16 Cayley plains have a higher percentage of fresh craters than the Apollo 17 Taurus Littrow (TL) plains. A combination of a less-cohesive target material and/or seismic shaking resulting from moonquakes or the impact of Tycho crater secondaries was likely responsible for a higher degradation rate in the TL-plains compared to the Cayley plains. This study explores the relationship between the symmetry and probability densities of key morphological traits like d/D, mean wall slope and rate of degradation. We show that the shape of d/D probability density function of SLCs in a study area encodes their rate of degradation. Comparison of power-law fitting and probabilistic modeling of depth-diameter relations shows that probabilistic methods complement regression models and are necessary for robust prediction of SLC depths from diameter (and vice versa) for different geological targets.

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 increase in volume during the development of the pharate adult. PMID:28182298

Evaluation of the fossil fish-specific diversity in a chadian continental assemblage: Exploration of morphological continuous variation in Synodontis (Ostariophysi, Siluriformes).

PubMed

Pinton, Aurélie; Le Fur, Soizic; Otero, Olga

2016-11-01

In the fossil record, the quantification of continuous morphological variation has become a central issue when dealing with species identification and speciation. In this context, fossil taxa with living representatives hold great promise, because of the potential to characterise patterns of intraspecific morphological variation in extant species prior to any interpretation in the fossil record. The vast majority of catfish families fulfil this prerequisite, as most of them are represented by extant genera. However, although they constitute a major fish group in terms of distribution, and ecological and taxonomic diversity, the quantitative study of their past morphological variation has been neglected, as fossil specimens are generally identified based on the scarcest remains, that is, complete neurocrania that bear discrete characters. Consequently, a part of freshwater catfish history is unprospected and unknown. In this study, we explored the morphological continuous variation of the humeral plate shape in Synodontis catfishes using Elliptic Fourier Analysis (EFA), and compared extant members and fossil counterparts. We analysed 153 extant specimens of 11 Synodontis species present in the Chad basin, in addition to 23 fossil specimens from the Chadian fossiliferous area of Toros Menalla which is dated around 7 Ma. This highly speciose genus, which is one of the most diversified in Africa, exhibits a rich fossil record with several hundred remains mostly identified as Synodontis sp. The analysis of the outline of the humeral plate reveals that some living morphological types were already represented in the Chad Basin 7 My ago, and allows for the discovery of extinct species. Beside illuminating the complex Neogene evolutionary history of Synodontis, these results underline the interest in the ability of isolated remains to reconstruct a past dynamic history and to validate the relevance of EFA as a tool to explore specific diversity through time. J. Morphol. 277:1486-1496, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Channel degradation and restoration of an Alpine river and related morphological changes

NASA Astrophysics Data System (ADS)

Campana, Daniela; Marchese, Enrico; Theule, Joshua I.; Comiti, Francesco

2014-09-01

River degradation and thus necessity for restoration are major issues worldwide. However, adequate methodologies to assess morphological variations linked to these actions and the morphological success of restoration interventions are still to be determined. The Ahr River (South Tyrol, Italian Alps) was characterized until the mid-twentieth century by an anabranching and meandering pattern, but starting from the 1960s it underwent intense channel degradation in terms of narrowing, incision, and floodplain disconnection. In the period 2003-2011, several reaches of the Ahr River were restored by widening and raising the channel bed. The planimetric changes that occurred historically in the Ahr River were determined by the interpretation of 10 maps and aerial photos covering the period 1820-2011. The estimation of the incision that occurred during the degradation phase was assessed by the difference in elevation between gravel surfaces, whereas the changes introduced by restoration interventions in two reaches were evaluated through the comparison of topographic cross sections surveyed in year 2000 and a high-resolution bathymetric LiDAR survey flown in late 2012. The MQI (Morphological Quality Index) was applied to different reaches in order to test how assessment methodologies respond to degradation and restoration actions. The combined analysis of planform and vertical changes indicates that gravel mining has been the largest pressure for the river, but a change in sediment/flow regimes probably led to the channel adjustments that occurred during the early twentieth century. The restoration measures have locally increased channel width, elevation, and morphometrical diversity compared to the unrestored reaches, as well as the morphological quality assessed by MQI. However, the extent of the modifications brought about by restoration works differs between the two restored reaches, pointing out the need for a quantitative analysis of the historical evolution of each river reach before designing and implementing restoration actions and to the necessity to monitor the subsequent morphological adjustments.

The better to eat you with: the comparative feeding morphology of phocid seals (Pinnipedia, Phocidae).

PubMed

Kienle, Sarah S; Berta, Annalisa

2016-03-01

One adaptation crucial to the survival of mammalian lineages that secondarily transitioned from land to water environments was the ability to capture and consume prey underwater. Phocid seals have evolved diverse feeding strategies to feed in the marine environment, and the objectives of this study were to document the specialized feeding morphologies and identify feeding strategies used by extant phocids. This study used principal component analysis (PCA) to determine the major axes of diversification in the skull for all extant phocid taxa and the recently extinct Caribbean monk seal (n = 19). Prey data gathered from the literature and musculoskeletal data from dissections were included to provide a comprehensive description of each feeding strategy. Random Forest analysis was used to determine the morphological, ecological and phylogenetic variables that best described each feeding strategy. There is morphological evidence for four feeding strategies in phocids: filter; grip and tear; suction; and pierce feeding. These feeding strategies are supported by quantitative cranial and mandibular characters, dietary information, musculoskeletal data and, for some species, behavioral observations. Most phocid species are pierce feeders, using a combination of biting and suction to opportunistically catch prey. Grip and tear and filter feeding are specialized strategies with specific morphological adaptations. These unique adaptations have allowed leopard seals (Hydrurga leptonyx) and crabeater seals (Lobodon carcinophaga) to exploit novel ecological niches and prey types. This study provides the first cranial and mandibular morphological evidence for the use of specialized suction feeding in hooded seals (Cystophora cristata), northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The most important variables in determining the feeding strategy of a given phocid species were cranial and mandibular shape, diet, and phylogeny. These results provide a framework for understanding the evolution and adaptability of feeding strategies employed by extant phocid species, and these findings can be applied to other pinniped lineages and extinct taxa. © 2015 Anatomical Society.

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, 45% specificity). CT perfusion measurements enable differentiation and better discrimination, in comparison with morphologic criteria, between cancer and diverticulitis. (c) RSNA, 2007.

Microstructural Organization of Elastomeric Polyurethanes with Siloxane-Containing Soft Segments

NASA Astrophysics Data System (ADS)

Choi, Taeyi; Weklser, Jadwiga; Padsalgikar, Ajay; Runt, James

2011-03-01

In the present study, we investigate the microstructure of two series of segmented polyurethanes (PUs) containing siloxane-based soft segments and the same hard segments, the latter synthesized from diphenylmethane diisocyanate and butanediol. The first series is synthesized using a hydroxy-terminated polydimethylsiloxane macrodiol and varying hard segment contents. The second series are derived from an oligomeric diol containing both siloxane and aliphatic carbonate species. Hard domain morphologies were characterized using tapping mode atomic force microscopy and quantitative analysis of hard/soft segment demixing was conducted using small-angle X-ray scattering. The phase transitions of all materials were investigated using DSC and dynamic mechanical analysis, and hydrogen bonding by FTIR spectroscopy.

Selective Laser Melting of Metal Powder Of Steel 3161

NASA Astrophysics Data System (ADS)

Smelov, V. G.; Sotov, A. V.; Agapovichev, A. V.; Tomilina, T. M.

2016-08-01

In this article the results of experimental study of the structure and mechanical properties of materials obtained by selective laser melting (SLM), metal powder steel 316L was carried out. Before the process of cultivation of samples as the input control, the morphology of the surface of the powder particles was studied and particle size analysis was carried out. Also, 3D X-ray quality control of the grown samples was carried out in order to detect hidden defects, their qualitative and quantitative assessment. To determine the strength characteristics of the samples synthesized by the SLM method, static tensile tests were conducted. To determine the stress X-ray diffraction analysis was carried out in the material samples.

Three-dimensional quantitative evaluation of midfacial skeletal changes after trans-sutural distraction osteogenesis for midfacial hypoplasia in growing patients with cleft lip and palate.

PubMed

Tong, Haizhou; Gao, Feng; Yin, Jiapeng; Shi, Zehong; Song, Tao; Li, Haidong; Sun, Xiaomei; Wang, Yongqian; Yin, Ningbei; Zhao, Zhenmin

2015-11-01

Trans-sutural distraction osteogenesis (TSDO) is an alternative method for the early treatment of midfacial hypoplasia in growing patients with cleft lip and palate (CLP). The purpose of this study was to analyze three-dimensional (3D) midfacial skeletal changes after TSDO and to explore the mechanism in this process. All patients with nonsyndromic CLP who underwent bone-borne TSDO for midfacial hypoplasia from 2005 to 2014 were reviewed in this retrospective study. 3D morphological and quantitative measurement analyses were performed to evaluate midfacial skeletal changes by superimposition of preoperative and postoperative computed tomographic images. Twenty-six patients with mean age of 11.5 years met the inclusion criteria. The 3D morphological findings exhibited the most significant suture stress changes at the pterygomaxillary suture area, with obvious bone generation in all patients. The whole midfacial skeleton had progressively increased advancement in a craniocaudal direction along the midface segment, associated with morphological changes in skeleton itself. The 3D quantitative measurement findings showed differential advancement of each landmark at the maxillary alveolar, zygomatic bone, orbital rim, and nasal bone, which was consistent with morphological findings. TSDO allows rotation advancement of the midfacial skeleton to achieve occlusal correction and facial harmony through the mechanism of both suture remodeling and bone remodeling. Copyright © 2015 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Revision of Neacomys spinosus (Thomas, 1882) (Rodentia: Cricetidae) with emphasis on Peruvian populations and the description of a new species.

PubMed

Hurtado, Natali; Pacheco, Víctor

2017-03-13

The large spiny mouse Neacomys spinosus (Thomas, 1882) has been considered the widest ranging species of the genus, occurring in southern Colombia, eastern Peru, western Brazil and northern Bolivia. The morphological variation between subspecies and populations of N. spinosus has been noted; nonetheless, this variation has not been assessed in a morphological or molecular context. Here, we present a taxonomic revision of Neacomys spinosus s.l. using qualitative and quantitative morphological analyses. These analyses were complemented with molecular analysis to reconstruct the phylogenetic relationships among species of Neacomys, based on sequences of the cytochrome b gene. Our results reveal that N. spinosus s.l. is a monophyletic group, and morphological and molecular evidence to differentiate three taxa: N. spinosus s.s., an endemic species from mountain cloud forests in Peru; N. amoenus s.l. from the Cerrado between Bolivia and Brazil to the Amazonia between Ecuador and northern Peru, and Neacomys sp. nov. from mountain cloud forests from southern Peru to Bolivia. Also, our molecular results indicate that Neacomys is still far from being completely known. For instance, there are three candidate species pending of taxonomic revision. Finally, we propose three species groups within Neacomys: "paracou", "tenuipes" and "spinosus", and discuss biogeographical scenarios of the genus within South America.

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.

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.

Computer-assisted quantification of the skull deformity for craniosynostosis from 3D head CT images using morphological descriptor and hierarchical classification

NASA Astrophysics Data System (ADS)

Lee, Min Jin; Hong, Helen; Shim, Kyu Won; Kim, Yong Oock

2017-03-01

This paper proposes morphological descriptors representing the degree of skull deformity for craniosynostosis in head CT images and a hierarchical classifier model distinguishing among normal and different types of craniosynostosis. First, to compare deformity surface model with mean normal surface model, mean normal surface models are generated for each age range and the mean normal surface model is deformed to the deformity surface model via multi-level threestage registration. Second, four shape features including local distance and area ratio indices are extracted in each five cranial bone. Finally, hierarchical SVM classifier is proposed to distinguish between the normal and deformity. As a result, the proposed method showed improved classification results compared to traditional cranial index. Our method can be used for the early diagnosis, surgical planning and postsurgical assessment of craniosynostosis as well as quantitative analysis of skull deformity.

Quantifying Three-Dimensional Morphology and RNA from Individual Embryos

PubMed Central

Green, Rebecca M.; Leach, Courtney L.; Hoehn, Natasha; Marcucio, Ralph S.; Hallgrímsson, Benedikt

2017-01-01

Quantitative analysis of morphogenesis aids our understanding of developmental processes by providing a method to link changes in shape with cellular and molecular processes. Over the last decade many methods have been developed for 3D imaging of embryos using microCT scanning to quantify the shape of embryos during development. These methods generally involve a powerful, cross-linking fixative such as paraformaldehyde to limit shrinkage during the CT scan. However, the extended time frames that these embryos are incubated in such fixatives prevent use of the tissues for molecular analysis after microCT scanning. This is a significant problem because it limits the ability to correlate variation in molecular data with morphology at the level of individual embryos. Here, we outline a novel method that allows RNA, DNA or protein isolation following CT scan while also allowing imaging of different tissue layers within the developing embryo. We show shape differences early in craniofacial development (E11.5) between common mouse genetic backgrounds, and demonstrate that we are able to generate RNA from these embryos after CT scanning that is suitable for downstream RT-PCR and RNAseq analyses. PMID:28152580

QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology.

PubMed

Guarani, Virginia; McNeill, Elizabeth M; Paulo, Joao A; Huttlin, Edward L; Fröhlich, Florian; Gygi, Steven P; Van Vactor, David; Harper, J Wade

2015-05-21

The mitochondrial contact site and cristae junction (CJ) organizing system (MICOS) dynamically regulate mitochondrial membrane architecture. Through systematic proteomic analysis of human MICOS, we identified QIL1 (C19orf70) as a novel conserved MICOS subunit. QIL1 depletion disrupted CJ structure in cultured human cells and in Drosophila muscle and neuronal cells in vivo. In human cells, mitochondrial disruption correlated with impaired respiration. Moreover, increased mitochondrial fragmentation was observed upon QIL1 depletion in flies. Using quantitative proteomics, we show that loss of QIL1 resulted in MICOS disassembly with the accumulation of a MIC60-MIC19-MIC25 sub-complex and degradation of MIC10, MIC26, and MIC27. Additionally, we demonstrated that in QIL1-depleted cells, overexpressed MIC10 fails to significantly restore its interaction with other MICOS subunits and SAMM50. Collectively, our work uncovers a previously unrecognized subunit of the MICOS complex, necessary for CJ integrity, cristae morphology, and mitochondrial function and provides a resource for further analysis of MICOS architecture.

QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology

PubMed Central

Guarani, Virginia; McNeill, Elizabeth M; Paulo, Joao A; Huttlin, Edward L; Fröhlich, Florian; Gygi, Steven P; Van Vactor, David; Harper, J Wade

2015-01-01

The mitochondrial contact site and cristae junction (CJ) organizing system (MICOS) dynamically regulate mitochondrial membrane architecture. Through systematic proteomic analysis of human MICOS, we identified QIL1 (C19orf70) as a novel conserved MICOS subunit. QIL1 depletion disrupted CJ structure in cultured human cells and in Drosophila muscle and neuronal cells in vivo. In human cells, mitochondrial disruption correlated with impaired respiration. Moreover, increased mitochondrial fragmentation was observed upon QIL1 depletion in flies. Using quantitative proteomics, we show that loss of QIL1 resulted in MICOS disassembly with the accumulation of a MIC60-MIC19-MIC25 sub-complex and degradation of MIC10, MIC26, and MIC27. Additionally, we demonstrated that in QIL1-depleted cells, overexpressed MIC10 fails to significantly restore its interaction with other MICOS subunits and SAMM50. Collectively, our work uncovers a previously unrecognized subunit of the MICOS complex, necessary for CJ integrity, cristae morphology, and mitochondrial function and provides a resource for further analysis of MICOS architecture. DOI: http://dx.doi.org/10.7554/eLife.06265.001 PMID:25997101

Facile one-pot synthesis of hexagons of NaSrB5O9:Tb3+ phosphor for solid-state lighting

NASA Astrophysics Data System (ADS)

Ramesh, B.; Dillip, G. R.; Deva Prasad Raju, B.; Somasundaram, K.; Prasad Peddi, Siva; de Carvalho dos Anjos, Virgilio; Joo, S. W.

2017-04-01

NaSrB5O9:Tb3+ hexagons were synthesized by a facile solid-state reaction method. The synthesized powders were structurally examined by x-ray diffraction analysis (XRD), and Rietveld refinement was performed using the XRD data and Fullprof software. Hexagon-like morphology was observed using field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). The elemental composition of the phosphors was investigated qualitatively by energy dispersive x-ray analysis (EDS) and quantitatively by x-ray photoelectron spectroscopy (XPS). The phosphor has a strong green emission at 545 nm under excitation of 379 nm, which is due to the 5{{\\text{D}}4}{{\\to}7}{{\\text{F}}5} transition of the Tb3+ ion. A lifetime of 3.48 ms was obtained for the phosphor. The important parameters of the light source were determined, such as the thermal quenching, critical distance, the nature of the dopant ion interaction, color coordinates, and quantum yield values. Other reported properties include the site occupancy of the dopant, surface properties, morphological properties, and optical properties.

Automatic Cell Segmentation in Fluorescence Images of Confluent Cell Monolayers Using Multi-object Geometric Deformable Model.

PubMed

Yang, Zhen; Bogovic, John A; Carass, Aaron; Ye, Mao; Searson, Peter C; Prince, Jerry L

2013-03-13

With the rapid development of microscopy for cell imaging, there is a strong and growing demand for image analysis software to quantitatively study cell morphology. Automatic cell segmentation is an important step in image analysis. Despite substantial progress, there is still a need to improve the accuracy, efficiency, and adaptability to different cell morphologies. In this paper, we propose a fully automatic method for segmenting cells in fluorescence images of confluent cell monolayers. This method addresses several challenges through a combination of ideas. 1) It realizes a fully automatic segmentation process by first detecting the cell nuclei as initial seeds and then using a multi-object geometric deformable model (MGDM) for final segmentation. 2) To deal with different defects in the fluorescence images, the cell junctions are enhanced by applying an order-statistic filter and principal curvature based image operator. 3) The final segmentation using MGDM promotes robust and accurate segmentation results, and guarantees no overlaps and gaps between neighboring cells. The automatic segmentation results are compared with manually delineated cells, and the average Dice coefficient over all distinguishable cells is 0.88.

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

Hydrocarbon productivities in different Botryococcus strains: comparative methods in product quantification.

PubMed

Eroglu, Ela; Okada, Shigeru; Melis, Anastasios

2011-08-01

Six different strains of the green microalgae Botryococcus belonging to the A-race or B-race, accumulating alkadiene or botryococcene hydrocarbons, respectively, were compared for biomass and hydrocarbon productivities. Biomass productivity was assessed gravimetrically upon strain growth in the laboratory under defined conditions. Hydrocarbon productivities were measured by three different and independent experimental approaches, including density equilibrium of the intact cells and micro-colonies, spectrophotometric analysis of hydrocarbon extracts, and gravimetric quantitation of eluted hydrocarbons. All three hydrocarbon-quantitation methods yielded similar results for each of the strains examined. The B-race microalgae Botryococcus braunii var. Showa and Kawaguchi-1 constitutively accumulated botryococcene hydrocarbons equivalent to 30% and 20%, respectively, of their overall biomass. The A-race microalgae Botryococcus braunii, varieties Yamanaka, UTEX 2441 and UTEX LB572 constitutively accumulated alkadiene hydrocarbons ranging from 14% to 13% and 10% of their overall biomass, respectively. Botryococcus sudeticus (UTEX 2629), a morphologically different green microalga, had the lowest hydrocarbon accumulation, equal to about 3% of its overall biomass. Results validate the density equilibrium and spectrophotometric analysis methods in the quantitation of botryococcene-type hydrocarbons. These analytical advances will serve in the screening and selection of B. braunii and of other microalgae in efforts to identify those having a high hydrocarbon content for use in commercial applications.

Contrast-enhanced magnetic resonance imaging of pulmonary lesions: description of a technique aiming clinical practice.

PubMed

Koenigkam-Santos, Marcel; Optazaite, Elzbieta; Sommer, Gregor; Safi, Seyer; Heussel, Claus Peter; Kauczor, Hans-Ulrich; Puderbach, Michael

2015-01-01

To propose a technique for evaluation of pulmonary lesions using contrast-enhanced MRI; to assess morphological patterns of enhancement and correlate quantitative analysis with histopathology. Thirty-six patients were prospectively studied. Volumetric-interpolated T1W images were obtained during consecutive breath holds after bolus triggered contrast injection. Volume coverage of first three acquisitions was limited (higher temporal resolution) and last acquisition obtained at 4th min. Two radiologists individually evaluated the patterns of enhancement. Region-of-interest-based signal intensity (SI)-time curves were created to assess quantitative parameters. Readers agreed moderately to substantially concerning lesions' enhancement pattern. SI-time curves could be created for all lesions. In comparison to benign, malignant lesions showed higher values of maximum enhancement, early peak, slope and 4th min enhancement. Early peak >15% showed 100% sensitivity to detect malignancy, maximum enhancement >40% showed 100% specificity. The proposed technique is robust, simple to perform and can be applied in clinical scenario. It allows visual evaluation of enhancement pattern/progression together with creation of SI-time curves and assessment of derived quantitative parameters. Perfusion analysis was highly sensitive to detect malignancy, in accordance to what is recommended by most recent guidelines on imaging evaluation of pulmonary lesions. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Quantitative 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.

Proteomic and transcriptional analysis of Lactobacillus johnsonii PF01 during bile salt exposure by iTRAQ shotgun proteomics and quantitative RT-PCR.

PubMed

Lee, Ji Yoon; Pajarillo, Edward Alain B; Kim, Min Jeong; Chae, Jong Pyo; Kang, Dae-Kyung

2013-01-04

Lactobacillus johnsonii PF01 has been reported to be highly resistant to bile, a key property of probiotic microorganisms. Here, we examine the nature of the bile-salt tolerance of L. johnsonii PF01. Growth inhibition and surface morphology and physiology aberrations were observed after overnight exposure to bile stress. Quantitative proteomic profiles using iTRAQ-LC-MS/MS technology identified 8307 peptides from both untreated PF01 cells and those exposed to 0.1%, 0.2%, and 0.3% bile salts. Some 215 proteins exhibited changed levels in response to bile stress; of these, levels of 94 peptides increased while those of 121 decreased. These were classified into the following categories: stress responses, cell division, transcription, translation, nucleotide metabolism, carbohydrate transport and metabolism, cell wall biosynthesis, and amino acid biosynthesis, and 16 of unidentified function. Analysis of the mRNA expression of selected genes by quantitative reverse transcriptase-PCR verified the proteomic data. Both proteomic and mRNA data provided evidence for increased phosphotransferase activity and cell wall biosynthesis. In addition, three bile salt hydrolases were significantly upregulated by bile exposure. These findings provide a basis for future evaluations of the tolerance of potential probiotic strains toward the various gastrointestinal challenges, including bile stress.

Biomass particle models with realistic morphology and resolved microstructure for simulations of intraparticle transport phenomena

DOE PAGES

Ciesielski, Peter N.; Crowley, Michael F.; Nimlos, Mark R.; ...

2014-12-09

Biomass exhibits a complex microstructure of directional pores that impact how heat and mass are transferred within biomass particles during conversion processes. However, models of biomass particles used in simulations of conversion processes typically employ oversimplified geometries such as spheres and cylinders and neglect intraparticle microstructure. In this study, we develop 3D models of biomass particles with size, morphology, and microstructure based on parameters obtained from quantitative image analysis. We obtain measurements of particle size and morphology by analyzing large ensembles of particles that result from typical size reduction methods, and we delineate several representative size classes. Microstructural parameters, includingmore » cell wall thickness and cell lumen dimensions, are measured directly from micrographs of sectioned biomass. A general constructive solid geometry algorithm is presented that produces models of biomass particles based on these measurements. Next, we employ the parameters obtained from image analysis to construct models of three different particle size classes from two different feedstocks representing a hardwood poplar species ( Populus tremuloides, quaking aspen) and a softwood pine ( Pinus taeda, loblolly pine). Finally, we demonstrate the utility of the models and the effects explicit microstructure by performing finite-element simulations of intraparticle heat and mass transfer, and the results are compared to similar simulations using traditional simplified geometries. In conclusion, we show how the behavior of particle models with more realistic morphology and explicit microstructure departs from that of spherical models in simulations of transport phenomena and that species-dependent differences in microstructure impact simulation results in some cases.« less

Image-based quantification and mathematical modeling of spatial heterogeneity in ESC colonies.

PubMed

Herberg, Maria; Zerjatke, Thomas; de Back, Walter; Glauche, Ingmar; Roeder, Ingo

2015-06-01

Pluripotent embryonic stem cells (ESCs) have the potential to differentiate into cells of all three germ layers. This unique property has been extensively studied on the intracellular, transcriptional level. However, ESCs typically form clusters of cells with distinct size and shape, and establish spatial structures that are vital for the maintenance of pluripotency. Even though it is recognized that the cells' arrangement and local interactions play a role in fate decision processes, the relations between transcriptional and spatial patterns have not yet been studied. We present a systems biology approach which combines live-cell imaging, quantitative image analysis, and multiscale, mathematical modeling of ESC growth. In particular, we develop quantitative measures of the morphology and of the spatial clustering of ESCs with different expression levels and apply them to images of both in vitro and in silico cultures. Using the same measures, we are able to compare model scenarios with different assumptions on cell-cell adhesions and intercellular feedback mechanisms directly with experimental data. Applying our methodology to microscopy images of cultured ESCs, we demonstrate that the emerging colonies are highly variable regarding both morphological and spatial fluorescence patterns. Moreover, we can show that most ESC colonies contain only one cluster of cells with high self-renewing capacity. These cells are preferentially located in the interior of a colony structure. The integrated approach combining image analysis with mathematical modeling allows us to reveal potential transcription factor related cellular and intercellular mechanisms behind the emergence of observed patterns that cannot be derived from images directly. © 2015 International Society for Advancement of Cytometry.

The nest-concealment hypothesis: New insights from a comparative analysis

USGS Publications Warehouse

Borgmann, Kathi L.; Conway, Courtney J.

2015-01-01

Selection of a breeding site is critical for many animals, especially for birds whose offspring are stationary during development. Thus, birds are often assumed to prefer concealed nest sites. However, 74% of studies (n = 106) that have evaluated this relationship for open-cup nesting songbirds in North America failed to support the nest-concealment hypothesis. We conducted a comparative analysis to identify factors that contribute to variation in the ability of researchers to find support for the nest-concealment hypothesis. We found that some of the discrepancy among studies can be explained by interspecific differences in morphological and extrinsic factors that affect nest predation. Moreover, methods that investigators used to estimate concealment affected whether studies found support for the nest-concealment hypothesis; 33% of the studies that used quantitative estimates found support for the nest-concealment hypothesis whereas only 10% of the studies that used qualitative estimates found support. The timing of measurements also explained some of the ambiguity; studies that provided little information regarding the timing of their foliage density estimates were less likely to support the nest-concealment hypothesis. Species with more conspicuous male plumage were less likely to support the nest-concealment hypothesis when we analyzed studies that used visual estimates. Whereas species with more conspicuous female plumage were more likely to support the nest-concealment hypothesis when we analyzed studies that used quantitative measures. Our results demonstrate that support for the nest-concealment hypothesis has been equivocal, but that some of the ambiguity can be explained by morphological traits and methods used to measure concealment.

Mapping Quantitative Trait Loci Associated with Toot Traits Using Sequencing-Based Genotyping Chromosome Segment Substitution Lines Derived from 9311 and Nipponbare in Rice (Oryza sativa L.).

PubMed

Zhou, Yong; Dong, Guichun; Tao, Yajun; Chen, Chen; Yang, Bin; Wu, Yue; Yang, Zefeng; Liang, Guohua; Wang, Baohe; Wang, Yulong

2016-01-01

Identification of quantitative trait loci (QTLs) associated with rice root morphology provides useful information for avoiding drought stress and maintaining yield production under the irrigation condition. In this study, a set of chromosome segment substitution lines derived from 9311 as the recipient and Nipponbare as donor, were used to analysis root morphology. By combining the resequencing-based bin-map with a multiple linear regression analysis, QTL identification was conducted on root number (RN), total root length (TRL), root dry weight (RDW), maximum root length (MRL), root thickness (RTH), total absorption area (TAA) and root vitality (RV), using the CSSL population grown under hydroponic conditions. A total of thirty-eight QTLs were identified: six for TRL, six for RDW, eight for the MRL, four for RTH, seven for RN, two for TAA, and five for RV. Phenotypic effect variance explained by these QTLs ranged from 2.23% to 37.08%, and four single QTLs had more than 10% phenotypic explanations on three root traits. We also detected the correlations between grain yield (GY) and root traits, and found that TRL, RTH and MRL had significantly positive correlations with GY. However, TRL, RDW and MRL had significantly positive correlations with biomass yield (BY). Several QTLs identified in our population were co-localized with some loci for grain yield or biomass. This information may be immediately exploited for improving rice water and fertilizer use efficiency for molecular breeding of root system architectures.

Investigation of quartz grain surface textures by atomic force microscopy for forensic analysis.

PubMed

Konopinski, D I; Hudziak, S; Morgan, R M; Bull, P A; Kenyon, A J

2012-11-30

This paper presents a study of quartz sand grain surface textures using atomic force microscopy (AFM) to image the surface. Until now scanning electron microscopy (SEM) has provided the primary technique used in the forensic surface texture analysis of quartz sand grains as a means of establishing the provenance of the grains for forensic reconstructions. The ability to independently corroborate the grain type classifications is desirable and provides additional weight to the findings of SEM analysis of the textures of quartz grains identified in forensic soil/sediment samples. AFM offers a quantitative means of analysis that complements SEM examination, and is a non-destructive technique that requires no sample preparation prior to scanning. It therefore has great potential to be used for forensic analysis where sample preservation is highly valuable. By taking quantitative topography scans, it is possible to produce 3D representations of microscopic surface textures and diagnostic features for examination. Furthermore, various empirical measures can be obtained from analysing the topography scans, including arithmetic average roughness, root-mean-square surface roughness, skewness, kurtosis, and multiple gaussian fits to height distributions. These empirical measures, combined with qualitative examination of the surfaces can help to discriminate between grain types and provide independent analysis that can corroborate the morphological grain typing based on the surface textures assigned using SEM. Furthermore, the findings from this study also demonstrate that quartz sand grain surfaces exhibit a statistically self-similar fractal nature that remains unchanged across scales. This indicates the potential for a further quantitative measure that could be utilised in the discrimination of quartz grains based on their provenance for forensic investigations. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

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.

Distinctive fingerprints of erosional regimes in terrestrial channel networks

NASA Astrophysics Data System (ADS)

Grau Galofre, A.; Jellinek, M.

2017-12-01

Satellite imagery and digital elevation maps capture the large scale morphology of channel networks attributed to long term erosional processes, such as fluvial, glacial, groundwater sapping and subglacial erosion. Characteristic morphologies associated with each of these styles of erosion have been studied in detail, but there exists a knowledge gap related to their parameterization and quantification. This knowledge gap prevents a rigorous analysis of the dominant processes that shaped a particular landscape, and a comparison across styles of erosion. To address this gap, we use previous morphological descriptions of glaciers, rivers, sapping valleys and tunnel valleys to identify and measure quantitative metrics diagnostic of these distinctive styles of erosion. From digital elevation models, we identify four geometric metrics: The minimum channel width, channel aspect ratio (longest length to channel width at the outlet), presence of undulating longitudinal profiles, and tributary junction angle. We also parameterize channel network complexity in terms of its stream order and fractal dimension. We then perform a statistical classification of the channel networks using a Principal Component Analysis on measurements of these six metrics on a dataset of 70 channelized systems. We show that rivers, glaciers, groundwater seepage and subglacial meltwater erode the landscape in rigorously distinguishable ways. Our methodology can more generally be applied to identify the contributions of different processes involved in carving a channel network. In particular, we are able to identify transitions from fluvial to glaciated landscapes or vice-versa.

Unsupervised color normalisation for H and E stained histopathology image analysis

NASA Astrophysics Data System (ADS)

Celis, Raúl; Romero, Eduardo

2015-12-01

In histology, each dye component attempts to specifically characterise different microscopic structures. In the case of the Hematoxylin-Eosin (H&E) stain, universally used for routine examination, quantitative analysis may often require the inspection of different morphological signatures related mainly to nuclei patterns, but also to stroma distribution. Nevertheless, computer systems for automatic diagnosis are often fraught by color variations ranging from the capturing device to the laboratory specific staining protocol and stains. This paper presents a novel colour normalisation method for H&E stained histopathology images. This method is based upon the opponent process theory and blindly estimates the best color basis for the Hematoxylin and Eosin stains without relying on prior knowledge. Stain Normalisation and Color Separation are transversal to any Framework of Histopathology Image Analysis.

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.

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.

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.

Glycol Methacrylate Embedding for the Histochemical Study of the Gastrointestinal Tract of Dogs Naturally Infected with Leishmania Infantum

PubMed Central

Pinto, A.J.W.; de Amorim, I.F.G.; Pinheiro, L.J.; Madeira, I.M.V.M.; Souza, C.C.; Chiarini-Garcia, H.; Caliari, M.V.

2015-01-01

In canine visceral leishmaniasis a diffuse chronic inflammatory exudate and an intense parasite load throughout the gastrointestinal tract (GIT) has been previously reported. However, these studies did not allow a properly description of canine cellular morphology details. The aim of our study was to better characterize these cells in carrying out a qualitative and quantitative histological study in the gastrointestinal tract of dogs naturally infected with Leishmania infantum by examining gut tissues embedded in glycol methacrylate. Twelve infected adult dogs were classified in asymptomatic and symptomatic. Five uninfected dogs were used as controls. After necropsy, three samples of each gut segment, including oesophagus, stomach, duodenum, jejunum, ileum, cecum, colon, and rectum were collected and fixed in Carnoy’s solution for glycol methacrylate protocols. Sections were stained with hematoxylin-eosin, toluidine blue borate, and periodic acid-Schiff stain. Leishmania amastigotes were detected by immunohistochemistry employed in both glycol methacrylate and paraffin embedded tissues. The quantitative histological analysis showed higher numbers of plasma cells, lymphocytes and macrophages in lamina propria of all segments of GIT of infected dogs compared with controls. The parasite load was more intense and cecum and colon, independently of the clinical status of these dogs. Importantly, glycol methacrylate embedded tissue stained with toluidine blue borate clearly revealed mast cell morphology, even after mast cell degranulation. Infected dogs showed lower numbers of mast cells in all gut segments than controls. Despite the glycol methacrylate (GMA) protocol requires more attention and care than the conventional paraffin processing, this embedding procedure proved to be especially suitable for the present histological study, where it allowed to preserve and observe cell morphology in fine detail. PMID:26708180

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.

Morphological classification and microanalysis of tire tread particles worn by abrasion or corrosion

NASA Astrophysics Data System (ADS)

Crosta, Giovanni F.

2011-06-01

Two types of tread wear particles are investigated: tread wear particles from a steel brush abrader (TrBP) and particles produced during a steering pad run (TrSP). A leaching experiment in water at pH = 7.5 for 24 and 48h was carried out on TrBP to simulate environmental degradation. Images of all materials were collected by a scanning electron microscope (SEM) together with element microanalytical (EDX) data. Surface morphology is described by a function of wave number (the "enhanced spectrum") obtained from SEM image analysis and non-linear filtering. A surface roughness index, ρ, is derived from the enhanced spectrum. The innovative contribution of this work is the representation of morphology by means of ρ, which, together with EDX data, allows the quantitative characterization of the materials. In particular, the surface roughness of leached TrBP is shown to decay in time and is related to the corresponding microanalytical data for the first time. The morphology of steering pad TrSP, affected by included mineral particles, is shown to be more heterogeneous. Differences in morphology (enhanced spectra and ρ), elemental composition and surface chemistry of TrBP and TrSP are discussed. All methods described and implemented herewith can be immediately applied to other types of tread wear material. The arguments put forward herewith should help in the proper design of those experiments aimed at assessing the impact of tread wear materials on the environment and on human health.

The impact of engineered log jams on bed morphology, flow characteristics and habitat diversity under low flow

NASA Astrophysics Data System (ADS)

Ockelford, A.; Crabbe, E.; Crowe Curran, J.; Parsons, D. R.; Shugar, D. H.; Burr, A.; Kennedy, K.; Coe, T.

2017-12-01

Wood jams are an important and ubiquitous feature of many river channels with their number, placement and spatial configuration determining their influence on channel morphology and flow characteristics. Further, engineered log jams are increasingly being constructed to develop, restore or maintain habitat diversity for key indicator specie such as salmon. However, questions remain as to the inter relationships between the logjams, the channel morphology, the flow characteristics and the habitat diversity under low flow conditions. Four engineered and one natural logjam were analyzed over a 3km reach of the South Fork Nooksack River, North Cascades National Park, USA during the summer low flow period. Non-intrusive three-dimensional topographic surveys of the river bed morphology surrounding the logjams was collected using a shallow water multibeam system. This was combined with terrestrial laser scans of the structure of the log jams above the waterline. Co-located high resolution flow velocity data was collected using an Acoustic Doppler Current Profiler. Discussion concentrates on providing a quantitative understanding of the effect of logjams on reach scale morphodynamics under low flow conditions. Multivariate statistical analysis of flow and topographic data in combination with log jam morphology allow the influences of the logjam on habitat suitability for key indicator species to be quantified. Results will be framed in terms of the effectiveness of the different logjam configurations on generating and promoting habitat diversity such as to aid future design and implementation.

Quantitative non-invasive intracellular imaging of Plasmodium falciparum infected human erythrocytes

NASA Astrophysics Data System (ADS)

Edward, Kert; Farahi, Faramarz

2014-05-01

Malaria is a virulent pathological condition which results in over a million annual deaths. The parasitic agent Plasmodium falciparum has been extensively studied in connection with this epidemic but much remains unknown about its development inside the red blood cell host. Optical and fluorescence imaging are among the two most common procedures for investigating infected erythrocytes but both require the introduction of exogenous contrast agents. In this letter, we present a procedure for the non-invasive in situ imaging of malaria infected red blood cells. The procedure is based on the utilization of simultaneously acquired quantitative phase and independent topography data to extract intracellular information. Our method allows for the identification of the developmental stages of the parasite and facilitates in situ analysis of the morphological changes associated with the progression of this disease. This information may assist in the development of efficacious treatment therapies for this condition.

Cell classification using big data analytics plus time stretch imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Jalali, Bahram; Chen, Claire L.; Mahjoubfar, Ata

2016-09-01

We show that blood cells can be classified with high accuracy and high throughput by combining machine learning with time stretch quantitative phase imaging. Our diagnostic system captures quantitative phase images in a flow microscope at millions of frames per second and extracts multiple biophysical features from individual cells including morphological characteristics, light absorption and scattering parameters, and protein concentration. These parameters form a hyperdimensional feature space in which supervised learning and cell classification is performed. We show binary classification of T-cells against colon cancer cells, as well classification of algae cell strains with high and low lipid content. The label-free screening averts the negative impact of staining reagents on cellular viability or cell signaling. The combination of time stretch machine vision and learning offers unprecedented cell analysis capabilities for cancer diagnostics, drug development and liquid biopsy for personalized genomics.

Character of skin on photo-thermal response and its regeneration process using second-harmonic generation microscopy.

PubMed

Wu, Shu-lian; Li, Hui; Zhang, Xiao-man; Chen, Wei R; Wang, Yun-Xia

2014-01-01

Quantitative characterization of skin collagen on photo-thermal response and its regeneration process is an important but difficult task. In this study, morphology and spectrum characteristics of collagen during photo-thermal response and its light-induced remodeling process were obtained by second-harmonic generation microscope in vivo. The texture feature of collagen orientation index and fractal dimension was extracted by image processing. The aim of this study is to detect the information hidden in skin texture during the process of photo-thermal response and its regeneration. The quantitative relations between injured collagen and texture feature were established for further analysis of the injured characteristics. Our results show that it is feasible to determine the main impacts of phototherapy on the skin. It is important to understand the process of collagen remodeling after photo-thermal injuries from texture feature.

Advanced image fusion algorithms for Gamma Knife treatment planning. Evaluation and proposal for clinical use.

PubMed

Apostolou, N; Papazoglou, Th; Koutsouris, D

2006-01-01

Image fusion is a process of combining information from multiple sensors. It is a useful tool implemented in the treatment planning programme of Gamma Knife Radiosurgery. In this paper we evaluate advanced image fusion algorithms for Matlab platform and head images. We develop nine level grayscale image fusion methods: average, principal component analysis (PCA), discrete wavelet transform (DWT) and Laplacian, filter - subtract - decimate (FSD), contrast, gradient, morphological pyramid and a shift invariant discrete wavelet transform (SIDWT) method in Matlab platform. We test these methods qualitatively and quantitatively. The quantitative criteria we use are the Root Mean Square Error (RMSE), the Mutual Information (MI), the Standard Deviation (STD), the Entropy (H), the Difference Entropy (DH) and the Cross Entropy (CEN). The qualitative are: natural appearance, brilliance contrast, presence of complementary features and enhancement of common features. Finally we make clinically useful suggestions.

LC-MS/MS method development for quantitative analysis of acetaminophen uptake by the aquatic fungus Mucor hiemalis.

PubMed

Esterhuizen-Londt, Maranda; Schwartz, Katrin; Balsano, Evelyn; Kühn, Sandra; Pflugmacher, Stephan

2016-06-01

Acetaminophen is a pharmaceutical, frequently found in surface water as a contaminant. Bioremediation, in particular, mycoremediation of acetaminophen is a method to remove this compound from waters. Owing to the lack of quantitative analytical method for acetaminophen in aquatic organisms, the present study aimed to develop a method for the determination of acetaminophen using LC-MS/MS in the aquatic fungus Mucor hiemalis. The method was then applied to evaluate the uptake of acetaminophen by M. hiemalis, cultured in pellet morphology. The method was robust, sensitive and reproducible with a lower limit of quantification of 5 pg acetaminophen on column. It was found that M. hiemalis internalize the pharmaceutical, and bioaccumulate it with time. Therefore, M. hiemalis was deemed a suitable candidate for further studies to elucidate its pharmaceutical tolerance and the longevity in mycoremediation applications. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantification of texture match of the skin graft: function and morphology of the stratum corneum.

PubMed

Inoue, K; Matsumoto, K

1986-01-01

In an attempt to analyze the "texture match" of grafted skin, functional and morphological aspects of the stratum corneum were studied using the Skin Surface Hydrometer (IBS Inc.) and the scanning electron microscope. The results showed that hygroscopicity and water holding capacity of the stratum corneum played a crucial role in making the skin surface soft and smooth. Morphologically there were regional differences in the surface pattern and the mean area of corneocytes, suggesting that these differences affect skin texture. It is suggested that the present functional and morphological studies of the stratum corneum can provide a quantitative measure of the "texture match".

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.

Quantification of MagLIF stagnation morphology using the Mallat Scattering Transformation

NASA Astrophysics Data System (ADS)

Glinsky, Michael; Weis, Matthew; Jennings, Christopher; Ampleford, David; Harding, Eric; Knapp, Patrick; Gomez, Matthew

2017-10-01

The morphology of the stagnated plasma resulting from MagLIF is measured by imaging the self-emission x-rays coming from the multi-keV plasma. Equivalent diagnostic response can be derived from integrated rad-hydro simulations from programs such as Hydra and Gorgon. There have been only limited quantitative ways to compare the image morphology, that is the texture, of the simulations to that of the experiments, to compare one experiment to another, or to compare one simulation to another. We have developed a metric of image morphology based on the Mallat Scattering Transformation, a transformation that has proved to be effective at distinguishing textures, sounds, and written characters. This metric has demonstrated excellent performance in classifying an ensemble of synthetic stagnations images. A good regression of the scattering coefficients to the parameters used to generate the synthetic images was found. Finally, the metric has been used to quantitatively compare simulations to experimental self-emission images. Sandia National Laboratories is a multi-mission laboratory managed and operated by NTESS, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the USDoEs NNSA under contract DE-NA0003525.

A Method for Quantifying, Visualising, and Analysing Gastropod Shell Form

PubMed Central

Liew, Thor-Seng; Schilthuizen, Menno

2016-01-01

Quantitative analysis of organismal form is an important component for almost every branch of biology. Although generally considered an easily-measurable structure, the quantification of gastropod shell form is still a challenge because many shells lack homologous structures and have a spiral form that is difficult to capture with linear measurements. In view of this, we adopt the idea of theoretical modelling of shell form, in which the shell form is the product of aperture ontogeny profiles in terms of aperture growth trajectory that is quantified as curvature and torsion, and of aperture form that is represented by size and shape. We develop a workflow for the analysis of shell forms based on the aperture ontogeny profile, starting from the procedure of data preparation (retopologising the shell model), via data acquisition (calculation of aperture growth trajectory, aperture form and ontogeny axis), and data presentation (qualitative comparison between shell forms) and ending with data analysis (quantitative comparison between shell forms). We evaluate our methods on representative shells of the genera Opisthostoma and Plectostoma, which exhibit great variability in shell form. The outcome suggests that our method is a robust, reproducible, and versatile approach for the analysis of shell form. Finally, we propose several potential applications of our methods in functional morphology, theoretical modelling, taxonomy, and evolutionary biology. PMID:27280463

Characterization and application of a quantitative DNA marker that discriminates sex in Chinook salmon (Oncorhynchus tshawytscha)

USGS Publications Warehouse

Clifton, D.R.; Rodriguez, R.J.

1997-01-01

A qualitative male-specific DNA marker (OT-24) was amplified by spPCR (single-primer polymerase chain reaction) from chinook salmon (Oncorhynchus tshawytscha) DNA along with several non-sex-linked products. The termini of the male-specific product were sequenced, and a pair of PeR primers were constructed for marker-specific PCR amplification. Dual primer PCR (dpPCR), with the marker-specific primers, amplified a product from both nudes and females. The amount of dpPCR product amplified from males was at least 100-fold greater than that from females. The quantitative difference between males and females was consistent among geographically distinct populations from western U.S. rivers. In addition, DNA sequence analysis indicated that OT-24 was highly conserved among geographically distinct salmon populations. The qualitative spPCR product segregated through several genetic crosses indicating equal sex ratios among progeny. Identification of the male and female juveniles by dpPCR was consistent with the spPCR analysis. There was no tissue specificity observed by spPCR or dpPCR analysis of this marker. A rapid DNA extraction method and dpPCR analysis were used to nonlethally determine sex ratios in wild spring chinook salmon adults, withheld for genetic and behavioral studies, prior to their development of gross sexual differences in their external morphology.

Characterization and application of a quantitative DNA marker that discriminates sex in chinook salmon (Oncorhynchus tshawytscha)

USGS Publications Warehouse

Clifton, D.R.; Rodriguez, R.J.

1997-01-01

A qualitative male-specific DNA marker (OT-24) was amplified by spPCR (single-primer polymerase chain reaction) from chinook salmon (Oncorhynchus tshawytscha) DNA along with several non-sex-linked products. The termini of the male-specific product were sequenced, and a pair of PeR primers were constructed for marker-specific PCR amplification. Dual primer PCR (dpPCR), with the marker-specific primers, amplified a product from both nudes and females. The amount of dpPCR product amplified from males was at least 100-fold greater than that from females. The quantitative difference between males and females was consistent among geographically distinct populations from western U.S. rivers. In addition, DNA sequence analysis indicated that OT-24 was highly conserved among geographically distinct salmon populations. The qualitative spPCR product segregated through several genetic crosses indicating equal sex ratios among progeny. Identification of the male and female juveniles by dpPCR was consistent with the spPCR analysis. There was no tissue specificity observed by spPCR or dpPCR analysis of this marker. A rapid DNA extraction method and dpPCR analysis were used to nonlethally determine sex ratios in wild spring chinook salmon adults, withheld for genetic and behavioral studies, prior to their development of gross sexual differences in their external morphology.

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.

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 small fraction (5--10%) of their stellar mass in young stars. I extend the study of recent star formation in ETGs to intermediate-redshift 0.35 intermediate-redshift 0.35 < z < 1.5 with the ERS data. Comparing the mass fraction and age of young stellar populations identified in these ETGs from two-component SED analysis with the morphology of the ETG and the frequency of companions, I find that at this redshift many ETGs are likely to have experienced a minor burst of recent star formation. The mechanisms driving this recent star formation are varied, and evidence for both minor merger driven recent star formation as well as the evolution of transitioning ETGs is identified.

Characterization of corneal damage from Pseudomonas aeruginosa infection by the use of multiphoton microscopy

NASA Astrophysics Data System (ADS)

Chang, Yu-Lin; Chen, Wei-Liang; Lo, Wen; Chen, Shean-Jen; Tan, Hsin-Yuan; Dong, Chen-Yuan

2010-11-01

Using multiphoton autofluorescence (MAF) and second harmonic generation (SHG) microscopy, we investigate the morphology and the structure of the corneal epithelium and stroma collagen of bovine cornea following injection of Pseudomonas aeruginosa. We found that corneal epithelial cells are damaged and stromal collagen becoming increasingly autofluorescent with time. We also characterized infected cornea cultured for 0, 6, 12, and 24 h by quantitative ratiometric MAF to SHG index (MAFSI) analysis. MAFSI results show that the destruction of the stromal collagen corresponds to a decrease in SHG intensity and increase of MAF signal with time.

Three-dimensional real-time imaging of bi-phasic flow through porous media

NASA Astrophysics Data System (ADS)

Sharma, Prerna; Aswathi, P.; Sane, Anit; Ghosh, Shankar; Bhattacharya, S.

2011-11-01

We present a scanning laser-sheet video imaging technique to image bi-phasic flow in three-dimensional porous media in real time with pore-scale spatial resolution, i.e., 35 μm and 500 μm for directions parallel and perpendicular to the flow, respectively. The technique is illustrated for the case of viscous fingering. Using suitable image processing protocols, both the morphology and the movement of the two-fluid interface, were quantitatively estimated. Furthermore, a macroscopic parameter such as the displacement efficiency obtained from a microscopic (pore-scale) analysis demonstrates the versatility and usefulness of the method.

Combined use of optical and electron microscopic techniques for the measurement of hygroscopic property, chemical composition, and morphology of individual aerosol particles.

PubMed

Ahn, Kang-Ho; Kim, Sun-Man; Jung, Hae-Jin; Lee, Mi-Jung; Eom, Hyo-Jin; Maskey, Shila; Ro, Chul-Un

2010-10-01

In this work, an analytical method for the characterization of the hygroscopic property, chemical composition, and morphology of individual aerosol particles is introduced. The method, which is based on the combined use of optical and electron microscopic techniques, is simple and easy to apply. An optical microscopic technique was used to perform the visual observation of the phase transformation and hygroscopic growth of aerosol particles on a single particle level. A quantitative energy-dispersive electron probe X-ray microanalysis, named low-Z particle EPMA, was used to perform a quantitative chemical speciation of the same individual particles after the measurement of the hygroscopic property. To validate the analytical methodology, the hygroscopic properties of artificially generated NaCl, KCl, (NH(4))(2)SO(4), and Na(2)SO(4) aerosol particles of micrometer size were investigated. The practical applicability of the analytical method for studying the hygroscopic property, chemical composition, and morphology of ambient aerosol particles is demonstrated.

Vascular Corrosion Casting: Review of Advantages and Limitations in the Application of Some Simple Quantitative Methods.

PubMed

Hossler, Fred E.; Douglas, John E.

2001-05-01

Vascular corrosion casting has been used for about 40 years to produce replicas of normal and abnormal vasculature and microvasculature of various tissues and organs that could be viewed at the ultrastructural level. In combination with scanning electron microscopy (SEM), the primary application of corrosion casting has been to describe the morphology and anatomical distribution of blood vessels in these tissues. However, such replicas should also contain quantitative information about that vasculature. This report summarizes some simple quantitative applications of vascular corrosion casting. Casts were prepared by infusing Mercox resin or diluted Mercox resin into the vasculature. Surrounding tissues were removed with KOH, hot water, and formic acid, and the resulting dried casts were observed with routine SEM. The orientation, size, and frequency of vascular endothelial cells were determined from endothelial nuclear imprints on various cast surfaces. Vascular volumes of heart, lung, and avian salt gland were calculated using tissue and resin densities, and weights. Changes in vascular volume and functional capillary density in an experimentally induced emphysema model were estimated from confocal images of casts. Clearly, corrosion casts lend themselves to quantitative analysis. However, because blood vessels differ in their compliances, in their responses to the toxicity of casting resins, and in their response to varying conditions of corrosion casting procedures, it is prudent to use care in interpreting this quantitative data. Some of the applications and limitations of quantitative methodology with corrosion casts are reviewed here.

Subtle changes in myelination due to childhood experiences: label-free microscopy to infer nerve fibers morphology and myelination in brain (Conference Presentation)

NASA Astrophysics Data System (ADS)

Gasecka, Alicja; Tanti, Arnaud; Lutz, Pierre-Eric; Mechawar, Naguib; Cote, Daniel C.

2017-02-01

Adverse childhood experiences have lasting detrimental effects on mental health and are strongly associated with impaired cognition and increased risk of developing psychopathologies. Preclinical and neuroimaging studies have suggested that traumatic events during brain development can affect cerebral myelination particularly in areas and tracts implicated in mood and emotion. Although current neuroimaging techniques are quite powerful, they lack the resolution to infer myelin integrity at the cellular level. Recently demonstrated coherent Raman microscopy has accomplished cellular level imaging of myelin sheaths in the nervous system. However, a quantitative morphometric analysis of nerve fibers still remains a challenge. In particular, in brain, where fibres exhibit small diameters and varying local orientation. In this work, we developed an automated myelin identification and analysis method that is capable of providing a complete picture of axonal myelination and morphology in brain samples. This method performs three main procedures 1) detects molecular anisotropy of membrane phospholipids based on polarization resolved coherent Raman microscopy, 2) identifies regions of different molecular organization, 3) calculates morphometric features of myelinated axons (e.g. myelin thickness, g-ratio). We applied this method to monitor white matter areas from suicides adults that suffered from early live adversity and depression compared to depressed suicides adults and psychiatrically healthy controls. We demonstrate that our method allows for the rapid acquisition and automated analysis of neuronal networks morphology and myelination. This is especially useful for clinical and comparative studies, and may greatly enhance the understanding of processes underlying the neurobiological and psychopathological consequences of child abuse.

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.

Biochemical evaluation of articular cartilage in patients with osteochondrosis dissecans by means of quantitative T2- and T2-mapping at 3T MRI: a feasibility study.

PubMed

Marik, W; Apprich, S; Welsch, G H; Mamisch, T C; Trattnig, S

2012-05-01

To perform an in vivo evaluation comparing overlying articular cartilage in patients suffering from osteochondrosis dissecans (OCD) in the talocrural joint and healthy volunteers using quantitative T2 mapping at 3.0 T. Ten patients with OCD of Grade II or lower and 9 healthy age matched volunteers were examined at a 3.0 T whole body MR scanner using a flexible multi-element coil. In all investigated persons MRI included proton-density (PD)-FSE and 3D GRE (TrueFisp) sequences for morphological diagnosis and location of anatomical site and quantitative T2 and T2 maps. Region of interest (ROI) analysis was performed for the cartilage layer above the OCD and for a morphologically healthy graded cartilage layer. Mean T2 and T2 values were then statistically analysed. The cartilage layer of healthy volunteers showed mean T2 and T2 values of 29.4 ms (SD 4.9) and 11.8 ms (SD 2.7), respectively. In patients with OCD of grade I and II lesions mean T2 values were 40.9 ms (SD 6.6), 48.7 ms (SD 11.2) and mean T2 values were 16.1 ms (SD 3.2), 16.2 ms (SD 4.8). Therefore statistically significantly higher mean T2 and T2 values were found in patients suffering from OCD compared to healthy volunteers. T2 and T2 mapping can help assess the microstructural composition of cartilage overlying osteochondral lesions. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Micro-anatomical quantitative optical imaging: toward automated assessment of breast tissues.

PubMed

Dobbs, Jessica L; Mueller, Jenna L; Krishnamurthy, Savitri; Shin, Dongsuk; Kuerer, Henry; Yang, Wei; Ramanujam, Nirmala; Richards-Kortum, Rebecca

2015-08-20

Pathologists currently diagnose breast lesions through histologic assessment, which requires fixation and tissue preparation. The diagnostic criteria used to classify breast lesions are qualitative and subjective, and inter-observer discordance has been shown to be a significant challenge in the diagnosis of selected breast lesions, particularly for borderline proliferative lesions. Thus, there is an opportunity to develop tools to rapidly visualize and quantitatively interpret breast tissue morphology for a variety of clinical applications. Toward this end, we acquired images of freshly excised breast tissue specimens from a total of 34 patients using confocal fluorescence microscopy and proflavine as a topical stain. We developed computerized algorithms to segment and quantify nuclear and ductal parameters that characterize breast architectural features. A total of 33 parameters were evaluated and used as input to develop a decision tree model to classify benign and malignant breast tissue. Benign features were classified in tissue specimens acquired from 30 patients and malignant features were classified in specimens from 22 patients. The decision tree model that achieved the highest accuracy for distinguishing between benign and malignant breast features used the following parameters: standard deviation of inter-nuclear distance and number of duct lumens. The model achieved 81 % sensitivity and 93 % specificity, corresponding to an area under the curve of 0.93 and an overall accuracy of 90 %. The model classified IDC and DCIS with 92 % and 96 % accuracy, respectively. The cross-validated model achieved 75 % sensitivity and 93 % specificity and an overall accuracy of 88 %. These results suggest that proflavine staining and confocal fluorescence microscopy combined with image analysis strategies to segment morphological features could potentially be used to quantitatively diagnose freshly obtained breast tissue at the point of care without the need for tissue preparation.

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

Preprocessing film-copied MRI for studying morphological brain changes.

PubMed

Pham, Tuan D; Eisenblätter, Uwe; Baune, Bernhard T; Berger, Klaus

2009-06-15

The magnetic resonance imaging (MRI) of the brain is one of the important data items for studying memory and morbidity in elderly as these images can provide useful information through the quantitative measures of various regions of interest of the brain. As an effort to fully automate the biomedical analysis of the brain that can be combined with the genetic data of the same human population and where the records of the original MRI data are missing, this paper presents two effective methods for addressing this imaging problem. The first method handles the restoration of the film-copied MRI. The second method involves the segmentation of the image data. Experimental results and comparisons with other methods suggest the usefulness of the proposed image analysis methodology.

Real time blood testing using quantitative phase imaging.

PubMed

Pham, Hoa V; Bhaduri, Basanta; Tangella, Krishnarao; Best-Popescu, Catherine; Popescu, Gabriel

2013-01-01

We demonstrate a real-time blood testing system that can provide remote diagnosis with minimal human intervention in economically challenged areas. Our instrument combines novel advances in label-free optical imaging with parallel computing. Specifically, we use quantitative phase imaging for extracting red blood cell morphology with nanoscale sensitivity and NVIDIA's CUDA programming language to perform real time cellular-level analysis. While the blood smear is translated through focus, our system is able to segment and analyze all the cells in the one megapixel field of view, at a rate of 40 frames/s. The variety of diagnostic parameters measured from each cell (e.g., surface area, sphericity, and minimum cylindrical diameter) are currently not available with current state of the art clinical instruments. In addition, we show that our instrument correctly recovers the red blood cell volume distribution, as evidenced by the excellent agreement with the cell counter results obtained on normal patients and those with microcytic and macrocytic anemia. The final data outputted by our instrument represent arrays of numbers associated with these morphological parameters and not images. Thus, the memory necessary to store these data is of the order of kilobytes, which allows for their remote transmission via, for example, the cellular network. We envision that such a system will dramatically increase access for blood testing and furthermore, may pave the way to digital hematology.

Heterogeneity mapping of protein expression in tumors using quantitative immunofluorescence.

PubMed

Faratian, Dana; Christiansen, Jason; Gustavson, Mark; Jones, Christine; Scott, Christopher; Um, InHwa; Harrison, David J

2011-10-25

Morphologic heterogeneity within an individual tumor is well-recognized by histopathologists in surgical practice. While this often takes the form of areas of distinct differentiation into recognized histological subtypes, or different pathological grade, often there are more subtle differences in phenotype which defy accurate classification (Figure 1). Ultimately, since morphology is dictated by the underlying molecular phenotype, areas with visible differences are likely to be accompanied by differences in the expression of proteins which orchestrate cellular function and behavior, and therefore, appearance. The significance of visible and invisible (molecular) heterogeneity for prognosis is unknown, but recent evidence suggests that, at least at the genetic level, heterogeneity exists in the primary tumor(1,2), and some of these sub-clones give rise to metastatic (and therefore lethal) disease. Moreover, some proteins are measured as biomarkers because they are the targets of therapy (for instance ER and HER2 for tamoxifen and trastuzumab (Herceptin), respectively). If these proteins show variable expression within a tumor then therapeutic responses may also be variable. The widely used histopathologic scoring schemes for immunohistochemistry either ignore, or numerically homogenize the quantification of protein expression. Similarly, in destructive techniques, where the tumor samples are homogenized (such as gene expression profiling), quantitative information can be elucidated, but spatial information is lost. Genetic heterogeneity mapping approaches in pancreatic cancer have relied either on generation of a single cell suspension(3), or on macrodissection(4). A recent study has used quantum dots in order to map morphologic and molecular heterogeneity in prostate cancer tissue(5), providing proof of principle that morphology and molecular mapping is feasible, but falling short of quantifying the heterogeneity. Since immunohistochemistry is, at best, only semi-quantitative and subject to intra- and inter-observer bias, more sensitive and quantitative methodologies are required in order to accurately map and quantify tissue heterogeneity in situ. We have developed and applied an experimental and statistical methodology in order to systematically quantify the heterogeneity of protein expression in whole tissue sections of tumors, based on the Automated QUantitative Analysis (AQUA) system(6). Tissue sections are labeled with specific antibodies directed against cytokeratins and targets of interest, coupled to fluorophore-labeled secondary antibodies. Slides are imaged using a whole-slide fluorescence scanner. Images are subdivided into hundreds to thousands of tiles, and each tile is then assigned an AQUA score which is a measure of protein concentration within the epithelial (tumor) component of the tissue. Heatmaps are generated to represent tissue expression of the proteins and a heterogeneity score assigned, using a statistical measure of heterogeneity originally used in ecology, based on the Simpson's biodiversity index(7). To date there have been no attempts to systematically map and quantify this variability in tandem with protein expression, in histological preparations. Here, we illustrate the first use of the method applied to ER and HER2 biomarker expression in ovarian cancer. Using this method paves the way for analyzing heterogeneity as an independent variable in studies of biomarker expression in translational studies, in order to establish the significance of heterogeneity in prognosis and prediction of responses to therapy.

Mitochondrial Fragmentation in Aspergillus fumigatus as Early Marker of Granulocyte Killing Activity

PubMed Central

Ruf, Dominik; Brantl, Victor; Wagener, Johannes

2018-01-01

The host's defense against invasive mold infections relies on diverse antimicrobial activities of innate immune cells. However, studying these mechanisms in vitro is complicated by the filamentous nature of such pathogens that typically form long, branched, multinucleated and compartmentalized hyphae. Here we describe a novel method that allows for the visualization and quantification of the antifungal killing activity exerted by human granulocytes against hyphae of the opportunistic pathogen Aspergillus fumigatus. The approach relies on the distinct impact of fungal cell death on the morphology of mitochondria that were visualized with green fluorescent protein (GFP). We show that oxidative stress induces complete fragmentation of the tubular mitochondrial network which correlates with cell death of affected hyphae. Live cell microscopy revealed a similar and non-reversible disruption of the mitochondrial morphology followed by fading of fluorescence in Aspergillus hyphae that were killed by human granulocytes. Quantitative microscopic analysis of fixed samples was subsequently used to estimate the antifungal activity. By utilizing this assay, we demonstrate that lipopolysaccharides as well as human serum significantly increase the killing efficacy of the granulocytes. Our results demonstrate that evaluation of the mitochondrial morphology can be utilized to assess the fungicidal activity of granulocytes against A. fumigatus hyphae. PMID:29868488

Effects of growth hormone on the ultrastructure of bovine preimplantation embryos.

PubMed

Kölle, Sabine; Stojkovic, Miodrag; Reese, Sven; Reichenbach, Horst-Dieter; Wolf, Eckhard; Sinowatz, Fred

2004-07-01

Growth hormone (GH) has recently been shown to promote the development of preimplantation embryos. The aim of our study was therefore to analyze the effects of GH on the morphology and ultrastructure of the cells of bovine preimplantation embryos produced by in vitro fertilization (IVF). In order to determine the physiologically optimal morphology of blastocysts, ex vivo embryos obtained by uterine flushing were also included in the study. As shown by transmission electron microscopy, treatment with GH induced the elimination of glycogen storage in cells of the inner cell mass of 7-day-old embryos. GH also stimulated the exocytosis of lipid vesicles in the inner cell mass and trophectoderm cells of these embryos. Quantitative analysis of micrographs demonstrated a higher volume density of embryonic mitochondria in 7-day-old embryos cultured with GH than in control embryos. Treatment with GH regularly resulted in an improvement of the ultrastructural features of embryos produced in vitro, thus resembling the morphology of ex vivo embryos. Scanning electron-microscopy studies demonstrated that GH altered the structure and the pore size of the zona pellucida of blastocysts. Our studies imply that GH can modulate carbohydrate, lipid, and energy metabolism and influence transportation processes in the early IVF embryo.

Palate anatomy and morphofunctional aspects of interpterygoid vacuities in temnospondyl cranial evolution

NASA Astrophysics Data System (ADS)

Lautenschlager, Stephan; Witzmann, Florian; Werneburg, Ingmar

2016-10-01

Temnospondyls were the morphologically and taxonomically most diverse group of early tetrapods with a near-global distribution during the Palaeozoic and Mesozoic. Members of this group occupied a range of different habitats (aquatic, amphibious, terrestrial), reflected by large morphological disparity of the cranium throughout their evolutionary history. A diagnostic feature of temnospondyls is the presence of an open palate with large interpterygoid vacuities, in contrast to the closed palate of most other early tetrapods and their fish-like relatives. Although the function of the interpterygoid vacuities has been discussed in the past, no quantitative studies have been performed to assess their biomechanical significance. Here, we applied finite element analysis, to test the possibility that the interpterygoid vacuities served for stress distribution during contraction of the jaw closing musculature. Different original and theoretical skull models, in which the vacuities differed in size or were completely absent, were compared for their mechanical performance. Our results demonstrate that palatal morphology played a considerable role in cranial biomechanics of temnospondyls. The presence of large cranial vacuities were found to offer the dual benefit of providing additional muscle attachment areas and allowing for more effective force transmission and thus an increase in bite force without compromising cranial stability.

Morphology of single inhalable particle inside public transit biodiesel fueled bus.

PubMed

Shandilya, Kaushik K; Kumar, Ashok

2010-01-01

In an urban-transit bus, fueled by biodiesel in Toledo, Ohio, single inhalable particle samples in October 2008 were collected and detected by scanning electron microscopy and energy dispersive X-ray spectrometry (SEM/EDS). Particle size analysis found bimodal distribution at 0.2 and 0.5 microm. The particle morphology was characterized by 14 different shape clusters: square, pentagon, hexagon, heptagon, octagon, nonagon, decagon, agglomerate, sphere, triangle, oblong, strip, line or stick, and unknown, by quantitative order. The square particles were common in the samples. Round and triangle particles are more, and pentagon, hexagon, heptagon, octagon, nonagon, decagon, strip, line or sticks are less. Agglomerate particles were found in abundance. The surface of most particles was coarse with a fractal edge that can provide a suitable chemical reaction bed in the polluted atmospheric environment. The three sorts of surface patterns of squares were smooth, semi-smooth, and coarse. The three sorts of square surface patterns represented the morphological characteristics of single inhalable particles in the air inside the bus in Toledo. The size and shape distribution results were compared to those obtained for a bus using ultra low sulfur diesel.

The Pore3D library package for the textural analysis of X-ray computed microtomographic images of rocks

NASA Astrophysics Data System (ADS)

Zandomeneghi, Daria; Mancini, Lucia; Voltolini, Marco; Brun, Francesco; Polacci, Margherita

2010-05-01

Many research fields in Geosciences require the knowledge of the three-dimensional (3D) texture of rocks. X-ray computed microtomography (μCT) supplies an effective method to directly acquire 3D information. Transmission X-ray μCT is a non-destructive technique based on the mapping of the linear attenuation coefficient of X-rays crossing the investigated sample. The 3D distribution of constituents and the contrast based on the different absorption properties of the components can be enhanced by phase-contrast imaging. On an X-ray tomographic dataset, if spatial resolution at the micron scale and proper software are available, a complete textural and morphological quantitative analysis can be carried out and a number of parameters can be extracted, including geometry and organization of discrete rock components (such as crystals, vesicles, fractures, alteration-compositional zones). In the case of volcanic rocks, μCT can be used to image and quantify the textural and morphological characteristics of the rock constituents, such as vesicles (gas bubbles in solidified, erupted products), crystals and glass fibers. For pyroclastic rocks, investigated parameters to characterize the vesicle portion are the size distribution, geometry and orientation of the pores, the pore-throat size and organization, the pore-surface roughness and the topology of the overall pore and pore-throat network. In this work we present several procedures able to extract quantitative information from CT images of volcanic rocks. The imaging experiments have been carried out at the Elettra Synchrotron Light Laboratory in Trieste (Italy) using both the synchrotron radiation at the SYRMEP beamline and a custom-developed μCT system, named TOMOLAB, equipped with a microfocus X-ray tube and based on a cone-beam geometry. The reconstructed 3D images (or volumes) have been elaborated with a software library, named Pore3D, custom-developed by the SYRMEP group at Elettra. The Pore3D software library allows a quantitative description of the morphology and topology of the sample components and it operates directly in the 3D domain, without inferring about the 3D behavior from stacked 2D information. The library has been elaborated to merge together in a common environment some of the features already available in previous research and commercial software, customizing in some cases their applications, adding new tools for the artifact reduction in the tomographic images and enhancing state-of-the-art methods for the quantitative analysis, as based on the specific know-how acquired by the SYRMEP group. The microtomographic experiments on selected pumices and scoriae have given us the opportunity to reconstruct and study the 3D internal structure of very different samples, originated at volcanoes with unique eruptive behavior and hazard potential. In particular, the analysis of vesicle size, shape, distribution, orientation and degree of interconnectivity, quantifies aspects that are directly related to the magma nature and dynamics. In fact, magma near the Earth's surface exists as a multiphase system, including gas bubbles and solid crystals in a liquid medium. The rheology of the magma and the processes that govern the transition between effusive and explosive eruptions can be fully understood if the gas permeability and flow through the bubble networks are quantified. As pyroclasts are natural records of the magma state, in terms of texture and composition, during the last phases of the conduit ascent, the textural 3D information can be coupled to physical, rheological and chemical properties of the parent magma.

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 present a preliminary study on the variation of morphological parameters in case of cell apoptosis induced by exposure to 10 μM cadmium chloride. We employ the same cell line, monitoring the process for 18 hours. In the vast group of environmental pollutants, the toxic heavy metal cadmium is considered a likely candidate as a causative agent of several types of cancers. Widely distributed and used in industry, and with a broad range of target organs and a long half-life (10-30 years) in the human body, this element has been long known for its multiple adverse effects on human health, through occupational or environmental exposure. In apoptosis, we measure cell volume decrease and cell shrinking. Both data of apoptosis and necrosis were analysed by means of a Sigmoidal Statistical Distribution function, which allows several quantitative data to be established, such as swelling and cell death time, flux of intracellular material from inside to outside the cell, initial and final volume versus time. In addition, we can quantitatively study the cytoplasmatic granularity that occurs during necrosis. As a future application, DH could be employed as a non-invasive and label-free method to distinguish between apoptosis and necrosis in terms of morphological parameters.

Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

PubMed Central

Carreira, Valeria Paula; Mensch, Julián; Hasson, Esteban; Fanara, Juan José

2016-01-01

Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact epistatically with mutant alleles. PMID:27459710

A surface curvature oscillation model for vapour-liquid-solid growth of periodic one-dimensional nanostructures

NASA Astrophysics Data System (ADS)

Wang, Hui; Wang, Jian-Tao; Cao, Ze-Xian; Zhang, Wen-Jun; Lee, Chun-Sing; Lee, Shuit-Tong; Zhang, Xiao-Hong

2015-03-01

While the vapour-liquid-solid process has been widely used for growing one-dimensional nanostructures, quantitative understanding of the process is still far from adequate. For example, the origins for the growth of periodic one-dimensional nanostructures are not fully understood. Here we observe that morphologies in a wide range of periodic one-dimensional nanostructures can be described by two quantitative relationships: first, inverse of the periodic spacing along the length direction follows an arithmetic sequence; second, the periodic spacing in the growth direction varies linearly with the diameter of the nanostructure. We further find that these geometric relationships can be explained by considering the surface curvature oscillation of the liquid sphere at the tip of the growing nanostructure. The work reveals the requirements of vapour-liquid-solid growth. It can be applied for quantitative understanding of vapour-liquid-solid growth and to design experiments for controlled growth of nanostructures with custom-designed morphologies.

The Skeletal Site-Specific Role of Connective Tissue Growth Factor in Prenatal Osteogenesis

PubMed Central

Lambi, Alex G.; Pankratz, Talia L.; Mundy, Christina; Gannon, Maureen; Barbe, Mary F.; Richtsmeier, Joan T.; Popoff, Steven N.

2013-01-01

Background Connective tissue growth factor (CTGF/CCN2) is a matricellular protein that is highly expressed during bone development. Mice with global CTGF ablation (knockout, KO) have multiple skeletal dysmorphisms and perinatal lethality. A quantitative analysis of the bone phenotype has not been conducted. Results We demonstrated skeletal site-specific changes in growth plate organization, bone microarchitecture, and shape and gene expression levels in CTGF KO compared with wild-type mice. Growth plate malformations included reduced proliferation zone and increased hypertrophic zone lengths. Appendicular skeletal sites demonstrated decreased metaphyseal trabecular bone, while having increased mid-diaphyseal bone and osteogenic expression markers. Axial skeletal analysis showed decreased bone in caudal vertebral bodies, mandibles, and parietal bones in CTGF KO mice, with decreased expression of osteogenic markers. Analysis of skull phenotypes demonstrated global and regional differences in CTGF KO skull shape resulting from allometric (size-based) and nonallometric shape changes. Localized differences in skull morphology included increased skull width and decreased skull length. Dysregulation of the transforming growth factor-β-CTGF axis coupled with unique morphologic traits provides a potential mechanistic explanation for the skull phenotype. Conclusions We present novel data on a skeletal phenotype in CTGF KO mice, in which ablation of CTGF causes site-specific aberrations in bone formation. PMID:23073844

Nanoscale morphological and chemical changes of high voltage lithium-manganese rich NMC composite cathodes with cycling.

PubMed

Yang, Feifei; Liu, Yijin; Martha, Surendra K; Wu, Ziyu; Andrews, Joy C; Ice, Gene E; Pianetta, Piero; Nanda, Jagjit

2014-08-13

Understanding the evolution of chemical composition and morphology of battery materials during electrochemical cycling is fundamental to extending battery cycle life and ensuring safety. This is particularly true for the much debated high energy density (high voltage) lithium-manganese rich cathode material of composition Li(1 + x)M(1 - x)O2 (M = Mn, Co, Ni). In this study we combine full-field transmission X-ray microscopy (TXM) with X-ray absorption near edge structure (XANES) to spatially resolve changes in chemical phase, oxidation state, and morphology within a high voltage cathode having nominal composition Li1.2Mn0.525Ni0.175Co0.1O2. Nanoscale microscopy with chemical/elemental sensitivity provides direct quantitative visualization of the cathode, and insights into failure. Single-pixel (∼ 30 nm) TXM XANES revealed changes in Mn chemistry with cycling, possibly to a spinel conformation and likely including some Mn(II), starting at the particle surface and proceeding inward. Morphological analysis of the particles revealed, with high resolution and statistical sampling, that the majority of particles adopted nonspherical shapes after 200 cycles. Multiple-energy tomography showed a more homogeneous association of transition metals in the pristine particle, which segregate significantly with cycling. Depletion of transition metals at the cathode surface occurs after just one cycle, likely driven by electrochemical reactions at the surface.

Nanoscale Morphological and Chemical Changes of High Voltage Lithium–Manganese Rich NMC Composite Cathodes with Cycling

PubMed Central

2015-01-01

Understanding the evolution of chemical composition and morphology of battery materials during electrochemical cycling is fundamental to extending battery cycle life and ensuring safety. This is particularly true for the much debated high energy density (high voltage) lithium–manganese rich cathode material of composition Li1 + xM1 – xO2 (M = Mn, Co, Ni). In this study we combine full-field transmission X-ray microscopy (TXM) with X-ray absorption near edge structure (XANES) to spatially resolve changes in chemical phase, oxidation state, and morphology within a high voltage cathode having nominal composition Li1.2Mn0.525Ni0.175Co0.1O2. Nanoscale microscopy with chemical/elemental sensitivity provides direct quantitative visualization of the cathode, and insights into failure. Single-pixel (∼30 nm) TXM XANES revealed changes in Mn chemistry with cycling, possibly to a spinel conformation and likely including some Mn(II), starting at the particle surface and proceeding inward. Morphological analysis of the particles revealed, with high resolution and statistical sampling, that the majority of particles adopted nonspherical shapes after 200 cycles. Multiple-energy tomography showed a more homogeneous association of transition metals in the pristine particle, which segregate significantly with cycling. Depletion of transition metals at the cathode surface occurs after just one cycle, likely driven by electrochemical reactions at the surface. PMID:25054780

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.

Hystricognathy vs Sciurognathy in the Rodent Jaw: A New Morphometric Assessment of Hystricognathy Applied to the Living Fossil Laonastes (Diatomyidae)

PubMed Central

Hautier, Lionel; Lebrun, Renaud; Saksiri, Soonchan; Michaux, Jacques; Vianey-Liaud, Monique; Marivaux, Laurent

2011-01-01

While exceptional for an intense diversification of lineages, the evolutionary history of the order Rodentia comprises only a limited number of morphological morphotypes for the mandible. This situation could partly explain the intense debates about the taxonomic position of the latest described member of this clade, the Laotian rock rat Laonastes aenigmamus (Diatomyidae). This discovery has re-launched the debate on the definition of the Hystricognathi suborder identified using the angle of the jaw relative to the plane of the incisors. Our study aims to end this ambiguity. For clarity, it became necessary to revisit the entire morphological diversity of the mandible in extant and extinct rodents. However, current and past rodent diversity brings out the limitations of the qualitative descriptive approach and highlights the need for a quantitative approach. Here, we present the first descriptive comparison of the masticatory apparatus within the Ctenohystrica clade, in combining classic comparative anatomy with morphometrical methods. First, we quantified the shape of the mandible in rodents using 3D landmarks. Then, the analysis of osteological features was compared to myological features in order to understand the biomechanical origin of this morphological diversity. Among the morphological variation observed, the mandible of Laonastes aenigmamus displays an intermediate association of features that could be considered neither as sciurognathous nor as hystricognathous. PMID:21490933

Emplacement of Basaltic Lava Flows: the Legacy of GPL Walker

NASA Astrophysics Data System (ADS)

Cashman, K. V.

2005-12-01

Through his early field measurements of lava flow morphology, G.P.L. Walker established a framework for examination of the dynamics of lava flow emplacement that is still in place today. I will examine this legacy as established by three early papers: (1) his 1967 paper, where he defined a relationship between the thickness of recent Etna lava flows and the slope over which they flowed, a relationship that he ascribed to lava viscosity; (2) his 1971 paper, which defined a relationship between lava flux and the formation of simple and compound flow units that he used to infer high effusion rates for the emplacement of some flood basalt lavas; and (3) his often-cited 1973 paper, which related the length of lava flows to their average effusion rate. These three papers, all similar in their basic approach of using field measurements of lava flow morphology to extract fundamental relationships between eruption conditions (magma flux and rheology) and emplacement style (flow length and thickness), firmly established the relationship between flow morphology and emplacement dynamics that has since been widely applied not only to subaerial lava flows, but also to the interpretation of flows in submarine and planetary environments. Important extensions of these concepts have been provided by improved field observation methods, particularly for analysis of flowing lava, by laboratory measurements of lava rheology, by the application of analog experiments to lava flow dynamics, and by steady improvement of numerical techniques to model the flow of lava over complex terrain. The real legacy of G.P.L. Walker's field measurement approach, however, may lie in the future, as new topographic measurement techniques such as LIDAR hold exciting promise for truly quantitative analysis of lava flow morphologies and their relationship to flow dynamics.

Quantitative cervical vertebral maturation assessment in adolescents with normal occlusion: a mixed longitudinal study.

PubMed

Chen, Li-Li; Xu, Tian-Min; Jiang, Jiu-Hui; Zhang, Xing-Zhong; Lin, Jiu-Xiang

2008-12-01

The purpose of this study was to establish a quantitative cervical vertebral maturation (CVM) system for adolescents with normal occlusion. Mixed longitudinal data were used. The subjects included 87 children and adolescents from 8 to 18 years old with normal occlusion (32 boys, 55 girls) selected from 901 candidates. Sequential lateral cephalograms and hand-wrist films were taken once a year for 6 years. The lateral cephalograms of all subjects were divided into 11 maturation groups according to the Fishman skeletal maturity indicators. The morphologic characteristics of the second, third, and fourth cervical vertebrae at 11 developmental stages were measured and analyzed. Three characteristic parameters (H4/W4, AH3/PH3, @2) were selected to determine the classification of CVM. With 3 morphologic variables, the quantitative CVM system including 4 maturational stages was established. An equation that can accurately estimate the maturation of the cervical vertebrae was established: CVM stage=-4.13+3.57xH4/W4+4.07xAH3/PH3+0.03x@2. The quantitative CVM method is an efficient, objective, and relatively simple approach to assess the level of skeletal maturation during adolescence.

Urban Heat Island in the city of Bari (Italy) ant its relationship with morphological features

NASA Astrophysics Data System (ADS)

Ceppi, C.; Balena, P.; Loconte, P.; Mancini, F.

2012-04-01

The investigation of an Urban Heat Island (UHI) and its relationship with the wide range of factors able to explain its behavior is a very difficult task: the main trouble is represented by the spatial variability of the urban temperature due to the extreme heterogeneousness of the urban coverage and morphological features. In literature it is known that the local surface temperatures are influenced by the changing characteristics in urban surface and modification of land surface processes affecting the surface energy balance and the shape of boundary layer. The whole processes could lead to distinct urban climates. This work is mainly focused on the mechanisms which are actually connecting the urban morphology with the surface temperature as derived by satellite data provided from the ASTER sensor. Urban morphology could be described by several factors depending on the selected scale of analysis. At the macroscale the UHI is more related to the land-use, environmental context and boundary conditions. At the microscale the surface characteristics, urban density, ratio between green and built areas and, construction and built typology are more involved in addition to the composite indicators such as the Sky View factor and the elevation of the built texture. The case study of the city of Bari is faced. It is a medium sized city in the southern Italy, characterized by the presence of a pervasive waterfront and presence of "lame", a natural erosive furrows shallow that are typical of the Apulia country side. Such ephemeral streams convey the stormwater from the plateau of the hilly Murgia areas to the sea. Moreover, the urban complexity of the city exacerbates the spatial variability of the phenomenon. The first step aim at the investigating of the relationship between the thermal behavior and the above mentioned factors by the construction of a set of homogeneous morphological units. The classification is built both in the urban and rural zone. The second step focuses on the development of a spatial statistical analysis based on qualitative and quantitative indicators able to link the classes of urban morphology with the satellite-based surface temperature. The relationships highlighted by such a spatial analysis can be used to model the urban climate and, consequently, develop a new kind of planning more addressed towards the mitigation of the UHI phenomenon.

Optical characterization of multi-scale morphologically complex heterogeneous media - Application to snow with soot impurities

NASA Astrophysics Data System (ADS)

Dai, Xiaoyu; Haussener, Sophia

2018-02-01

A multi-scale methodology for the radiative transfer analysis of heterogeneous media composed of morphologically-complex components on two distinct scales is presented. The methodology incorporates the exact morphology at the various scales and utilizes volume-averaging approaches with the corresponding effective properties to couple the scales. At the continuum level, the volume-averaged coupled radiative transfer equations are solved utilizing (i) effective radiative transport properties obtained by direct Monte Carlo simulations at the pore level, and (ii) averaged bulk material properties obtained at particle level by Lorenz-Mie theory or discrete dipole approximation calculations. This model is applied to a soot-contaminated snow layer, and is experimentally validated with reflectance measurements of such layers. A quantitative and decoupled understanding of the morphological effect on the radiative transport is achieved, and a significant influence of the dual-scale morphology on the macroscopic optical behavior is observed. Our results show that with a small amount of soot particles, of the order of 1ppb in volume fraction, the reduction in reflectance of a snow layer with large ice grains can reach up to 77% (at a wavelength of 0.3 μm). Soot impurities modeled as compact agglomerates yield 2-3% lower reduction of the reflectance in a thick show layer compared to snow with soot impurities modeled as chain-like agglomerates. Soot impurities modeled as equivalent spherical particles underestimate the reflectance reduction by 2-8%. This study implies that the morphology of the heterogeneities in a media significantly affects the macroscopic optical behavior and, specifically for the soot-contaminated snow, indicates the non-negligible role of soot on the absorption behavior of snow layers. It can be equally used in technical applications for the assessment and optimization of optical performance in multi-scale media.

Cryptic Speciation Patterns in Iranian Rock Lizards Uncovered by Integrative Taxonomy

PubMed Central

Ahmadzadeh, Faraham; Flecks, Morris; Carretero, Miguel A.; Mozaffari, Omid; Böhme, Wolfgang; Harris, D. James; Freitas, Susana; Rödder, Dennis

2013-01-01

While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overall resemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters) and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results support four new species, which are described herein. PMID:24324611

Neocortical neuronal morphology in the Siberian Tiger (Panthera tigris altaica) and the clouded leopard (Neofelis nebulosa).

PubMed

Johnson, Cameron B; Schall, Matthew; Tennison, Mackenzie E; Garcia, Madeleine E; Shea-Shumsky, Noah B; Raghanti, Mary Ann; Lewandowski, Albert H; Bertelsen, Mads F; Waller, Leona C; Walsh, Timothy; Roberts, John F; Hof, Patrick R; Sherwood, Chet C; Manger, Paul R; Jacobs, Bob

2016-12-01

Despite extensive investigations of the neocortex in the domestic cat, little is known about neuronal morphology in larger felids. To this end, the present study characterized and quantified the somatodendritic morphology of neocortical neurons in prefrontal, motor, and visual cortices of the Siberian tiger (Panthera tigris altaica) and clouded leopard (Neofelis nebulosa). After neurons were stained with a modified Golgi technique (N = 194), dendritic branching and spine distributions were analyzed using computer-assisted morphometry. Qualitatively, aspiny and spiny neurons in both species appeared morphologically similar to those observed in the domestic cat. Although the morphology of spiny neurons was diverse, with the presence of extraverted, inverted, horizontal, and multiapical pyramidal neurons, the most common variant was the typical pyramidal neuron. Gigantopyramidal neurons in the motor cortex were extremely large, confirming the observation of Brodmann ([1909] Vergleichende Lokalisationlehre der Grosshirnrinde in ihren Prinzipien dargestellt auf Grund des Zellenbaues. Leipzig, Germany: J.A. Barth), who found large somata for these neurons in carnivores in general, and felids in particular. Quantitatively, a MARSplines analysis of dendritic measures differentiated typical pyramidal neurons between the Siberian tiger and the clouded leopard with 93% accuracy. In general, the dendrites of typical pyramidal neurons were more complex in the tiger than in the leopards. Moreover, dendritic measures in tiger pyramidal neurons were disproportionally large relative to body/brain size insofar as they were nearly as extensive as those observed in much larger mammals (e.g., African elephant). Comparison of neuronal morphology in a more diverse collection of larger felids may elucidate the comparative context for the relatively large size of the pyramidal neurons observed in the present study. J. Comp. Neurol. 524:3641-3665, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Nuclear proliferomics: A new field of study to identify signatures of nuclear materials as demonstrated on alpha-UO3.

PubMed

Schwerdt, Ian J; Brenkmann, Alexandria; Martinson, Sean; Albrecht, Brent D; Heffernan, Sean; Klosterman, Michael R; Kirkham, Trenton; Tasdizen, Tolga; McDonald Iv, Luther W

2018-08-15

The use of a limited set of signatures in nuclear forensics and nuclear safeguards may reduce the discriminating power for identifying unknown nuclear materials, or for verifying processing at existing facilities. Nuclear proliferomics is a proposed new field of study that advocates for the acquisition of large databases of nuclear material properties from a variety of analytical techniques. As demonstrated on a common uranium trioxide polymorph, α-UO 3 , in this paper, nuclear proliferomics increases the ability to improve confidence in identifying the processing history of nuclear materials. Specifically, α-UO 3 was investigated from the calcination of unwashed uranyl peroxide at 350, 400, 450, 500, and 550 °C in air. Scanning electron microscopy (SEM) images were acquired of the surface morphology, and distinct qualitative differences are presented between unwashed and washed uranyl peroxide, as well as the calcination products from the unwashed uranyl peroxide at the investigated temperatures. Differential scanning calorimetry (DSC), UV-Vis spectrophotometry, powder X-ray diffraction (p-XRD), and thermogravimetric analysis-mass spectrometry (TGA-MS) were used to understand the source of these morphological differences as a function of calcination temperature. Additionally, the SEM images were manually segmented using Morphological Analysis for MAterials (MAMA) software to identify quantifiable differences in morphology for three different surface features present on the unwashed uranyl peroxide calcination products. No single quantifiable signature was sufficient to discern all calcination temperatures with a high degree of confidence; therefore, advanced statistical analysis was performed to allow the combination of a number of quantitative signatures, with their associated uncertainties, to allow for complete discernment by calcination history. Furthermore, machine learning was applied to the acquired SEM images to demonstrate automated discernment with at least 89% accuracy. Copyright © 2018 Elsevier B.V. All rights reserved.

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 the growing needs for user-friendly, straightforward solutions that facilitate large-scale, cell-based 3D assays in basic research, drug discovery, and target validation. PMID:24810913

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 oligodendrogliomas could be successfully used as an alternative method to the manual reading as well as to the digital images quantitation with CAMI software. According to our observation a need of a remote supervision/consultation and training for the effective use of remote quantitative analysis of WSI is necessary.

Fluvial drainage networks: the fractal approach as an improvement of quantitative geomorphic analyses

NASA Astrophysics Data System (ADS)

Melelli, Laura; Liucci, Luisa; Vergari, Francesca; Ciccacci, Sirio; Del Monte, Maurizio

2014-05-01

Drainage basins are primary landscape units for geomorphological investigations. Both hillslopes and river drainage system are fundamental components in drainage basins analysis. As other geomorphological systems, also the drainage basins aim to an equilibrium condition where the sequence of erosion, transport and sedimentation approach to a condition of minimum energy effort. This state is revealed by a typical geometry of landforms and of drainage net. Several morphometric indexes can measure how much a drainage basin is far from the theoretical equilibrium configuration, revealing possible external disarray. In active tectonic areas, the drainage basins have a primary importance in order to highlight style, amount and rate of tectonic impulses, and morphometric indexes allow to estimate the tectonic activity classes of different sectors in a study area. Moreover, drainage rivers are characterized by a self-similarity structure; this promotes the use of fractals theory to investigate the system. In this study, fractals techniques are employed together with quantitative geomorphological analysis to study the Upper Tiber Valley (UTV), a tectonic intermontane basin located in northern Apennines (Umbria, central Italy). The area is the result of different tectonic phases. From Late Pliocene until present time the UTV is strongly controlled by a regional uplift and by an extensional phase with different sets of normal faults playing a fundamental role in basin morphology. Thirty-four basins are taken into account for the quantitative analysis, twenty on the left side of the basin, the others on the right side. Using fractals dimension of drainage networks, Horton's laws results, concavity and steepness indexes, and hypsometric curves, this study aims to obtain an evolutionary model of the UTV, where the uplift is compared to local subsidence induced by normal fault activity. The results highlight a well defined difference between western and eastern tributary basins, suggesting a greater disequilibrium in the last ones. The quantitative analysis points out the segments of the basin boundaries where the fault activity is more efficient and the resulting geomorphological implications.

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.

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.

Computer-aided sperm analysis: a useful tool to evaluate patient's response to varicocelectomy.

PubMed

Ariagno, Julia I; Mendeluk, Gabriela R; Furlan, María J; Sardi, M; Chenlo, P; Curi, Susana M; Pugliese, Mercedes N; Repetto, Herberto E; Cohen, Mariano

2017-01-01

Preoperative and postoperative sperm parameter values from infertile men with varicocele were analyzed by computer-aided sperm analysis (CASA) to assess if sperm characteristics improved after varicocelectomy. Semen samples of men with proven fertility (n = 38) and men with varicocele-related infertility (n = 61) were also analyzed. Conventional semen analysis was performed according to WHO (2010) criteria and a CASA system was employed to assess kinetic parameters and sperm concentration. Seminal parameters values in the fertile group were very far above from those of the patients, either before or after surgery. No significant improvement in the percentage normal sperm morphology (P = 0.10), sperm concentration (P = 0.52), total sperm count (P = 0.76), subjective motility (%) (P = 0.97) nor kinematics (P = 0.30) was observed after varicocelectomy when all groups were compared. Neither was significant improvement found in percentage normal sperm morphology (P = 0.91), sperm concentration (P = 0.10), total sperm count (P = 0.89) or percentage motility (P = 0.77) after varicocelectomy in paired comparisons of preoperative and postoperative data. Analysis of paired samples revealed that the total sperm count (P = 0.01) and most sperm kinetic parameters: curvilinear velocity (P = 0.002), straight-line velocity (P = 0.0004), average path velocity (P = 0.0005), linearity (P = 0.02), and wobble (P = 0.006) improved after surgery. CASA offers the potential for accurate quantitative assessment of each patient's response to varicocelectomy.

Flow, Transport, and Reaction in Porous Media: Percolation Scaling, Critical-Path Analysis, and Effective Medium Approximation

NASA Astrophysics Data System (ADS)

Hunt, Allen G.; Sahimi, Muhammad

2017-12-01

We describe the most important developments in the application of three theoretical tools to modeling of the morphology of porous media and flow and transport processes in them. One tool is percolation theory. Although it was over 40 years ago that the possibility of using percolation theory to describe flow and transport processes in porous media was first raised, new models and concepts, as well as new variants of the original percolation model are still being developed for various applications to flow phenomena in porous media. The other two approaches, closely related to percolation theory, are the critical-path analysis, which is applicable when porous media are highly heterogeneous, and the effective medium approximation—poor man's percolation—that provide a simple and, under certain conditions, quantitatively correct description of transport in porous media in which percolation-type disorder is relevant. Applications to topics in geosciences include predictions of the hydraulic conductivity and air permeability, solute and gas diffusion that are particularly important in ecohydrological applications and land-surface interactions, and multiphase flow in porous media, as well as non-Gaussian solute transport, and flow morphologies associated with imbibition into unsaturated fractures. We describe new applications of percolation theory of solute transport to chemical weathering and soil formation, geomorphology, and elemental cycling through the terrestrial Earth surface. Wherever quantitatively accurate predictions of such quantities are relevant, so are the techniques presented here. Whenever possible, the theoretical predictions are compared with the relevant experimental data. In practically all the cases, the agreement between the theoretical predictions and the data is excellent. Also discussed are possible future directions in the application of such concepts to many other phenomena in geosciences.

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 is warranted to elucidate it. Systematic review registration International Prospective Register of Systematic Reviews, PROSPERO CRD42012002041 PMID:24710215

Features of morfological changes in primary thyroid gland CTLL cultures of rats descendants prenatally exposed by radioisotopes of iodine-131.

PubMed

Boiko, O A; Lavrenchuk, H Yo; Lypska, A I; Talko, V V; Asmolkov, V S

2017-12-01

to investigate morphological changes in the primary thyroid cell culture of rat infants whose parents were prenatally exposed by radioisotope iodine 131. obtaining and culturing of thyroid tissue primary cell cultures of newborn rats, cytological (receipt and analysis of cell cultures agents for optical microscopy), biophysical (flow cytometry), statistics. It was shown that cells in thyroid primary culture of offspring rats prenatally exposed by radioisotopes of iodine 131 signs of destructive degenerative changes were observed mostly when animals of both sexes were irra diated. Increased number of two and three nuclear cells and induction of ring like cells is an evidence of signifi cant genotoxic violation and points to the genome instability in offspring of animals exposed by radioisotope iodine 131. Analysis and quantitative morphological parameters of cells in thyroid primary culture of newborn rats whose parents were exposed prenatally by radioisotopes of iodine 131 showed that upon exposure to radiation thy roid undergoes destructive changes at the cellular level and, even in the second generation of offspring, leads to disruption of its functions. O. A. Boiko, H. Yo. Lavrenchuk, A. I. Lypska, V. V. Talko, V. S. Asmolkov.

Hemodynamic and morphologic responses in mouse brain during acute head injury imaged by multispectral structured illumination

NASA Astrophysics Data System (ADS)

Volkov, Boris; Mathews, Marlon S.; Abookasis, David

2015-03-01

Multispectral imaging has received significant attention over the last decade as it integrates spectroscopy, imaging, tomography analysis concurrently to acquire both spatial and spectral information from biological tissue. In the present study, a multispectral setup based on projection of structured illumination at several near-infrared wavelengths and at different spatial frequencies is applied to quantitatively assess brain function before, during, and after the onset of traumatic brain injury in an intact mouse brain (n=5). For the production of head injury, we used the weight drop method where weight of a cylindrical metallic rod falling along a metal tube strikes the mouse's head. Structured light was projected onto the scalp surface and diffuse reflected light was recorded by a CCD camera positioned perpendicular to the mouse head. Following data analysis, we were able to concurrently show a series of hemodynamic and morphologic changes over time including higher deoxyhemoglobin, reduction in oxygen saturation, cell swelling, etc., in comparison with baseline measurements. Overall, results demonstrates the capability of multispectral imaging based structured illumination to detect and map of brain tissue optical and physiological properties following brain injury in a simple noninvasive and noncontact manner.

Automatic segmentation of the left ventricle in a cardiac MR short axis image using blind morphological operation

NASA Astrophysics Data System (ADS)

Irshad, Mehreen; Muhammad, Nazeer; Sharif, Muhammad; Yasmeen, Mussarat

2018-04-01

Conventionally, cardiac MR image analysis is done manually. Automatic examination for analyzing images can replace the monotonous tasks of massive amounts of data to analyze the global and regional functions of the cardiac left ventricle (LV). This task is performed using MR images to calculate the analytic cardiac parameter like end-systolic volume, end-diastolic volume, ejection fraction, and myocardial mass, respectively. These analytic parameters depend upon genuine delineation of epicardial, endocardial, papillary muscle, and trabeculations contours. In this paper, we propose an automatic segmentation method using the sum of absolute differences technique to localize the left ventricle. Blind morphological operations are proposed to segment and detect the LV contours of the epicardium and endocardium, automatically. We test the benchmark Sunny Brook dataset for evaluation of the proposed work. Contours of epicardium and endocardium are compared quantitatively to determine contour's accuracy and observe high matching values. Similarity or overlapping of an automatic examination to the given ground truth analysis by an expert are observed with high accuracy as with an index value of 91.30% . The proposed method for automatic segmentation gives better performance relative to existing techniques in terms of accuracy.

Effects of plasticization and shear stress on phase structure development and properties of soy protein blends.

PubMed

Chen, Feng; Zhang, Jinwen

2010-11-01

In this study, soy protein concentrate (SPC) was used as a plastic component to blend with poly(butylene adipate-co-terephthalate) (PBAT). Effects of SPC plasticization and blend composition on its deformation during mixing were studied in detail. Influence of using water as the major plasticizer and glycerol as the co-plasticizer on the deformation of the SPC phase during mixing was explored. The effect of shear stress, as affected by SPC loading level, on the phase structure of SPC in the blends was also investigated. Quantitative analysis of the aspect ratio of SPC particles was conducted by using ImageJ software, and an empirical model predicting the formation of percolated structure was applied. The experimental results and the model prediction showed a fairly good agreement. The experimental results and statistic analysis suggest that both SPC loading level and its water content prior to compounding had significant influences on development of the SPC phase structure and were correlated in determining the morphological structures of the resulting blends. Consequently, physical and mechanical properties of the blends greatly depended on the phase morphology and PBAT/SPC ratio of the blends.

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

The roles of physicists in medical imaging have expanded over the years, from the study of imaging systems (sources and detectors) and dose to the assessment of image quality and perception, the development of image processing techniques, and the development of image analysis methods to assist in detection and diagnosis. The latter is a natural extension of medical physicists’ goals in developing imaging techniques to help physicians acquire diagnostic information and improve clinical decisions. Studies indicate that radiologists do not detect all abnormalities on images that are visible on retrospective review, and they do not always correctly characterize abnormalities that are found. Since the 1950s, the potential use of computers had been considered for analysis of radiographic abnormalities. In the mid-1980s, however, medical physicists and radiologists began major research efforts for computer-aided detection or computer-aided diagnosis (CAD), that is, using the computer output as an aid to radiologists—as opposed to a completely automatic computer interpretation—focusing initially on methods for the detection of lesions on chest radiographs and mammograms. Since then, extensive investigations of computerized image analysis for detection or diagnosis of abnormalities in a variety of 2D and 3D medical images have been conducted. The growth of CAD over the past 20 years has been tremendous—from the early days of time-consuming film digitization and CPU-intensive computations on a limited number of cases to its current status in which developed CAD approaches are evaluated rigorously on large clinically relevant databases. CAD research by medical physicists includes many aspects—collecting relevant normal and pathological cases; developing computer algorithms appropriate for the medical interpretation task including those for segmentation, feature extraction, and classifier design; developing methodology for assessing CAD performance; validating the 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

The roles of physicists in medical imaging have expanded over the years, from the study of imaging systems (sources and detectors) and dose to the assessment of image quality and perception, the development of image processing techniques, and the development of image analysis methods to assist in detection and diagnosis. The latter is a natural extension of medical physicists' goals in developing imaging techniques to help physicians acquire diagnostic information and improve clinical decisions. Studies indicate that radiologists do not detect all abnormalities on images that are visible on retrospective review, and they do not always correctly characterize abnormalities thatmore » are found. Since the 1950s, the potential use of computers had been considered for analysis of radiographic abnormalities. In the mid-1980s, however, medical physicists and radiologists began major research efforts for computer-aided detection or computer-aided diagnosis (CAD), that is, using the computer output as an aid to radiologists--as opposed to a completely automatic computer interpretation--focusing initially on methods for the detection of lesions on chest radiographs and mammograms. Since then, extensive investigations of computerized image analysis for detection or diagnosis of abnormalities in a variety of 2D and 3D medical images have been conducted. The growth of CAD over the past 20 years has been tremendous--from the early days of time-consuming film digitization and CPU-intensive computations on a limited number of cases to its current status in which developed CAD approaches are evaluated rigorously on large clinically relevant databases. CAD research by medical physicists includes many aspects--collecting relevant normal and pathological cases; developing computer algorithms appropriate for the medical interpretation task including those for segmentation, feature extraction, and classifier design; developing methodology for assessing CAD performance; validating the 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

Mycoplasma pneumoniae Protein P30 Is Required for Cytadherence and Associated with Proper Cell Development

PubMed Central

Romero-Arroyo, Cynthia E.; Jordan, Jarrat; Peacock, Susan J.; Willby, Melisa J.; Farmer, Mark A.; Krause, Duncan C.

1999-01-01

The attachment organelle of Mycoplasma pneumoniae is a polar, tapered cell extension containing an intracytoplasmic, electron-dense core. This terminal structure is the leading end in gliding motility, and its duplication is thought to precede cell division, raising the possibility that mutations affecting cytadherence also confer a defect in motility or cell development. Mycoplasma surface protein P30 is associated with the attachment organelle, and P30 mutants II-3 and II-7 do not cytadhere. In this study, the recombinant wild-type but not the mutant II-3 p30 allele restored cytadherence when transformed into P30 mutants by recombinant transposon delivery. The mutations associated with loss of P30 in mutant II-3 and reacquisition of P30 in cytadhering revertants thereof were identified by nucleotide sequencing of the p30 gene. Morphological abnormalities that included ovoid or multilobed cells having a poorly defined tip structure were associated with loss of P30. Digital image analysis confirmed quantitatively the morphological differences noted visually. Transformation of the P30 mutants with the wild-type p30 allele restored a normal morphology, as determined both visually and by digital image analysis, suggesting that P30 plays a role in mycoplasma cell development. Finally, the P30 mutants localized the adhesin protein P1 to the terminal organelle, indicating that P30 is not involved in P1 trafficking but may be required for its receptor-binding function. PMID:9973332

A geometric morphometric analysis of hominin upper second and third molars, with particular emphasis on European Pleistocene populations.

PubMed

Gómez-Robles, Aida; Bermúdez de Castro, José María; Martinón-Torres, María; Prado-Simón, Leyre; Arsuaga, Juan Luis

2012-09-01

The study of dental morphology by means of geometric morphometric methods allows for a detailed and quantitative comparison of hominin species that is useful for taxonomic assignment and phylogenetic reconstruction. Upper second and third molars have been studied in a comprehensive sample of Plio- and Pleistocene hominins from African, Asian and European sites in order to complete our analysis of the upper postcanine dentition. Intraspecific variation in these two molars is high, but some interspecific trends can be identified. Both molars exhibit a strong reduction of the distal cusps in recent hominin species, namely European Homo heidelbergensis, Homo neanderthalensis and Homo sapiens, but this reduction shows specific patterns and proportions in the three groups. Second molars tend to show four well developed cusps in earlier hominin species and their morphology is only marginally affected by allometric effects. Third molars can be incipiently reduced in earlier species and they evince a significant allometric component, identified both inter- and intraspecifically. European Middle Pleistocene fossils from Sima de los Huesos (SH) show a very strong reduction of these two molars, even more marked than the reduction observed in Neanderthals and in modern human populations. The highly derived shape of SH molars points to an early acquisition of typical Neanderthal dental traits by pre-Neanderthal populations and to a deviation of this population from mean morphologies of other European Middle Pleistocene groups. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

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.

Control of dental-derived induced pluripotent stem cells through modified surfaces for dental application.

PubMed

Choi, Hyunmin; Park, Kyu-Hyung; Lee, Ah-Reum; Mun, Chin Hee; Shin, Yong Dae; Park, Yong-Beom; Park, Young-Bum

2017-07-01

The aim of this study is to investigate the behaviour of iPSc derived from dental stem cells in terms of initial adhesion, differentiation potential on differently surface-treated titanium disc. iPSc derived from human gingival fibroblasts (hGFs) were established using 4-reprogramming factors transduction with Sendai virus. The hGF-iPSc established in this study exhibited the morphology and growth properties similar to human embryonic stem (ES) cells and expressed pluripotency makers. Alkaline Phosphatase (AP) staining, Embryoid Body (EB) formation and in vitro differentiation and karyotyping further confirmed pluripotency of hGF-iPSc. Then, hGF-iPSc were cultured on machined- and Sandblasted and acid etched (SLA)-treated titanium discs with osteogenic induction medium and their morphological as well as quantitative changes according to different surface types were investigated using Alizrin Red S staining, Scanning electron microscopy (SEM), Flow cytometry and RT-PCR. Time-dependent and surface-dependent morphological changes as well as quantitative change in osteogenic differentiation of hGF-iPSc were identified and osteogenic gene expression of hGF-iPSc cultured on SLA-treated titanium disc found to be greater than machined titanium disc, suggesting the fate of hGF-iPSc may be determined by the characteristics of surface to which hGF-iPSc first adhere. iPSc derived from dental stem cell can be one of the most promising and practical cell sources for personalized regenerative dentistry and their morphological change as well as quantitative change in osteogenic differentiation according to different surface types may be further utilized for future clinical application incorporated with dental implant.

Morphology Development During Deposition in OPV Low Band Gap Polymer:Bis-Fullerene Heterojunctions: Effect of a Second Solvent

NASA Astrophysics Data System (ADS)

Chen, Huipeng; Hsiao, Yu-Che; Hu, Bin; Dadmun, Mark

2014-03-01

Polymer based bulk-heterojunction solar cells, based on blends of conjugated polymers and fullerenes are one potential option for low cost renewable power generation. One way to improve power conversion efficiency (PCE) of this cell is to increase the open-circuit voltage (Voc) . It has been reported that replacing PCBM with bis-adduct fullerenes (i.e. ICBA) significantly improves Voc and PCE in P3HT device. However, for the most promising low band-gap polymer (LBP) system, replacing PCBM with ICBA gives very poor short-circuit current (Jsc) and PCE although Voc is significantly improved. As Jsc and PCE strongly depend on the morphology, we therefore tried to optimize the morphology of as-cast LBP/ICBA mixture by adding a second solvent with varying solubility to LBP and ICBA to the deposition solution. The results show that there is no change of LBP ordering by adding the second solvent regardless of its solubility. The morphology of all the as-cast samples is then determined by neutron scattering. A homogenous dispersion of ICBA in LBP is found in the sample where the second solvent is selective to LBP, giving poor PCE. Aggregates of ICBA are formed in those samples where the second solvent is selective to ICBA. The resultant morphology improves PCE by up to 246%. A quantitative analysis of neutron data shows that the interfacial area between ICBA aggregates and LBP/ICBA mixed phase is improved in these samples, which appears to facilitate charge transport and reduce the recombination of free charge carriers.

Characterization of the collagen component of cartilage repair tissue of the talus with quantitative MRI: comparison of T2 relaxation time measurements with a diffusion-weighted double-echo steady-state sequence (dwDESS).

PubMed

Kretzschmar, M; Bieri, O; Miska, M; Wiewiorski, M; Hainc, N; Valderrabano, V; Studler, U

2015-04-01

The purpose of this study was to characterize the collagen component of repair tissue (RT) of the talus after autologous matrix-induced chondrogenesis (AMIC) using quantitative T2 and diffusion-weighted imaging. Mean T2 values and diffusion coefficients of AMIC-RT and normal cartilage of the talus of 25 patients with posttraumatic osteochondral lesions and AMIC repair were compared in a cross-sectional design using partially spoiled steady-state free precession (pSSFP) for T2 quantification, and diffusion-weighted double-echo steady-state (dwDESS) for diffusion measurement. RT and cartilage were graded with modified Noyes and MOCART scores on morphological sequences. An association between follow-up interval and quantitative MRI measures was assessed using multivariate regression, after stratifying the cohort according to time interval between surgery and MRI. Mean T2 of the AMIC-RT and cartilage were 43.1 ms and 39.1 ms, respectively (p = 0.26). Mean diffusivity of the RT (1.76 μm(2)/ms) was significantly higher compared to normal cartilage (1.46 μm(2)/ms) (p = 0.0092). No correlation was found between morphological and quantitative parameters. RT diffusivity was lowest in the subgroup with follow-up >28 months (p = 0.027). Compared to T2-mapping, dwDESS demonstrated greater sensitivity in detecting differences in the collagen matrix between AMIC-RT and cartilage. Decreased diffusivity in patients with longer follow-up times may indicate an increased matrix organization of RT. • MRI is used to assess morphology of the repair tissue during follow-up. • Quantitative MRI allows an estimation of biochemical properties of the repair tissue. • Differences between repair tissue and cartilage were more significant with dwDESS than T2 mapping.

[The morphology of the peripheral blood erythrocytes in patients with tetralogy of Fallot before and after its surgical correction].

PubMed

Guliamov, D S; Vorozheĭkin, V M; Ikmatov, A A; Abdumadzhidov, Kh A

1995-01-01

Quantitative changes in red cells were studied by dark field scanning electron microscopy of native preparations obtained from patients with Fallot's tetralogy of varying severity and duration. Mainly echinocytic transformation of red cells was revealed that directly depended on the disease duration. Morphologic findings have confirmed the efficacy of surgical correction and drug therapy of Fallot's tetralogy.

Three-dimensional biofilm structure quantification.

PubMed

Beyenal, Haluk; Donovan, Conrad; Lewandowski, Zbigniew; Harkin, Gary

2004-12-01

Quantitative parameters describing biofilm physical structure have been extracted from three-dimensional confocal laser scanning microscopy images and used to compare biofilm structures, monitor biofilm development, and quantify environmental factors affecting biofilm structure. Researchers have previously used biovolume, volume to surface ratio, roughness coefficient, and mean and maximum thicknesses to compare biofilm structures. The selection of these parameters is dependent on the availability of software to perform calculations. We believe it is necessary to develop more comprehensive parameters to describe heterogeneous biofilm morphology in three dimensions. This research presents parameters describing three-dimensional biofilm heterogeneity, size, and morphology of biomass calculated from confocal laser scanning microscopy images. This study extends previous work which extracted quantitative parameters regarding morphological features from two-dimensional biofilm images to three-dimensional biofilm images. We describe two types of parameters: (1) textural parameters showing microscale heterogeneity of biofilms and (2) volumetric parameters describing size and morphology of biomass. The three-dimensional features presented are average (ADD) and maximum diffusion distances (MDD), fractal dimension, average run lengths (in X, Y and Z directions), aspect ratio, textural entropy, energy and homogeneity. We discuss the meaning of each parameter and present the calculations in detail. The developed algorithms, including automatic thresholding, are implemented in software as MATLAB programs which will be available at site prior to publication of the paper.

Mechanisms and Evidence of Genital Coevolution: The Roles of Natural Selection, Mate Choice, and Sexual Conflict

PubMed Central

Brennan, Patricia L.R.; Prum, Richard O.

2015-01-01

Genital coevolution between the sexes is expected to be common because of the direct interaction between male and female genitalia during copulation. Here we review the diverse mechanisms of genital coevolution that include natural selection, female mate choice, male–male competition, and how their interactions generate sexual conflict that can lead to sexually antagonistic coevolution. Natural selection on genital morphology will result in size coevolution to allow for copulation to be mechanically possible, even as other features of genitalia may reflect the action of other mechanisms of selection. Genital coevolution is explicitly predicted by at least three mechanisms of genital evolution: lock and key to prevent hybridization, female choice, and sexual conflict. Although some good examples exist in support of each of these mechanisms, more data on quantitative female genital variation and studies of functional morphology during copulation are needed to understand more general patterns. A combination of different approaches is required to continue to advance our understanding of genital coevolution. Knowledge of the ecology and behavior of the studied species combined with functional morphology, quantitative morphological tools, experimental manipulation, and experimental evolution have been provided in the best-studied species, all of which are invertebrates. Therefore, attention to vertebrates in any of these areas is badly needed. PMID:26134314

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein.

PubMed

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-30

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson's disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young's modulus).

Mitotic position and morphology of committed precursor cells in the zebrafish retina adapt to architectural changes upon tissue maturation.

PubMed

Weber, Isabell P; Ramos, Ana P; Strzyz, Paulina J; Leung, Louis C; Young, Stephen; Norden, Caren

2014-04-24

The development of complex neuronal tissues like the vertebrate retina requires the tight orchestration of cell proliferation and differentiation. Although the complexity of transcription factors and signaling pathways involved in retinogenesis has been studied extensively, the influence of tissue maturation itself has not yet been systematically explored. Here, we present a quantitative analysis of mitotic events during zebrafish retinogenesis that reveals three types of committed neuronal precursors in addition to the previously known apical progenitors. The identified precursor types present at distinct developmental stages and exhibit different mitotic location (apical versus nonapical), cleavage plane orientation, and morphology. Interestingly, the emergence of nonapically dividing committed bipolar cell precursors can be linked to an increase in apical crowding caused by the developing photoreceptor cell layer. Furthermore, genetic interference with neuronal subset specification induces ectopic divisions of committed precursors, underlining the finding that progressing morphogenesis can effect precursor division position. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Online quantitative analysis of multispectral images of human body tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.

2013-08-01

A method is developed for online monitoring of structural and morphological parameters of biological tissues (haemoglobin concentration, degree of blood oxygenation, average diameter of capillaries and the parameter characterising the average size of tissue scatterers), which involves multispectral tissue imaging, image normalisation to one of its spectral layers and determination of unknown parameters based on their stable regression relation with the spectral characteristics of the normalised image. Regression is obtained by simulating numerically the diffuse reflectance spectrum of the tissue by the Monte Carlo method at a wide variation of model parameters. The correctness of the model calculations is confirmed by the good agreement with the experimental data. The error of the method is estimated under conditions of general variability of structural and morphological parameters of the tissue. The method developed is compared with the traditional methods of interpretation of multispectral images of biological tissues, based on the solution of the inverse problem for each pixel of the image in the approximation of different analytical models.

Komagataeibacter rhaeticus as an alternative bacteria for cellulose production.

PubMed

Machado, Rachel T A; Gutierrez, Junkal; Tercjak, Agnieszka; Trovatti, Eliane; Uahib, Fernanda G M; Moreno, Gabriela de Padua; Nascimento, Andresa P; Berreta, Andresa A; Ribeiro, Sidney J L; Barud, Hernane S

2016-11-05

A strain isolated from Kombucha tea was isolated and used as an alternative bacterium for the biosynthesis of bacterial cellulose (BC). In this study, BC generated by this novel bacterium was compared to Gluconacetobacter xylinus biosynthesized BC. Kinetic studies reveal that Komagataeibacter rhaeticus was a viable bacterium to produce BC according to yield, thickness and water holding capacity data. Physicochemical properties of BC membranes were investigated by UV-vis and Fourier transform infrared spectroscopies (FTIR), thermogravimetrical analysis (TGA) and X-ray diffraction (XRD). Additionally, scanning electron microscopy (SEM) and atomic force microscopy (AFM) were also used for morphological characterization. Mechanical properties at nano and macroscale were studied employing PeakForce quantitative nanomechanical property mapping (QNM) and dynamic mechanical analyzer (DMA), respectively. Results confirmed that BC membrane biosynthesized by Komagataeibacter rhaeticus had similar physicochemical, morphological and mechanical properties than BC membrane produced by Gluconacetobacter xylinus and can be widely used for the same applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

NASA Astrophysics Data System (ADS)

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus).

Quantification of metallic nanoparticle morphology with tilt series imaging by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Dutta, Aniruddha; Yuan, Biao; Clukay, Christopher J.; Grabill, Christopher N.; Heinrich, Helge; Bhattacharya, Aniket; Kuebler, Stephen M.

2012-02-01

We report on the quantitative analysis of electrolessly deposited Au and Ag nanoparticles (NPs) on SU8 polymer with the help of High-Angle Annular Dark-Field Scanning Transmission Electron Microscopy (HAADF-STEM) in tilt series. Au NPs act as nucleating agents for the electroless deposition of silver. Au NPs were prepared by attachingAu^3+cations to amine functionalized SU8 polymeric surfaces and then reducing it with aqueous NaBH4. The nanoscale morphology of the deposited NPs on the surface of polymer has been studied from the dark field TEM cross sectional images. Ag NPs were deposited on the cross-linked polymeric surface from a silver citrate solution reduced by hydroquinone. HAADF-STEM enables us to determine the distances between the NPs and their exact locations at and near the surface. The particle distribution, sizes and densities provide us with the data necessary to control the parameters for the development of the electroless deposition technique for emerging nanoscale technologies.

Valley s'Asymmetric Characteristics of the Loess Plateau in Northwestern Shanxi Based on DEM

NASA Astrophysics Data System (ADS)

Duan, J.

2016-12-01

The valleys of the Loess Plateau in northwestern Shanxi show great asymmetry. This study using multi-scale DEMs, high-resolution satellite images and digital terrain analysis method, put forward a quantitative index to describe the asymmetric morphology. Several typical areas are selected to test and verify the spatial variability. Results show: (1) Considering the difference of spatial distribution, Pianguanhe basin, Xianchuanhe basin and Yangjiachuan basin are the areas where show most significant asymmetric characteristics . (2) Considering the difference of scale, the shape of large-scale valleys represents three characteristics: randomness, equilibrium and relative symmetry, while small-scale valleys show directionality and asymmetry. (3) Asymmetric morphology performs orientation, and the east-west valleys extremely obvious. Combined with field survey, its formation mechanism can be interpreted as follows :(1)Loess uneven distribution in the valleys. (2) The distribution diversities of vegetation, water , heat conditions and other factors, make a difference in water erosion capability which leads to asymmetric characteristics.

Reduction reactions and densification during in situ TEM heating of iron oxide nanochains

NASA Astrophysics Data System (ADS)

Bonifacio, Cecile S.; Das, Gautom; Kennedy, Ian M.; van Benthem, Klaus

2017-12-01

The reduction reactions and densification of nanochains assembled from γ-Fe2O3 nanoparticles were investigated using in situ transmission electron microscopy (TEM). Morphological changes and reduction of the metal oxide nanochains were observed during in situ TEM annealing through simultaneous imaging and quantitative analysis of the near-edge fine structures of Fe L2,3 absorption edges acquired by spatially resolved electron energy loss spectroscopy. A change in the oxidation states during annealing of the iron oxide nanochains was observed with phase transformations due to continuous reduction from Fe2O3 over Fe3O4, FeO to metallic Fe. Phase transitions during the in situ heating experiments were accompanied with morphological changes in the nanochains, specifically rough-to-smooth surface transitions below 500 °C, neck formation between adjacent particles around 500 °C, and subsequent neck growth. At higher temperatures, coalescence of FeO particles was observed, representing densification.

Micro-computed tomography of false starts produced on bone by different hand-saws.

PubMed

Pelletti, Guido; Viel, Guido; Fais, Paolo; Viero, Alessia; Visentin, Sindi; Miotto, Diego; Montisci, Massimo; Cecchetto, Giovanni; Giraudo, Chiara

2017-05-01

The analysis of macro- and microscopic characteristics of saw marks on bones can provide useful information about the class of the tool utilized to produce the injury. The aim of the present study was to test micro-computed tomography (micro-CT) for the analysis of false starts experimentally produced on 32 human bone sections using 4 different hand-saws in order to verify the potential utility of micro-CT for distinguishing false starts produced by different saws and to correlate the morphology of the tool with that of the bone mark. Each sample was analysed through stereomicroscopy and micro-CT. Stereomicroscopic analysis allowed the identification of the false starts and the detection of the number of tool marks left by each saw. Micro-CT scans, through the integration of 3D renders and multiplanar reconstructions (MPR), allowed the identification of the shape of each false start correlating it to the injuring tool. Our results suggest that micro-CT could be a useful technique for assessing false starts produced by different classes of saws, providing accurate morphological profiles of the bone marks with all the advantages of high resolution 3D imaging (e.g., high accuracy, non-destructive analysis, preservation and documentation of evidence). However, further studies are necessary to integrate qualitative data with quantitative metrical analysis in order to further characterize the false start and the related injuring tool. Copyright © 2017 Elsevier B.V. All rights reserved.

Morphometric characterisation of wing feathers of the barn owl Tyto alba pratincola and the pigeon Columba livia

PubMed Central

Bachmann, Thomas; Klän, Stephan; Baumgartner, Werner; Klaas, Michael; Schröder, Wolfgang; Wagner, Hermann

2007-01-01

Background Owls are known for their silent flight. Even though there is some information available on the mechanisms that lead to a reduction of noise emission, neither the morphological basis, nor the biological mechanisms of the owl's silent flight are known. Therefore, we have initiated a systematic analysis of wing morphology in both a specialist, the barn owl, and a generalist, the pigeon. This report presents a comparison between the feathers of the barn owl and the pigeon and emphasise the specific characteristics of the owl's feathers on macroscopic and microscopic level. An understanding of the features and mechanisms underlying this silent flight might eventually be employed for aerodynamic purposes and lead to a new wing design in modern aircrafts. Results A variety of different feathers (six remiges and six coverts), taken from several specimen in either species, were investigated. Quantitative analysis of digital images and scanning electron microscopy were used for a morphometric characterisation. Although both species have comparable body weights, barn owl feathers were in general larger than pigeon feathers. For both species, the depth and the area of the outer vanes of the remiges were typically smaller than those of the inner vanes. This difference was more pronounced in the barn owl than in the pigeon. Owl feathers also had lesser radiates, longer pennula, and were more translucent than pigeon feathers. The two species achieved smooth edges and regular surfaces of the vanes by different construction principles: while the angles of attachment to the rachis and the length of the barbs was nearly constant for the barn owl, these parameters varied in the pigeon. We also present a quantitative description of several characteristic features of barn owl feathers, e.g., the serrations at the leading edge of the wing, the fringes at the edges of each feather, and the velvet-like dorsal surface. Conclusion The quantitative description of the feathers and the specific structures of owl feathers can be used as a model for the construction of a biomimetic airplane wing or, in general, as a source for noise-reducing applications on any surfaces subjected to flow fields. PMID:18031576

Multi-Resolution Analysis of LiDAR data for Characterizing a Stabilized Aeolian Landscape in South Texas

NASA Astrophysics Data System (ADS)

Barrineau, C. P.; Dobreva, I. D.; Bishop, M. P.; Houser, C.

2014-12-01

Aeolian systems are ideal natural laboratories for examining self-organization in patterned landscapes, as certain wind regimes generate certain morphologies. Topographic information and scale dependent analysis offer the opportunity to study such systems and characterize process-form relationships. A statistically based methodology for differentiating aeolian features would enable the quantitative association of certain surface characteristics with certain morphodynamic regimes. We conducted a multi-resolution analysis of LiDAR elevation data to assess scale-dependent morphometric variations in an aeolian landscape in South Texas. For each pixel, mean elevation values are calculated along concentric circles moving outward at 100-meter intervals (i.e. 500 m, 600 m, 700 m from pixel). The calculated average elevation values plotted against distance from the pixel of interest as curves are used to differentiate multi-scalar variations in elevation across the landscape. In this case, it is hypothesized these curves may be used to quantitatively differentiate certain morphometries from others like a spectral signature may be used to classify paved surfaces from natural vegetation, for example. After generating multi-resolution curves for all the pixels in a selected area of interest (AOI), a Principal Components Analysis is used to highlight commonalities and singularities between generated curves from pixels across the AOI. Our findings suggest that the resulting components could be used for identification of discrete aeolian features like open sands, trailing ridges and active dune crests, and, in particular, zones of deflation. This new approach to landscape characterization not only works to mitigate bias introduced when researchers must select training pixels for morphometric investigations, but can also reveal patterning in aeolian landscapes that would not be as obvious without quantitative characterization.

Quantitative control of CaCO3 growth on quartz crystal microbalance sensors as a signal amplification method.

PubMed

Wu, Congcong; Sun, Zhaomei; Liu, Li-Shang

2017-07-10

The surface crystallization of CaCO 3 on gold was monitored by a quartz crystal microbalance (QCM). Quantitative control of the grown crystals was realized by adjusting the ratio of two functional groups, -N(CH 3 ) 3 and -COOH, on SAMs. Crystals with uniform size, morphology and polymorphism were obtained. The amount of crystals formed was found to increase with an increase in the -COOH group. The proposed quantitative control of crystallization can be an effective mass amplification strategy for QCM to enhance its assay sensitivity.

X-ray diffraction and SEM study of kidney stones in Israel: quantitative analysis, crystallite size determination, and statistical characterization.

PubMed

Uvarov, Vladimir; Popov, Inna; Shapur, Nandakishore; Abdin, Tamer; Gofrit, Ofer N; Pode, Dov; Duvdevani, Mordechai

2011-12-01

Urinary calculi have been recognized as one of the most painful medical disorders. Tenable knowledge of the phase composition of the stones is very important to elucidate an underlying etiology of the stone disease. We report here the results of quantitative X-ray diffraction phase analysis performed on 278 kidney stones from the 275 patients treated at the Department of Urology of Hadassah Hebrew University Hospital (Jerusalem, Israel). Quantification of biominerals in multicomponent samples was performed using the normalized reference intensity ratio method. According to the observed phase compositions, all the tested stones were classified into five chemical groups: oxalates (43.2%), phosphates (7.7%), urates (10.3%), cystines (2.9%), and stones composed of a mixture of different minerals (35.9%). A detailed analysis of each allocated chemical group is presented along with the crystallite size calculations for all the observed crystalline phases. The obtained results have been compared with the published data originated from different geographical regions. Morphology and spatial distribution of the phases identified in the kidney stones were studied with scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS). This type of detailed study of phase composition and structural characteristics of the kidney stones was performed in Israel for the first time.

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 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

Image Cytometric Analysis of Algal Spores for Evaluation of Antifouling Activities of Biocidal Agents.

PubMed

Il Koo, Bon; Lee, Yun-Soo; Seo, Mintae; Seok Choi, Hyung; Leng Seah, Geok; Nam, Taegu; Nam, Yoon Sung

2017-07-31

Chemical biocides have been widely used as marine antifouling agents, but their environmental toxicity impose regulatory restriction on their use. Although various surrogate antifouling biocides have been introduced, their comparative effectiveness has not been well investigated partly due to the difficulty of quantitative evaluation of their antifouling activity. Here we report an image cytometric method to quantitatively analyze the antifouling activities of seven commercial biocides using Ulva prolifera as a target organism, which is known to be a dominant marine species causing soft fouling. The number of spores settled on a substrate is determined through image analysis using the intrinsic fluorescence of chlorophylls in the spores. Pre-determined sets of size and shape of spores allow for the precise determination of the number of settled spores. The effects of biocide concentration and combination of different biocides on the spore settlement are examined. No significant morphological changes of Ulva spores are observed, but the amount of adhesive pad materials is appreciably decreased in the presence of biocides. It is revealed that the growth rate of Ulva is not directly correlated with the antifouling activities against the settlement of Ulva spores. This work suggests that image cytometric analysis is a very convenient, fast-processable method to directly analyze the antifouling effects of biocides and coating materials.

Technical Advance: Live-imaging analysis of human dendritic cell migrating behavior under the influence of immune-stimulating reagents in an organotypic model of lung

PubMed Central

Nguyen Hoang, Anh Thu; Chen, Puran; Björnfot, Sofia; Högstrand, Kari; Lock, John G.; Grandien, Alf; Coles, Mark; Svensson, Mattias

2014-01-01

This manuscript describes technical advances allowing manipulation and quantitative analyses of human DC migratory behavior in lung epithelial tissue. DCs are hematopoietic cells essential for the maintenance of tissue homeostasis and the induction of tissue-specific immune responses. Important functions include cytokine production and migration in response to infection for the induction of proper immune responses. To design appropriate strategies to exploit human DC functional properties in lung tissue for the purpose of clinical evaluation, e.g., candidate vaccination and immunotherapy strategies, we have developed a live-imaging assay based on our previously described organotypic model of the human lung. This assay allows provocations and subsequent quantitative investigations of DC functional properties under conditions mimicking morphological and functional features of the in vivo parental tissue. We present protocols to set up and prepare tissue models for 4D (x, y, z, time) fluorescence-imaging analysis that allow spatial and temporal studies of human DCs in live epithelial tissue, followed by flow cytometry analysis of DCs retrieved from digested tissue models. This model system can be useful for elucidating incompletely defined pathways controlling DC functional responses to infection and inflammation in lung epithelial tissue, as well as the efficacy of locally administered candidate interventions. PMID:24899587

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 exists. Though further study and integration with other date sets is required, a positive feedback mechanism between accumulation of material blocking the vent, eruption, and subsequent accumulation of material to re-block the vent remains possible.

Respiratory trace feature analysis for the prediction of respiratory-gated PET quantification.

PubMed

Wang, Shouyi; Bowen, Stephen R; Chaovalitwongse, W Art; Sandison, George A; Grabowski, Thomas J; Kinahan, Paul E

2014-02-21

The benefits of respiratory gating in quantitative PET/CT vary tremendously between individual patients. Respiratory pattern is among many patient-specific characteristics that are thought to play an important role in gating-induced imaging improvements. However, the quantitative relationship between patient-specific characteristics of respiratory pattern and improvements in quantitative accuracy from respiratory-gated PET/CT has not been well established. If such a relationship could be estimated, then patient-specific respiratory patterns could be used to prospectively select appropriate motion compensation during image acquisition on a per-patient basis. This study was undertaken to develop a novel statistical model that predicts quantitative changes in PET/CT imaging due to respiratory gating. Free-breathing static FDG-PET images without gating and respiratory-gated FDG-PET images were collected from 22 lung and liver cancer patients on a PET/CT scanner. PET imaging quality was quantified with peak standardized uptake value (SUV(peak)) over lesions of interest. Relative differences in SUV(peak) between static and gated PET images were calculated to indicate quantitative imaging changes due to gating. A comprehensive multidimensional extraction of the morphological and statistical characteristics of respiratory patterns was conducted, resulting in 16 features that characterize representative patterns of a single respiratory trace. The six most informative features were subsequently extracted using a stepwise feature selection approach. The multiple-regression model was trained and tested based on a leave-one-subject-out cross-validation. The predicted quantitative improvements in PET imaging achieved an accuracy higher than 90% using a criterion with a dynamic error-tolerance range for SUV(peak) values. The results of this study suggest that our prediction framework could be applied to determine which patients would likely benefit from respiratory motion compensation when clinicians quantitatively assess PET/CT for therapy target definition and response assessment.

Respiratory trace feature analysis for the prediction of respiratory-gated PET quantification

NASA Astrophysics Data System (ADS)

Wang, Shouyi; Bowen, Stephen R.; Chaovalitwongse, W. Art; Sandison, George A.; Grabowski, Thomas J.; Kinahan, Paul E.

2014-02-01

The benefits of respiratory gating in quantitative PET/CT vary tremendously between individual patients. Respiratory pattern is among many patient-specific characteristics that are thought to play an important role in gating-induced imaging improvements. However, the quantitative relationship between patient-specific characteristics of respiratory pattern and improvements in quantitative accuracy from respiratory-gated PET/CT has not been well established. If such a relationship could be estimated, then patient-specific respiratory patterns could be used to prospectively select appropriate motion compensation during image acquisition on a per-patient basis. This study was undertaken to develop a novel statistical model that predicts quantitative changes in PET/CT imaging due to respiratory gating. Free-breathing static FDG-PET images without gating and respiratory-gated FDG-PET images were collected from 22 lung and liver cancer patients on a PET/CT scanner. PET imaging quality was quantified with peak standardized uptake value (SUVpeak) over lesions of interest. Relative differences in SUVpeak between static and gated PET images were calculated to indicate quantitative imaging changes due to gating. A comprehensive multidimensional extraction of the morphological and statistical characteristics of respiratory patterns was conducted, resulting in 16 features that characterize representative patterns of a single respiratory trace. The six most informative features were subsequently extracted using a stepwise feature selection approach. The multiple-regression model was trained and tested based on a leave-one-subject-out cross-validation. The predicted quantitative improvements in PET imaging achieved an accuracy higher than 90% using a criterion with a dynamic error-tolerance range for SUVpeak values. The results of this study suggest that our prediction framework could be applied to determine which patients would likely benefit from respiratory motion compensation when clinicians quantitatively assess PET/CT for therapy target definition and response assessment.

Very high elevation water ice clouds on Mars: Their morphology and temporal behavior

NASA Technical Reports Server (NTRS)

Jaquin, Fred

1988-01-01

Quantitative analysis of Viking images of the martian planetary limb has uncovered the existence and temporal behavior of water ice clouds that form between 50 and 90 km elevation. These clouds show a seasonal behavior that may be correlated with lower atmosphere dynamics. Enhanced vertical mixing of the atmosphere as Mars nears perihelion is hypothesized as the cause of the seasonal dependence, and the diurnal dependence is explained by the temporal behavior of the martian diurnal thermal tide. Viking images also provide a data set of the vertical distribution of aerosols in the martian atmosphere. The temporal and spatial distribution of aerosols are characterized.

Estimating ankle rotational constraints from anatomic structure

NASA Astrophysics Data System (ADS)

Baker, H. H.; Bruckner, Janice S.; Langdon, John H.

1992-09-01

Three-dimensional biomedical data obtained through tomography provide exceptional views of biological anatomy. While visualization is one of the primary purposes for obtaining these data, other more quantitative and analytic uses are possible. These include modeling of tissue properties and interrelationships, simulation of physical processes, interactive surgical investigation, and analysis of kinematics and dynamics. As an application of our research in modeling tissue structure and function, we have been working to develop interactive and automated tools for studying joint geometry and kinematics. We focus here on discrimination of morphological variations in the foot and determining the implications of these on both hominid bipedal evolution and physical therapy treatment for foot disorders.

A systems-biology approach to yeast actin cables.

PubMed

Drake, Tyler; Yusuf, Eddy; Vavylonis, Dimitrios

2012-01-01

We focus on actin cables in yeast as a model system for understanding cytoskeletal organization and the workings of actin itself. In particular, we highlight quantitative approaches on the kinetics of actin-cable assembly and methods of measuring their morphology by image analysis. Actin cables described by these studies can span greater lengths than a thousand end-to-end actin-monomers. Because of this difference in length scales, control of the actin-cable system constitutes a junction between short-range interactions - among actin-monomers and nucleating, polymerization-facilitating, side-binding, severing, and cross-linking proteins - and the emergence of cell-scale physical form as embodied by the actin cables themselves.

Modeling the Spatiotemporal Evolution of the Melanoma Tumor Microenvironment

NASA Astrophysics Data System (ADS)

Signoriello, Alexandra; Bosenberg, Marcus; Shattuck, Mark; O'Hern, Corey

The tumor microenvironment, which includes tumor cells, tumor-associated macrophages (TAM), cancer-associated fibroblasts, and endothelial cells, drives the formation and progression of melanoma tumors. Using quantitative analysis of in vivo confocal images of melanoma tumors in three spatial dimensions, we examine the physical properties of the melanoma tumor microenvironment, including the numbers of different cells types, cell size, and morphology. We also compute the nearest neighbor statistics and measure intermediate range spatial correlations between different cell types. We also calculate the step size distribution, mean-square displacement, and non-Gaussian parameter from the spatial trajectories of different cell types in the tumor microenvironment.

Three-dimensional analysis by electron diffraction methods of nanocrystalline materials.

PubMed

Gammer, Christoph; Mangler, Clemens; Karnthaler, Hans-Peter; Rentenberger, Christian

2011-12-01

To analyze nanocrystalline structures quantitatively in 3D, a novel method is presented based on electron diffraction. It allows determination of the average size and morphology of the coherently scattering domains (CSD) in a straightforward way without the need to prepare multiple sections. The method is applicable to all kinds of bulk nanocrystalline materials. As an example, the average size of the CSD in nanocrystalline FeAl made by severe plastic deformation is determined in 3D. Assuming ellipsoidal CSD, it is deduced that the CSD have a width of 19 ± 2 nm, a length of 18 ± 1 nm, and a height of 10 ± 1 nm.

In vivo automated quantification of quality of apples during storage using optical coherence tomography images

NASA Astrophysics Data System (ADS)

Srivastava, Vishal; Dalal, Devjyoti; Kumar, Anuj; Prakash, Surya; Dalal, Krishna

2018-06-01

Moisture content is an important feature of fruits and vegetables. As 80% of apple content is water, so decreasing the moisture content will degrade the quality of apples (Golden Delicious). The computational and texture features of the apples were extracted from optical coherence tomography (OCT) images. A support vector machine with a Gaussian kernel model was used to perform automated classification. To evaluate the quality of wax coated apples during storage in vivo, our proposed method opens up the possibility of fully automated quantitative analysis based on the morphological features of apples. Our results demonstrate that the analysis of the computational and texture features of OCT images may be a good non-destructive method for the assessment of the quality of apples.

Genetical genomics of Populus leaf shape variation

DOE PAGES

Drost, Derek R.; Puranik, Swati; Novaes, Evandro; ...

2015-06-30

Leaf morphology varies extensively among plant species and is under strong genetic control. Mutagenic screens in model systems have identified genes and established molecular mechanisms regulating leaf initiation, development, and shape. However, it is not known whether this diversity across plant species is related to naturally occurring variation at these genes. Quantitative trait locus (QTL) analysis has revealed a polygenic control for leaf shape variation in different species suggesting that loci discovered by mutagenesis may only explain part of the naturally occurring variation in leaf shape. Here we undertook a genetical genomics study in a poplar intersectional pseudo-backcross pedigree tomore » identify genetic factors controlling leaf shape. Here, the approach combined QTL discovery in a genetic linkage map anchored to the Populus trichocarpa reference genome sequence and transcriptome analysis.« less

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

PubMed Central

Irie, Naoki; Kuratani, Shigeru

2011-01-01

One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. PMID:21427719

Measurement of Galactic Logarithmic Spiral Arm Pitch Angle Using Two-dimensional Fast Fourier Transform Decomposition

NASA Astrophysics Data System (ADS)

Davis, Benjamin L.; Berrier, Joel C.; Shields, Douglas W.; Kennefick, Julia; Kennefick, Daniel; Seigar, Marc S.; Lacy, Claud H. S.; Puerari, Ivânio

2012-04-01

A logarithmic spiral is a prominent feature appearing in a majority of observed galaxies. This feature has long been associated with the traditional Hubble classification scheme, but historical quotes of pitch angle of spiral galaxies have been almost exclusively qualitative. We have developed a methodology, utilizing two-dimensional fast Fourier transformations of images of spiral galaxies, in order to isolate and measure the pitch angles of their spiral arms. Our technique provides a quantitative way to measure this morphological feature. This will allow comparison of spiral galaxy pitch angle to other galactic parameters and test spiral arm genesis theories. In this work, we detail our image processing and analysis of spiral galaxy images and discuss the robustness of our analysis techniques.

Quantitative genetic correlation between trait and preference supports a sexually selected sperm process

PubMed Central

Simmons, Leigh W.; Kotiaho, Janne S.

2007-01-01

Sperm show patterns of rapid and divergent evolution that are characteristic of sexual selection. Sperm competition has been proposed as an important selective agent in the evolution of sperm morphology. However, several comparative analyses have revealed evolutionary associations between sperm length and female reproductive tract morphology that suggest patterns of male–female coevolution. In the dung beetle Onthophagus taurus, males with short sperm have a fertilization advantage that depends on the size of the female's sperm storage organ, the spermatheca; large spermathecae select for short sperm. Sperm length is heritable and is genetically correlated with male condition. Here we report significant additive genetic variation and heritability for spermatheca size and genetic covariance between spermatheca size and sperm length predicted by both the “good-sperm” and “sexy-sperm” models of postcopulatory female preference. Our data thus provide quantitative genetic support for the role of a sexually selected sperm process in the evolutionary divergence of sperm morphology, in much the same manner as precopulatory female preferences drive the evolutionary divergence of male secondary sexual traits. PMID:17921254

Semi-quantitative assessment of pulmonary perfusion in children using dynamic contrast-enhanced MRI

NASA Astrophysics Data System (ADS)

Fetita, Catalin; Thong, William E.; Ou, Phalla

2013-03-01

This paper addresses the study of semi-quantitative assessment of pulmonary perfusion acquired from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in a study population mainly composed of children with pulmonary malformations. The automatic analysis approach proposed is based on the indicator-dilution theory introduced in 1954. First, a robust method is developed to segment the pulmonary artery and the lungs from anatomical MRI data, exploiting 2D and 3D mathematical morphology operators. Second, the time-dependent contrast signal of the lung regions is deconvolved by the arterial input function for the assessment of the local hemodynamic system parameters, ie. mean transit time, pulmonary blood volume and pulmonary blood flow. The discrete deconvolution method implements here a truncated singular value decomposition (tSVD) method. Parametric images for the entire lungs are generated as additional elements for diagnosis and quantitative follow-up. The preliminary results attest the feasibility of perfusion quantification in pulmonary DCE-MRI and open an interesting alternative to scintigraphy for this type of evaluation, to be considered at least as a preliminary decision in the diagnostic due to the large availability of the technique and to the non-invasive aspects.

Nuclear apoptotic volume decrease in individual cells: Confocal microscopy imaging and kinetic modeling.

PubMed

Khalo, Irina V; Konokhova, Anastasiya I; Orlova, Darya Y; Trusov, Konstantin V; Yurkin, Maxim A; Bartova, Eva; Kozubek, Stanislav; Maltsev, Valeri P; Chernyshev, Andrei V

2018-05-30

The dynamics of nuclear morphology changes during apoptosis remains poorly investigated and understood. Using 3D time-lapse confocal microscopy we performed a study of early-stage apoptotic nuclear morphological changes induced by etoposide in single living HepG2 cells. These observations provide a definitive evidence that nuclear apoptotic volume decrease (AVD) is occurring simultaneously with peripheral chromatin condensation (so called "apoptotic ring"). In order to describe quantitatively the dynamics of nuclear morphological changes in the early stage of apoptosis we suggest a general molecular kinetic model, which fits well the obtained experimental data in our study. Results of this work may clarify molecular mechanisms of nuclear morphology changes during apoptosis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multispectral Imaging Broadens Cellular Analysis

NASA Technical Reports Server (NTRS)

2007-01-01

Amnis Corporation, a Seattle-based biotechnology company, developed ImageStream to produce sensitive fluorescence images of cells in flow. The company responded to an SBIR solicitation from Ames Research Center, and proposed to evaluate several methods of extending the depth of field for its ImageStream system and implement the best as an upgrade to its commercial products. This would allow users to view whole cells at the same time, rather than just one section of each cell. Through Phase I and II SBIR contracts, Ames provided Amnis the funding the company needed to develop this extended functionality. For NASA, the resulting high-speed image flow cytometry process made its way into Medusa, a life-detection instrument built to collect, store, and analyze sample organisms from erupting hydrothermal vents, and has the potential to benefit space flight health monitoring. On the commercial end, Amnis has implemented the process in ImageStream, combining high-resolution microscopy and flow cytometry in a single instrument, giving researchers the power to conduct quantitative analyses of individual cells and cell populations at the same time, in the same experiment. ImageStream is also built for many other applications, including cell signaling and pathway analysis; classification and characterization of peripheral blood mononuclear cell populations; quantitative morphology; apoptosis (cell death) assays; gene expression analysis; analysis of cell conjugates; molecular distribution; and receptor mapping and distribution.

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 skeletal evaluation based on cervical vertebral maturation: a longitudinal study of adolescents with normal occlusion.

PubMed

Chen, L; Liu, J; Xu, T; Long, X; Lin, J

2010-07-01

The study aims were to investigate the correlation between vertebral shape and hand-wrist maturation and to select characteristic parameters of C2-C5 (the second to fifth cervical vertebrae) for cervical vertebral maturation determination by mixed longitudinal data. 87 adolescents (32 males, 55 females) aged 8-18 years with normal occlusion were studied. Sequential lateral cephalograms and hand-wrist radiographs were taken annually for 6 consecutive years. Lateral cephalograms were divided into 11 maturation groups according to Fishman Skeletal Maturity Indicators (SMI). 62 morphological measurements of C2-C5 at 11 different developmental stages (SMI1-11) were measured and analysed. Locally weighted scatterplot smoothing, correlation coefficient analysis and variable cluster analysis were used for statistical analysis. Of the 62 cervical vertebral parameters, 44 were positively correlated with SMI, 6 were negatively correlated and 12 were not correlated. The correlation coefficients between cervical vertebral parameters and SMI were relatively high. Characteristic parameters for quantitative analysis of cervical vertebral maturation were selected. In summary, cervical vertebral maturation could be used reliably to evaluate the skeletal stage instead of the hand-wrist radiographic method. Selected characteristic parameters offered a simple and objective reference for the assessment of skeletal maturity and timing of orthognathic surgery. Copyright 2010 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

iTRAQ-Based Quantitative Proteomic Analysis of the Antimicrobial Mechanism of Peptide F1 against Escherichia coli.

PubMed

Miao, Jianyin; Chen, Feilong; Duan, Shan; Gao, Xiangyang; Liu, Guo; Chen, Yunjiao; Dixon, William; Xiao, Hang; Cao, Yong

2015-08-19

Antimicrobial peptides have received increasing attention in the agricultural and food industries due to their potential to control pathogens. However, to facilitate the development of novel peptide-based antimicrobial agents, details regarding the molecular mechanisms of these peptides need to be elucidated. The aim of this study was to investigate the antimicrobial mechanism of peptide F1, a bacteriocin found in Tibetan kefir, against Escherichia coli at protein levels using iTRAQ-based quantitative proteomic analysis. In response to treatment with peptide F1, 31 of the 280 identified proteins in E. coli showed alterations in their expression, including 10 down-regulated proteins and 21 up-regulated proteins. These 31 proteins all possess different molecular functions and are involved in different molecular pathways, as is evident in referencing the Kyoto Encyclopedia of Genes and Genomes pathways. Specifically, pathways that were significantly altered in E. coli in response to peptide F1 treatment include the tricarboxylic acid cycle, oxidative phosphorylation, glycerophospholipid metabolism, and the cell cycle-caulobacter pathways, which was also associated with inhibition of the cell growth, induction of morphological changes, and cell death. The results provide novel insights into the molecular mechanisms of antimicrobial peptides.

Spectral imaging of histological and cytological specimens

NASA Astrophysics Data System (ADS)

Rothmann, Chana; Malik, Zvi

1999-05-01

Evaluation of cell morphology by bright field microscopy is the pillar of histopathological diagnosis. The need for quantitative and objective parameters for diagnosis has given rise to the development of morphometric methods. The development of spectral imaging for biological and medical applications introduced both fields to large amounts of information extracted from a single image. Spectroscopic analysis is based on the ability of a stained histological specimen to absorb, reflect, or emit photons in ways characteristic to its interactions with specific dyes. Spectral information obtained from a histological specimen is stored in a cube whose appellate signifies the two spatial dimensions of a flat sample (x and y) and the third dimension, the spectrum, representing the light intensity for every wavelength. The spectral information stored in the cube can be further processed by morphometric analysis and quantitative procedures. Such a procedure is spectral-similarity mapping (SSM), which enables the demarcation of areas occupied by the same type of material. SSM constructs new images of the specimen, revealing areas with similar stain-macromolecule characteristics and enhancing subcellular features. Spectral imaging combined with SSM reveals nuclear organization through the differentiation stages as well as in apoptotic and necrotic conditions and identifies specifically the nucleoli domains.

Qualitative and quantitative analysis of four species of Curcuma rhizomes using twice development thin layer chromatography.

PubMed

Zhang, J S; Guan, J; Yang, F Q; Liu, H G; Cheng, X J; Li, S P

2008-11-04

The rhizomes of Curcuma phaeocaulis, Curcuma kwangsiensis, Curcuma wenyujin and Curcuma longa are used as Ezhu or Jianghuang in traditional Chinese medicine for a long time. Due to their similar morphological characters, it is difficult to distinguish their origins of raw materials used in clinic. In this study, a simple, rapid and reliable twice development TLC method was developed for qualitative and quantitative analysis of the four species of Curcuma rhizomes. The chromatography was performed on silica gel 60F(254) plate with chloroform-methanol-formic acid (80:4:0.8, v/v/v) and petroleum ether-ethyl acetate (90:10, v/v) as mobile phase for twice development. The TLC markers were colorized with 1% vanillin-H(2)SO(4) solution. The four species of Curcuma were easily discriminated based on their characteristic TLC profiles, and simultaneous quantification of eight compounds, including bisdemethoxycurcumin, demethoxycurcumin, curcumine, curcumenol, curcumol, curdione, furanodienone and curzerene, in Curcuma were also performed densitometrically at lambda(scan)=518nm and lambda(reference)=800 nm. The investigated compounds had good linearity (r(2)>0.9905) within test ranges. Therefore, the developed TLC method can be used for quality control of Curcuma rhizomes.

Field Research Facility Data Integration Framework Data Management Plan: Survey Lines Dataset

DTIC Science & Technology

2016-08-01

CHL and its District partners. The beach morphology surveys on which this report focuses provide quantitative measures of the dynamic nature of...topography • volume change 1.4 Data description The morphology surveys are conducted over a series of 26 shore- perpendicular profile lines spaced 50...dataset input data and products. Table 1. FRF survey lines dataset input data and products. Input Data FDIF Product Description ASCII LARC survey text

An Automated Energy Detection Algorithm Based on Morphological Filter Processing with a Modified Watershed Transform

DTIC Science & Technology

2018-01-01

collected data. These statistical techniques are under the area of descriptive statistics, which is a methodology to condense the data in quantitative ...ARL-TR-8270 ● JAN 2018 US Army Research Laboratory An Automated Energy Detection Algorithm Based on Morphological Filter...report when it is no longer needed. Do not return it to the originator. ARL-TR-8270 ● JAN 2017 US Army Research Laboratory An

The Use of Atomic Force Microscopy for 3D Analysis of Nucleic Acid Hybridization on Microarrays.

PubMed

Dubrovin, E V; Presnova, G V; Rubtsova, M Yu; Egorov, A M; Grigorenko, V G; Yaminsky, I V

2015-01-01

Oligonucleotide microarrays are considered today to be one of the most efficient methods of gene diagnostics. The capability of atomic force microscopy (AFM) to characterize the three-dimensional morphology of single molecules on a surface allows one to use it as an effective tool for the 3D analysis of a microarray for the detection of nucleic acids. The high resolution of AFM offers ways to decrease the detection threshold of target DNA and increase the signal-to-noise ratio. In this work, we suggest an approach to the evaluation of the results of hybridization of gold nanoparticle-labeled nucleic acids on silicon microarrays based on an AFM analysis of the surface both in air and in liquid which takes into account of their three-dimensional structure. We suggest a quantitative measure of the hybridization results which is based on the fraction of the surface area occupied by the nanoparticles.

Contribution of flow-volume curves to the detection of central airway obstruction*

PubMed Central

Raposo, Liliana Bárbara Perestrelo de Andrade e; Bugalho, António; Gomes, Maria João Marques

2013-01-01

OBJECTIVE: To assess the sensitivity and specificity of flow-volume curves in detecting central airway obstruction (CAO), and to determine whether their quantitative and qualitative criteria are associated with the location, type and degree of obstruction. METHODS: Over a four-month period, we consecutively evaluated patients with bronchoscopy indicated. Over a one-week period, all patients underwent clinical evaluation, flow-volume curve, bronchoscopy, and completed a dyspnea scale. Four reviewers, blinded to quantitative and clinical data, and bronchoscopy results, classified the morphology of the curves. A fifth reviewer determined the morphological criteria, as well as the quantitative criteria. RESULTS: We studied 82 patients, 36 (44%) of whom had CAO. The sensitivity and specificity of the flow-volume curves in detecting CAO were, respectively, 88.9% and 91.3% (quantitative criteria) and 30.6% and 93.5% (qualitative criteria). The most prevalent quantitative criteria in our sample were FEF50%/FIF50% ≥ 1, in 83% of patients, and FEV1/PEF ≥ 8 mL . L–1 . min–1, in 36%, both being associated with the type, location, and degree of obstruction (p < 0.05). There was concordance among the reviewers as to the presence of CAO. There is a relationship between the degree of obstruction and dyspnea. CONCLUSIONS: The quantitative criteria should always be calculated for flow-volume curves in order to detect CAO, because of the low sensitivity of the qualitative criteria. Both FEF50%/FIF50% ≥ 1 and FEV1/PEF ≥ 8 mL . L–1 . min–1 were associated with the location, type and degree of obstruction. PMID:24068266

Quantitative Analysis of {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography Identifies Novel Prognostic Imaging Biomarkers in Locally Advanced Pancreatic Cancer Patients Treated With Stereotactic Body Radiation Therapy

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

Cui, Yi; Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo; Song, Jie

Purpose: To identify prognostic biomarkers in pancreatic cancer using high-throughput quantitative image analysis. Methods and Materials: In this institutional review board–approved study, we retrospectively analyzed images and outcomes for 139 locally advanced pancreatic cancer patients treated with stereotactic body radiation therapy (SBRT). The overall population was split into a training cohort (n=90) and a validation cohort (n=49) according to the time of treatment. We extracted quantitative imaging characteristics from pre-SBRT {sup 18}F-fluorodeoxyglucose positron emission tomography, including statistical, morphologic, and texture features. A Cox proportional hazard regression model was built to predict overall survival (OS) in the training cohort using 162more » robust image features. To avoid over-fitting, we applied the elastic net to obtain a sparse set of image features, whose linear combination constitutes a prognostic imaging signature. Univariate and multivariate Cox regression analyses were used to evaluate the association with OS, and concordance index (CI) was used to evaluate the survival prediction accuracy. Results: The prognostic imaging signature included 7 features characterizing different tumor phenotypes, including shape, intensity, and texture. On the validation cohort, univariate analysis showed that this prognostic signature was significantly associated with OS (P=.002, hazard ratio 2.74), which improved upon conventional imaging predictors including tumor volume, maximum standardized uptake value, and total legion glycolysis (P=.018-.028, hazard ratio 1.51-1.57). On multivariate analysis, the proposed signature was the only significant prognostic index (P=.037, hazard ratio 3.72) when adjusted for conventional imaging and clinical factors (P=.123-.870, hazard ratio 0.53-1.30). In terms of CI, the proposed signature scored 0.66 and was significantly better than competing prognostic indices (CI 0.48-0.64, Wilcoxon rank sum test P<1e-6). Conclusion: Quantitative analysis identified novel {sup 18}F-fluorodeoxyglucose positron emission tomography image features that showed improved prognostic value over conventional imaging metrics. If validated in large, prospective cohorts, the new prognostic signature might be used to identify patients for individualized risk-adaptive therapy.« 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.

Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae).

PubMed

Bessega, C; Pometti, C; Ewens, M; Saidman, B O; Vilardi, J C

2015-02-01

Signals of selection on quantitative traits can be detected by the comparison between the genetic differentiation of molecular (neutral) markers and quantitative traits, by multivariate extensions of the same model and by the observation of the additive covariance among relatives. We studied, by three different tests, signals of occurrence of selection in Prosopis alba populations over 15 quantitative traits: three economically important life history traits: height, basal diameter and biomass, 11 leaf morphology traits that may be related with heat-tolerance and physiological responses and spine length that is very important from silvicultural purposes. We analyzed 172 G1-generation trees growing in a common garden belonging to 32 open pollinated families from eight sampling sites in Argentina. The multivariate phenotypes differ significantly among origins, and the highest differentiation corresponded to foliar traits. Molecular genetic markers (SSR) exhibited significant differentiation and allowed us to provide convincing evidence that natural selection is responsible for the patterns of morphological differentiation. The heterogeneous selection over phenotypic traits observed suggested different optima in each population and has important implications for gene resource management. The results suggest that the adaptive significance of traits should be considered together with population provenance in breeding program as a crucial point prior to any selecting program, especially in Prosopis where the first steps are under development.

Depth-resolved imaging of colon tumor using optical coherence tomography and fluorescence laminar optical tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tang, Qinggong; Frank, Aaron; Wang, Jianting; Chen, Chao-wei; Jin, Lily; Lin, Jon; Chan, Joanne M.; Chen, Yu

2016-03-01

Early detection of neoplastic changes remains a critical challenge in clinical cancer diagnosis and treatment. Many cancers arise from epithelial layers such as those of the gastrointestinal (GI) tract. Current standard endoscopic technology is unable to detect those subsurface lesions. Since cancer development is associated with both morphological and molecular alterations, imaging technologies that can quantitative image tissue's morphological and molecular biomarkers and assess the depth extent of a lesion in real time, without the need for tissue excision, would be a major advance in GI cancer diagnostics and therapy. In this research, we investigated the feasibility of multi-modal optical imaging including high-resolution optical coherence tomography (OCT) and depth-resolved high-sensitivity fluorescence laminar optical tomography (FLOT) for structural and molecular imaging. APC (adenomatous polyposis coli) mice model were imaged using OCT and FLOT and the correlated histopathological diagnosis was obtained. Quantitative structural (the scattering coefficient) and molecular imaging parameters (fluorescence intensity) from OCT and FLOT images were developed for multi-parametric analysis. This multi-modal imaging method has demonstrated the feasibility for more accurate diagnosis with 87.4% (87.3%) for sensitivity (specificity) which gives the most optimal diagnosis (the largest area under receiver operating characteristic (ROC) curve). This project results in a new non-invasive multi-modal imaging platform for improved GI cancer detection, which is expected to have a major impact on detection, diagnosis, and characterization of GI cancers, as well as a wide range of epithelial cancers.

Transplantation analysis of developmental mechanisms in Hydra.

PubMed

Shimizu, Hiroshi

2012-01-01

Since the pioneering work of Ethel Browne (1909) who demonstrated for the first time the concept of organizer activity, i.e. the potency of an apical Hydra tissue to induce a secondary axis when transplanted onto a host, Hydra flourished as a fruitful model system for developmental studies. Over the next 60 years this efficient transplantation approach identified graded biological activities along the body column of Hydra named Head Acti-vation and Head Inhibition. These properties inspired theoretical modelers including Lewis Wolpert, Alfred Gierer and Hans Meinhardt to propose models for morphogenesis, respectively the positional information (1969) and reaction-diffusion (1972) models. In 1973, Tsutomu Sugiyama and Toshitaka Fujisawa initiated in Mishima a unique project to analyze the properties of Hydra strains with distinct morphological and developmental characters. To this end, they collected in several areas of Japan multiple Hydra strains that they subsequently characterized and crossed. They also established a lateral transplantation strategy that was much more powerful than the previous ones, as it combined quantitative measurements with cellular analyses thanks to the chimera procedures developed by Campbell and colleagues. In-deed this approach provided a paradigm to quantify in any morphological phenotype the Head Activation and Head Inhibition levels along the body column. In this article, I review the various strains identified by Sugiyama and colleagues, the principles and the main results deduced from the quantitative lateral transplantation strategy. In addition, I briefly discuss the relevance of this approach in the era of molecular biology.

Impact of specific language impairment and type of school on different language subsystems.

PubMed

Puglisi, Marina Leite; Befi-Lopes, Debora Maria

2016-01-01

This study aimed to explore quantitative and qualitative effects of type of school and specific language impairment (SLI) on different language abilities. 204 Brazilian children aged from 4 to 6 years old participated in the study. Children were selected to form three groups: 1) 63 typically developing children studying in private schools (TDPri); 2) 102 typically developing children studying in state schools (TDSta); and 39 children with SLI studying in state schools (SLISta). All individuals were assessed regarding expressive vocabulary, number morphology and morphosyntactic comprehension. All language subsystems were vulnerable to both environmental (type of school) and biological (SLI) effects. The relationship between the three language measures was exactly the same to all groups: vocabulary growth correlated with age and with the development of morphological abilities and morphosyntactic comprehension. Children with SLI showed atypical errors in the comprehension test at the age of 4, but presented a pattern of errors that gradually resembled typical development. The effect of type of school was marked by quantitative differences, while the effect of SLI was characterised by both quantitative and qualitative differences.

A quantitative comparison of plaque types in Alzheimer's disease and senile dementia of the Lewy body type.

PubMed

McKenzie, J E; Edwards, R J; Gentleman, S M; Ince, P G; Perry, R H; Royston, M C; Roberts, G W

1996-01-01

In a previous study we reported no difference in the overall beta-amyloid protein (beta AP) load between Alzheimer's disease (AD) and senile dementia of the Lewy body type (SDLT). However, it is possible that differences in the morphology of beta AP plaque types exist, analogous to the differences in cytoskeletal pathology found in these two disorders. We have carried out a quantitative image analysis of plaque subtypes in the temporal lobe of AD (n = 8), SDLT (n = 9) and control (n = 11) cases. Measurements of beta AP load and plaque density were consistently higher in AD and SDLT than in controls. When AD and SDLT cases were compared no differences were seen in either the density or relative proportions of classic and diffuse plaques. Based on these results we suggest that the variation in the clinical course of these diseases reflects differences in the cytoskeletal pathology, whereas the final stages of profound dementia common to both disorders is associated with the deposition of beta AP.

Dissection and Downstream Analysis of Zebra Finch Embryos at Early Stages of Development

PubMed Central

Murray, Jessica R.; Stanciauskas, Monika E.; Aralere, Tejas S.; Saha, Margaret S.

2014-01-01

The zebra finch (Taeniopygiaguttata) has become an increasingly important model organism in many areas of research including toxicology1,2, behavior3, and memory and learning4,5,6. As the only songbird with a sequenced genome, the zebra finch has great potential for use in developmental studies; however, the early stages of zebra finch development have not been well studied. Lack of research in zebra finch development can be attributed to the difficulty of dissecting the small egg and embryo. The following dissection method minimizes embryonic tissue damage, which allows for investigation of morphology and gene expression at all stages of embryonic development. This permits both bright field and fluorescence quality imaging of embryos, use in molecular procedures such as in situ hybridization (ISH), cell proliferation assays, and RNA extraction for quantitative assays such as quantitative real-time PCR (qtRT-PCR). This technique allows investigators to study early stages of development that were previously difficult to access. PMID:24999108

Surface Plasmon Damping Quantified with an Electron Nanoprobe

PubMed Central

Bosman, Michel; Ye, Enyi; Tan, Shu Fen; Nijhuis, Christian A.; Yang, Joel K. W.; Marty, Renaud; Mlayah, Adnen; Arbouet, Arnaud; Girard, Christian; Han, Ming-Yong

2013-01-01

Fabrication and synthesis of plasmonic structures is rapidly moving towards sub-nanometer accuracy in control over shape and inter-particle distance. This holds the promise for developing device components based on novel, non-classical electro-optical effects. Monochromated electron energy-loss spectroscopy (EELS) has in recent years demonstrated its value as a qualitative experimental technique in nano-optics and plasmonic due to its unprecedented spatial resolution. Here, we demonstrate that EELS can also be used quantitatively, to probe surface plasmon kinetics and damping in single nanostructures. Using this approach, we present from a large (>50) series of individual gold nanoparticles the plasmon Quality factors and the plasmon Dephasing times, as a function of energy/frequency. It is shown that the measured general trend applies to regular particle shapes (rods, spheres) as well as irregular shapes (dendritic, branched morphologies). The combination of direct sub-nanometer imaging with EELS-based plasmon damping analysis launches quantitative nanoplasmonics research into the sub-nanometer realm. PMID:23425921

Networks of plants: how to measure similarity in vegetable species.

PubMed

Vivaldo, Gianna; Masi, Elisa; Pandolfi, Camilla; Mancuso, Stefano; Caldarelli, Guido

2016-06-07

Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome similar problems and to exploit possibilities from environment. In this paper we introduce various quantitative measures based on recent advancements in complex network theory that allow to measure the effective similarities of various species. By using this approach on the similarity in fruit-typology ecological traits we obtain a clear plant classification in a way similar to traditional taxonomic classification. This result is not trivial, since a similar analysis done on the basis of diaspore morphological properties do not provide any clear parameter to classify plants species. Complex network theory can then be used in order to determine which feature amongst many can be used to distinguish scope and possibly evolution of plants. Future uses of this approach range from functional classification to quantitative determination of plant communities in nature.

Quantitative assessment of interfacial interactions with rough membrane surface and its implications for membrane selection and fabrication in a MBR.

PubMed

Chen, Jianrong; Mei, Rongwu; Shen, Liguo; Ding, Linxian; He, Yiming; Lin, Hongjun; Hong, Huachang

2015-03-01

The interfacial interactions between a foulant particle and rough membrane surface in a submerged membrane bioreactor (MBR) were quantitatively assessed by using a new-developed method. It was found that the profile of total interaction versus separation distance was complicated. There were an energy barrier and two negative energy ranges in the profile. Further analysis showed that roughness scale significantly affected the strength and properties of interfacial interactions. It was revealed that there existed a critical range of roughness scale within which the total energy in the separation distance ranged from 0 to several nanometers was continually repulsive. Decrease in foulant size would increase the strength of specific interaction energy, but did not change the existence of a critical roughness scale range. These findings suggested the possibility to "tailor" membrane surface morphology for membrane fouling mitigation, and thus gave significant implications for membrane selection and fabrication in MBRs. Copyright © 2014 Elsevier Ltd. All rights reserved.

OH 83: A new early modern human fossil cranium from the Ndutu beds of Olduvai Gorge, Tanzania.

PubMed

Reiner, Whitney B; Masao, Fidelis; Sholts, Sabrina B; Songita, Agustino Venance; Stanistreet, Ian; Stollhofen, Harald; Taylor, R E; Hlusko, Leslea J

2017-11-01

Herein we introduce a newly recovered partial calvaria, OH 83, from the upper Ndutu Beds of Olduvai Gorge, Tanzania. We present the geological context of its discovery and a comparative analysis of its morphology, placing OH 83 within the context of our current understanding of the origins and evolution of Homo sapiens. We comparatively assessed the morphology of OH 83 using quantitative and qualitative data from penecontemporaneous fossils and the W.W. Howells modern human craniometric dataset. OH 83 is geologically dated to ca. 60-32 ka. Its morphology is indicative of an early modern human, falling at the low end of the range of variation for post-orbital cranial breadth, the high end of the range for bifrontal breadth, and near average in frontal length. There have been numerous attempts to use cranial anatomy to define the species Homo sapiens and identify it in the fossil record. These efforts have not met wide agreement by the scientific community due, in part, to the mosaic patterns of cranial variation represented by the fossils. The variable, mosaic pattern of trait expression in the crania of Middle and Late Pleistocene fossils implies that morphological modernity did not occur at once. However, OH 83 demonstrates that by ca. 60-32 ka modern humans in Africa included individuals that are at the fairly small and gracile range of modern human cranial variation. © 2017 Wiley Periodicals, Inc.