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Sample records for quantitative ultrastructural analysis

  1. Image analysis techniques. The problem of the quantitative evaluation of thechromatin ultrastructure.

    PubMed

    Maraldi, N M; Marinelli, F; Squarzoni, S; Santi, S; Barbieri, M

    1991-02-01

    these images and especially to those referring to nuclei, is limited by several drawbacks: i) the thin section represents only a small fraction of the nuclear volume entirely visible in optical microscope specimens; ii) the identification of nucleosomes, of the solenoid fibres and of the higher levels of compaction of the heterochromatin is not thinsectioned specimens; iii) the differences between heterochromatin and euchromatin are based only on their grey level but do not reveal possible variations of their structural organization. Therefore, the applications of image analysis to the nuclear content does not utilzes the high resolution power of e.m. images and simply quantify the areas occupied by electron-dense chromatin with respect to the more electron-transparent ones. This result is less significative of those obtainable by optical microscopy, since the electron staining is not quantitative as the Fulgen reaction. On the other hand, the following problems still remain unresolved and should be clarified only by the use of quantitative image analysis: ultrastructural organization of the different types of heterochromatin (1); relationships between gene activation, transcription and chromatin decondensation; chromatin arrangement transformation induced by exogenous agents. In order to face these problems, in the last years we applied image analysis to cell or tissue specimens frozen in liquid nitrogen and then fractured in order to expose the inner content of the nucleus (Fig. 1). The obtained metal replicas represent very suitable specimens for digitalized image elaboration, since the fibers which give rise to the chromatin domains are exposed by the fracturing and evidentiated by the shadowing as black dots with a clear white shadow (Fig. 2). Therefore, their size and shape can be quantitatively evaluated by a digital image processor; in this vay the structural elements of the chromatin fibres are also detectable inside a fractured nucleus and their relative

  2. Synchrotron radiation CT methods for 3D quantitative assessment of mechanically relevant ultrastructural properties in murine bone

    NASA Astrophysics Data System (ADS)

    Schneider, Philipp; Voide, Romain; Stampanoni, Marco; Müller, Ralph

    2008-03-01

    Recent data have shown that predicting bone strength can be greatly improved by including microarchitectural parameters in the analysis. Moreover, bone ultrastructure has been implicated as an important contributor to bone strength. We therefore hypothesized that a better understanding of phenotypes linked to bone ultrastructure will provide new insight in the assessment of bone quality and its contribution to bone strength and fracture risk. Therefore, we first developed an experimental design to assess quantitatively ultrastructural murine bone tissue properties non-invasively in three dimensions by using synchrotron radiation-based (SR) computed tomography (CT) methods with resolutions on the order of one micrometer and below. New morphometric indices were introduced to quantify ultrastructural phenotypes of murine cortical bone assessed by our SR CT-based setup, namely the canal network and the osteocyte lacunar system. These ultrastructural phenotypes were then successfully studied in two genetically distinct mouse strains. Finally, we provided strong evidence for a significant influence of the canal network on murine bone mechanics. In the long run, we believe that the morphometric analysis of the ultrastructural phenotypes and the study of bone phenotypes at different hierarchy levels, in conjunction with bone mechanics, will provide new insights in the assessment of bone quality.

  3. Ultrastructural Analysis of Myoblast Fusion in Drosophila

    PubMed Central

    Zhang, Shiliang; Chen, Elizabeth H.

    2015-01-01

    Summary Myoblast fusion in Drosophila has become a powerful genetic system with which to unravel the mechanisms underlying cell fusion. The identification of important components of myoblast fusion by genetic analysis has led to a molecular pathway toward our understanding of this cellular process. In addition to the application of immunohistochemistry and live imaging techniques to visualize myoblast fusion at the light microscopic level, ultrastructural analysis using electron microscopy remains an indispensable tool to reveal fusion intermediates and specific membrane events at sites of fusion. In this chapter, we describe conventional chemical fixation and high-pressure freezing/freeze substitution methods for visualizing fusion intermediates during Drosophila myoblast fusion. Furthermore, we describe an immunoelectron microscopic method for localizing specific proteins relative to the fusion apparatus. PMID:18979250

  4. Ultrastructural cytochemical analysis of intranuclear arsenic inclusions

    SciTech Connect

    Sorensen, E.M.B.

    1987-01-01

    To establish the chemical composition of the arsenic inclusion, freshly isolated preparations of inclusions and epon-embedded thin sections of inclusions were subjected to ultrastructural cytochemical analysis. Intranuclear inclusions are composed of amorphous, arsenic-containing subunits aligned linearly to form a coiled complex. Lipase, ribonuclease, deoxyribonuclease, trypsin, pepsin, protease, amylase, or ethylenediaminetetraacetic acid (EDTA) was used to digest or chelate these inclusions. Following enzymatic digestion or chelation, the electron opacity of inclusions was compared with that of control sections exposed for equal times to equivalent solutions lacking the enzymes. Exposure to amylase caused a consistent reduction in the electron opacity of thin sections of inclusions and almost complete digestion of the freshly isolated preparations of inclusions. This was indicative of the presence of a carbohydrate moiety within arsenic inclusions. Incubation of inclusions with EDTA resulted in solubilization of freshly isolated and thin-sectioned embedded material. These data indicated that the intranuclear arsenic inclusion is composed of both metallic and carbohydrate moieties, confirming earlier studies which identified arsenic within inclusions using instrumental neutron activation analysis and x-ray microprobe analysis.

  5. Ultrastructural Analysis of Vascular Calcifications in Uremia

    PubMed Central

    Aretz, Anke; Verberckmoes, Steven C.; Krüger, Thilo; Behets, Geert J.; Ghadimi, Reza; Weirich, Thomas E.; Rohrmann, Dorothea; Langer, Stephan; Tordoir, Jan H.; Amann, Kerstin; Westenfeld, Ralf; Brandenburg, Vincent M.; D'Haese, Patrick C.; Mayer, Joachim; Ketteler, Markus; McKee, Marc D.; Floege, Jürgen

    2010-01-01

    Accelerated intimal and medial calcification and sclerosis accompany the increased cardiovascular mortality of dialysis patients, but the pathomechanisms initiating microcalcifications of the media are largely unknown. In this study, we systematically investigated the ultrastructural properties of medial calcifications from patients with uremia. We collected iliac artery segments from 30 dialysis patients before kidney transplantation and studied them by radiography, microcomputed tomography, light microscopy, and transmission electron microscopy including electron energy loss spectrometry, energy dispersive spectroscopy, and electron diffraction. In addition, we performed synchrotron x-ray analyses and immunogold labeling to detect inhibitors of calcification. Von Kossa staining revealed calcification of 53% of the arteries. The diameter of these microcalcifications ranged from 20 to 500 nm, with a core-shell structure consisting of up to three layers (subshells). Many of the calcifications consisted of 2- to 10-nm nanocrystals and showed a hydroxyapatite and whitlockite crystalline structure and mineral phase. Immunogold labeling of calcification foci revealed the calcification inhibitors fetuin-A, osteopontin, and matrix gla protein. These observations suggest that uremic microcalcifications originate from nanocrystals, are chemically diverse, and intimately associate with proteinaceous inhibitors of calcification. Furthermore, considering the core-shell structure of the calcifications, apoptotic bodies or matrix vesicles may serve as a calcification nidus. PMID:20203159

  6. Quantitative differences in the pineal ultrastructure of perinatal and adult harp (Phoca groenlandica) and hooded seals (Cystophora cristata).

    PubMed

    Aarseth, Jo Jorem; Stokkan, Karl-Arne

    2003-10-01

    Seals are unique among mammals in that newborns have a large pineal gland and extremely high plasma levels of melatonin at birth. Melatonin levels are also high in the seal fetus but decline rapidly during the first few days of life. The aim of the present study was to provide quantitative information about the ultrastructure of the seal pineal gland using fetal, newborn, and adult hooded seals (Cystophora cristata), and newborn and adult harp seals (Phoca groenlandica). The relative and absolute volumes of pinealocytes (Pi), arteries and veins, nerves, connective tissue, capillaries and glial cells, as well as mitocondria and lipid droplets in Pi, were calculated by use of point count analysis. Whereas the pineal ultrastructure was similar in fetuses and newborns, both seal species showed a pronounced and particular reduction in the volume of Pi and a similar reduction in pinealocyte mitochondria. There was also a shift from unmyelinated to myelinated pineal nerves in adults compared with fetal/newborns. The selective and marked reduction of Pi may explain the zonated pineal structure typical of the adult seal. The results demonstrate that the fetal gland is as large and active as that of the newborn seal and support the notion that the large size and high activity of the pineal gland in the newborn seal is a fading consequence of its prenatal condition.

  7. A quantitative approach to scar analysis.

    PubMed

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

    2011-02-01

    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.

  8. 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

  9. Ultrastructural analysis of Candida albicans when exposed to silver nanoparticles.

    PubMed

    Vazquez-Muñoz, Roberto; Avalos-Borja, Miguel; Castro-Longoria, Ernestina

    2014-01-01

    Candida albicans is the most common fungal pathogen in humans, and recently some studies have reported the antifungal activity of silver nanoparticles (AgNPs) against some Candida species. However, ultrastructural analyses on the interaction of AgNPs with these microorganisms have not been reported. In this work we evaluated the effect of AgNPs on C. albicans, and the minimum inhibitory concentration (MIC) was found to have a fungicidal effect. The IC50 was also determined, and the use of AgNPs with fluconazole (FLC), a fungistatic drug, reduced cell proliferation. In order to understand how AgNPs interact with living cells, the ultrastructural distribution of AgNPs in this fungus was determined. Transmission electron microscopy (TEM) analysis revealed a high accumulation of AgNPs outside the cells but also smaller nanoparticles (NPs) localized throughout the cytoplasm. Energy dispersive spectroscopy (EDS) analysis confirmed the presence of intracellular silver. From our results it is assumed that AgNPs used in this study do not penetrate the cell, but instead release silver ions that infiltrate into the cell leading to the formation of NPs through reduction by organic compounds present in the cell wall and cytoplasm.

  10. Ultrastructural Analysis of Candida albicans When Exposed to Silver Nanoparticles

    PubMed Central

    Vazquez-Muñoz, Roberto; Avalos-Borja, Miguel; Castro-Longoria, Ernestina

    2014-01-01

    Candida albicans is the most common fungal pathogen in humans, and recently some studies have reported the antifungal activity of silver nanoparticles (AgNPs) against some Candida species. However, ultrastructural analyses on the interaction of AgNPs with these microorganisms have not been reported. In this work we evaluated the effect of AgNPs on C. albicans, and the minimum inhibitory concentration (MIC) was found to have a fungicidal effect. The IC50 was also determined, and the use of AgNPs with fluconazole (FLC), a fungistatic drug, reduced cell proliferation. In order to understand how AgNPs interact with living cells, the ultrastructural distribution of AgNPs in this fungus was determined. Transmission electron microscopy (TEM) analysis revealed a high accumulation of AgNPs outside the cells but also smaller nanoparticles (NPs) localized throughout the cytoplasm. Energy dispersive spectroscopy (EDS) analysis confirmed the presence of intracellular silver. From our results it is assumed that AgNPs used in this study do not penetrate the cell, but instead release silver ions that infiltrate into the cell leading to the formation of NPs through reduction by organic compounds present in the cell wall and cytoplasm. PMID:25290909

  11. Ultrastructural analysis of the lamina cribrosa after radial optic neurotomy.

    PubMed

    Hasselbach, H; Thale, A; Bunse, A; Paulsen, F; Roider, J

    2009-06-01

    Radial optic neurotomy (RON) has been proposed for alleviation of the "scleral outlet compartment syndrome" at the level of the lamina cribrosa, which is thought to play a pathoetiologic role in central retinal vein occlusion (CRVO). The aim of this study has been to analyze the ultrastructural alterations of the lamina cribrosa after RON to gain new insights in the underlying pathomechanical factors. Fifteen donor eyes underwent a standardized open-sky-vitrectomy and RON after removal of the anterior eye segment for keratoplasty. Using a microvitreoretinal blade, a radial incision was performed on the nasal hemisphere of the optic nerve head radial to the optic disc and parallel to the nerve fibre layer. The lamina cribrosa and the surrounding scleral ring were then prepared for light microscopy, scanning (SEM) and transmission electron microscopy (TEM). Ultrastructural analysis demonstrated that in 60% (n=9) of the evaluated cases the scleral ring was dissected completely and in 40% (n=6) only partially. The adjacent neuronal tissue to the dissection area showed only minimal injury. The central retinal vessels were not injured in all cases. Only complete incision of the circular ring of collagen fibrils surrounding the lamina cribrosa via RON resulted in effective relaxation of the scleral outlet and was achieved in 60% of all eyes under standardized conditions. In all cases the adjacent tissue showed only minimal injury. The high rate of incomplete dissection of the scleral outlet may be an explanation for the variable outcome seen in different studies on RON.

  12. Multivariate Quantitative Chemical Analysis

    NASA Technical Reports Server (NTRS)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

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

  13. Quantitative and qualitative morphologic, cytochemical, and ultrastructural characteristics of blood cells in captive Asian water monitors.

    PubMed

    Salakij, Chaleow; Salakij, Jarernsak; Prihirunkit, Kreangsak; Narkkong, Naul-Anong; Sanyathitiseree, Pornchai; Kranjanapitukkul, Kwanjai

    2014-12-01

    The Asian water monitor (Varanus salvator) is the most common monitor lizard in Thailand. Reported data regarding hematology and morphology of blood cells for this species are scarce. The objective of this study was to assess routine hematologic variables and characterize the morphology, cytochemical staining, and ultrastructural features of blood cells in the Asian water monitor. Blood samples from 55 monitors (22 males and 33 females) were obtained for a CBC. Cytochemical staining (Sudan black B [SBB], peroxidase [PO], α-naphthyl acetate esterase [ANAE], and beta-glucuronidase [BG]), and scanning and transmission electron microscopy were performed using standard methods. Determined mean (range) hematologic results of all monitors included PCV 0.32 L/L (0.20-0.44 L/L), HGB 106 g/L (62-157 g/L), WBC 15.9 × 10(9) /L (4.0-34.0 × 10(9) /L), heterophil 6.3 × 10(9) /L (1.5-17.1 × 10(9) /L, azurophil 2.6 × 10(9) /L (0.7-9.5 × 10(9) /L), basophil 0.1 (0.1-0.5 × 10(9) /L), lymphocyte 6.8 × 10(9) /L (0.5-13.1 × 10(9) /L), and monocyte 0.2 × 10(9) /L (0.04-1 × 10(9) /L) counts. Heterophils and basophils stained strongly positive with SBB, ANAE, and BG. Heterophils contained 2 types of granules, round SBB-positive and PO-negative granules, and electron-dense, large rod-shaped granules. Gamonts of Hepatozoon sp. were found in <1% RBC of 43 monitors. There was no significant difference between hematologic variables in Hepatozoon-positive and -negative monitors. Heterophils in Asian water monitors may also function as eosinophils based on cytochemical and ultrastructural features. The quantitative results may be used as base for further studies in healthy and diseased Asian water monitors. © 2014 American Society for Veterinary Clinical Pathology.

  14. Quantitative Hydrocarbon Surface Analysis

    NASA Technical Reports Server (NTRS)

    Douglas, Vonnie M.

    2000-01-01

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

  15. Quantitative Hydrocarbon Surface Analysis

    NASA Technical Reports Server (NTRS)

    Douglas, Vonnie M.

    2000-01-01

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

  16. An Ultrastructural Analysis of Nocardia During Experimental Infections in Mice

    PubMed Central

    Beaman, Blaine L.

    1973-01-01

    Several strains of Nocardia that varied from virulent to avirulent were injected intraperitoneally into young mice. Histological and ultrastructural analysis of the resultant infections revealed that the bacteria and the lesions they induced were different depending upon the strain of organism used. Further, the morphological and tinctorial characteristics of the bacteria grown in vitro changes during growth in vivo. These observations strongly suggested that chemical and physical alterations occurred in the cell envelope of the Nocardia when grown in mice. Electron microscopy confirmed that significant structural modification occurred, especially in the cell envelope, when the nocardial cells established themselves within the host tissue. It was shown that the least virulent strain exhibited the most dramatic changes whereas the most virulent organism appeared to be affected the least. Images PMID:4584055

  17. [Quantitative changes in the ultrastructure of myocardial cells in Japanese quail during hypergravity, hypodynamia and space flight].

    PubMed

    Bózner, A; Boda, K; Dostál, J; Matĕjková, Z; Devecka, V

    1993-03-01

    The experimental work aimed at the quantitative ultrastructure of the myocardial cells of the Japanese quail Coturnix coturnix japonica during hypergravitation, hypodynamism and space flight in a Soviet satellite. For the determination of quantitative changes of the myocardial ultrastructure a morphometrical method was used with parameters like the number of mitochondria, average mitochondrial size, relative mitochondrial volume, deficiency of cristae and relative volume of myofibrils. The quails were observed in 3 groups. The absolute control consisted of quails living in normal Earth conditions, in the laboratory group the quails were exposed to conditions of hypergravitation and hypodynamism in a specially constructed centrifuge, and in the flying group the quails were exposed to space flight in a Soviet orbital station MIR. In the group of absolute controls no pathological changes of the myocardial ultrastructure were found. In the flying group there were no significant changes, with the exception of decreased relative volume of myofibrils, which however agrees with the findings on symptoms corresponding to human and animal heart weakness during space flights. In the laboratory group, pathological changes were observed in each of the fractions. The most significant pathological findings were found in the group controls in the center and in hypergravitation combined with hypodynamism. It can be concluded that the laboratories can simulate conditions induced by the start and flight of space ships. (Fig. 2, Ref, 8.)

  18. Ultrastructural and quantitative immunohistochemical changes induced by nonsteroid antiandrogens on pituitary gonadotroph population of prepubertal male rats.

    PubMed

    Cónsole, G M; Jurado, S B; Rulli, S B; Calandra, R S; Gómez Dumm, C L

    2001-01-01

    Specific blockade of the androgen receptor by the nonsteroid antiandrogens flutamide and Casodex has proven to be a useful tool for studying androgens in vivo. The aim of the present study was to investigate the effect of antiandrogen administration at the pituitary level by evaluating the ultrastructural changes in gonadotrophs, in correlation with the quantitative immunohistochemical findings, and by comparing these alterations with the effect of androgen deprivation by castration either with or without subsequent androgen replacement. Male Sprague-Dawley rats (23 days old) were grouped as follows: (1) controls, (2) flutamide-injected (10 mg/rat/day), (3) Casodex-injected (10 mg/rat/day), (4) castrated, and (5) castrated plus androgen-replaced (dihydrotestosterone propionate; 40 microg/rat/day). Groups were sacrificed after 10 days of maintenance under each condition. Pituitaries were processed for both light and electron microscopy. Serial sections (4 microm) were obtained at different levels and immunostained by means of the primary murine monoclonal antibodies anti-FSH and anti-LH and a peroxidase-mediated EnVision System (Dako). Volume density, cell density and mean cell area were measured with an image analysis system (Imaging Technology, Software Optimas 5.2). The mean cell area (p < 0.001) and the volume density (p < 0.05) increased significantly in the flutamide- and Casodex-treated groups as well as the castrated group of FSH and LH cells. On the other hand, androgen replacement in the castrated rats, however, reduced in both parameters related to control animals. The cell density of FSH-secreting cells was increased (p < 0.05) in the Casodex and flutamide treatment as well as castrated group. The cell density of LH-secreting cells was augmented (p < 0.05) in the Casodex-treated group, while there was no increase in such parameter with flutamide and castration. The ultrastructure of all groups showed two types of gonadotrophs. Type I cells contained

  19. Ultrastructural analysis of different-made staplers' staples.

    PubMed

    Gentilli, S; Portigliotti, L; Aronici, M; Ferrante, D; Surico, D; Milanesio, M; Gianotti, V; Gatti, G; Addante, A; Garavoglia, M

    2012-10-01

    Recently, Chinese-made mechanical staplers with lower price respect to American-made ones have been introduced in clinical practice. In literature, small case series compare the clinical outcomes of different staplers concluding that the new stapler devices perform as well as the American ones. The aim of this study is to compare with an ultrastructural analysis the staples of different staplers in order to verify the existence of differences that might explain significant price disparity and condition clinical outcomes. Each stapler was subjected to morphological analysis, energy dispersive X-Ray spectroscopy, metal release assessment followed by inductively coupled plasma mass spectroscopy. P-values were considered statistically significant when <0.05. Autosuture staples have square section whereas the other American one and Chinese made staples have round sections. Roughness index and chips presence before and after ageing tests were comparable for all samples except for Ethicon Endo-Surgery stapler. Energy dispersive X-Ray spectroscopy showed that all staplers are made of pure Titanium but Ethicon Endo-Surgery staples are made with an alloy. Metal release analysis release statistically significant differences between samples in simulated body fluid 20 days solution (P=0.002) and in Aquaregia at 14 days solution. Discussion. Stapling devices have became routinely used in gastrointestinal surgery mainly because of operative time reduction. Recently, new Chinese-made mechanical staplers, with significantly lower prices, have been introduced in clinical practice. In literature, there are some studies that compare clinical outcomes of American-made and Chinese-made staplers on small groups of patients but doesn't exist any work which consider structural differences between traditional and new devices. In our study, for the first time, we propose a comparison between two American-made staplers and three Chinese-made staplers which evaluate morphology, metal

  20. Quantitative environmental risk analysis

    SciTech Connect

    Klovning, J.; Nilsen, E.F.

    1995-12-31

    According to regulations relating to implementation and rise of risk analysis in the petroleum activities issued by the Norwegian Petroleum Directorate, it is mandatory for an operator on the Norwegian Continental Shelf to establish acceptance criteria for environmental risk in the activities and carry out environmental risk analysis. This paper presents a {open_quotes}new{close_quotes} method for environmental risk analysis developed by the company. The objective has been to assist the company to meet rules and regulations and to assess and describe the environmental risk in a systematic manner. In the environmental risk analysis the most sensitive biological resource in the affected area is used to assess the environmental damage. The analytical method is based on the methodology for quantitative risk analysis related to loss of life. In addition it incorporates the effect of seasonal fluctuations in the environmental risk evaluations. The paper is describing the function of the main analytical sequences exemplified through an analysis of environmental risk related to exploration drilling in an environmental sensitive area on the Norwegian Continental Shelf.

  1. Morphometric and ultrastructural analysis of different pituitary cell populations in undernourished monkeys.

    PubMed

    Cónsole, G M; Jurado, S B; Oyhenart, E; Ferese, C; Pucciarelli, H; Gómez Dumm, C L

    2001-01-01

    Undernutrition elicited by a low-protein diet determines a marked reduction of hypophyseal activity and affects the function of the respective target organs. The objective of the present investigation was to study the ultrastructural and quantitative immunohistochemical changes of the different pituitary cell populations in undernourished monkeys that had been previously shown to have significant changes in craniofacial growth. Twenty Saimiri sciureus boliviensis monkeys of both sexes were used. The animals were born in captivity and were separated into two groups at one year of age, i.e., control and undernourished animals. The monkeys were fed ad libitum a 20% (control group) and a 10% (experimental group) protein diet for two years. Pituitaries were processed for light and electron microscopy. The former was immunolabeled with anti-GH, -PRL, -LH, -FSH, -ACTH, and -TSH sera. Volume density and cell density were measured using an image analyzer. Quantitative immunohistochemistry revealed a decrease in these parameters with regard to somatotrophs, lactotrophs, gonadotrophs and thyrotrophs from undernourished animals compared to control ones. In these populations, the ultrastructural study showed changes suggesting compensatory hyperfunction. On the contrary, no significant changes were found in the morphometric parameters or the ultrastructure of the corticotroph population. We conclude that in undernourished monkeys the somatotroph, lactotroph, gonadotroph, and thyrotroph cell populations showed quantitative immunohistochemical changes that can be correlated with ultrastructural findings.

  2. Quantitative and qualitative morphologic, cytochemical and ultrastructural characteristics of blood cells in the Crested Serpent eagle and Shikra.

    PubMed

    Salakij, Chaleow; Kasorndorkbua, Chaiyan; Salakij, Jarernsak; Suwannasaeng, Pimsuda; Jakthong, Pattarapong

    2015-08-01

    The Crested Serpent eagle (Spilornis cheela) is a bird of prey found in the tropical rain forest in Thailand. The Shikra (Accipiter badius) is a sparrow hawk and common resident in Thailand. Blood samples from 9 Crested Serpent eagles and 12 Shikras were obtained from September 2010 to November 2014. They were clinically healthy and negative for blood parasites detectable by light microscopy and molecular techniques (partial cytochrome b gene for avian malaria and partial 18S rRNA gene for trypanosome). Cytochemical staining (Sudan black B, peroxidase, α-naphthyl acetate esterase, and β-glucuronidase) and transmission electron microscopy were performed. Hematological results were reported as the mean ± standard deviation and median. Heterophils were the most prevalent leukocytes in the Crested Serpent eagle, but in the Shikra, lymphocytes were the most prevalent leukocytes. In the Shikra, some vacuoles were observed in the cytoplasm of the eosinophils. All blood cells in both types of raptors stained positively for β-glucuronidase but negatively for peroxidase. The ultrastructure of heterophils showed more clearly differentiate long rod granules in Crested Serpent eagle and spindle-shaped granules in Shikra. The ultrastructure of the eosinophils in the Crested Serpent eagle revealed varied electron-dense, round-shaped granules with round, different electron-dense areas in the centers of some granules, which differed from the structure reported for other raptors. These quantitative results may be useful for clinical evaluations of Crested Serpent eagles and Shikras that are undergoing rehabilitation for release.

  3. Quantitative Techniques in Volumetric Analysis

    NASA Astrophysics Data System (ADS)

    Zimmerman, John; Jacobsen, Jerrold J.

    1996-12-01

    Quantitative Techniques in Volumetric Analysis is a visual library of techniques used in making volumetric measurements. This 40-minute VHS videotape is designed as a resource for introducing students to proper volumetric methods and procedures. The entire tape, or relevant segments of the tape, can also be used to review procedures used in subsequent experiments that rely on the traditional art of quantitative analysis laboratory practice. The techniques included are: Quantitative transfer of a solid with a weighing spoon Quantitative transfer of a solid with a finger held weighing bottle Quantitative transfer of a solid with a paper strap held bottle Quantitative transfer of a solid with a spatula Examples of common quantitative weighing errors Quantitative transfer of a solid from dish to beaker to volumetric flask Quantitative transfer of a solid from dish to volumetric flask Volumetric transfer pipet A complete acid-base titration Hand technique variations The conventional view of contemporary quantitative chemical measurement tends to focus on instrumental systems, computers, and robotics. In this view, the analyst is relegated to placing standards and samples on a tray. A robotic arm delivers a sample to the analysis center, while a computer controls the analysis conditions and records the results. In spite of this, it is rare to find an analysis process that does not rely on some aspect of more traditional quantitative analysis techniques, such as careful dilution to the mark of a volumetric flask. Figure 2. Transfer of a solid with a spatula. Clearly, errors in a classical step will affect the quality of the final analysis. Because of this, it is still important for students to master the key elements of the traditional art of quantitative chemical analysis laboratory practice. Some aspects of chemical analysis, like careful rinsing to insure quantitative transfer, are often an automated part of an instrumental process that must be understood by the

  4. Electron microscopy for ultrastructural analysis and protein localization in Saccharomyces cerevisiae

    PubMed Central

    Frankl, Andri; Mari, Muriel; Reggiori, Fulvio

    2015-01-01

    The yeast Saccharomyces cerevisiae is a key model system for studying of a multitude of cellular processes because of its amenability to genetics, molecular biology and biochemical procedures. Ultrastructural examinations of this organism, though, are traditionally difficult because of the presence of a thick cell wall and the high density of cytoplasmic proteins. A series of recent methodological and technical developments, however, has revived interest in morphological analyses of yeast (e.g. 123). Here we present a review of established and new methods, from sample preparation to imaging, for the ultrastructural analysis of S. cerevisiae. We include information for the use of different fixation methods, embedding procedures, approaches for contrast enhancement, and sample visualization techniques, with references to successful examples. The goal of this review is to guide researchers that want to investigate a particular process at the ultrastructural level in yeast by aiding in the selection of the most appropriate approach to visualize a specific structure or subcellular compartment. PMID:28357267

  5. Histologic and ultrastructural analysis of melasma after fractional resurfacing.

    PubMed

    Goldberg, David J; Berlin, Alexander L; Phelps, Robert

    2008-02-01

    Fractional photothermolysis is a popular treatment option for photodamaged skin and other cutaneous conditions. Recently, successful improvement in melasma has been achieved with this laser system. We undertook this study to evaluate the ultrastructural changes associated with fractional laser treatment of melasma. Ten subjects with skin types III and IV and a clinical diagnosis of epidermal melasma were treated with a 1,550-nm erbium:glass laser delivering light in a fractional manner (Fraxel SR 750, Reliant Technologies, Inc., Mountain View, CA) every 2 weeks for a total of four sessions. Biopsies were obtained from all subjects both before treatment and at 3 months following the final treatment. All biopsies were analyzed by light and electron microscopy for treatment-induced changes. In addition, a secondary endpoint of the study was to assess for clinical improvement in melasma following fractional resurfacing. This assessment was performed by the investigator using pre- and post-treatment photographs. Light microscopy on post-treatment specimens showed a relative decrease in melanocytes compared to the pre-treatment ones. Post-treatment electron microscopy revealed fewer melanocytes and a relative absence of melanin in the surrounding keratinocytes compared to pre-treatment specimens. In addition, six subjects with skin type III were determined to have good improvement, whereas four subjects with skin type IV had fair improvement, as assessed by the investigator. Post-treatment ultrastructural changes are consistent with an elimination process and may help to explain clinical improvement following laser treatment.

  6. Quantitative analysis of PET studies.

    PubMed

    Weber, Wolfgang A

    2010-09-01

    Quantitative analysis can be included relatively easily in clinical PET-imaging protocols, but in order to obtain meaningful quantitative results one needs to follow a standardized protocol for image acquisition and data analysis. Important factors to consider are the calibration of the PET scanner, the radiotracer uptake time and the approach for definition of regions of interests. Using such standardized acquisition protocols quantitative parameters of tumor metabolism or receptor status can be derived from tracer kinetic analysis and simplified approaches such as calculation of standardized uptake values (SUVs).

  7. Quantitative analysis in megageomorphology

    NASA Technical Reports Server (NTRS)

    Mayer, L.

    1985-01-01

    Megageomorphology is the study of regional topographic features and their relations to independent geomorphic variables that operate at the regional scale. These independent variables can be classified as either tectonic or climatic in nature. Quantitative megageomorphology stresses the causal relations between plate tectonic factors and landscape features or correlations between climatic factors and geomorphic processes. In addition, the cumulative effects of tectonics and climate on landscape evolution that simultaneously operate in a complex system of energy transfer is of interst. Regional topographic differentiation, say between continents and ocean floors, is largely the result of the different densities and density contrasts within the oceanic and continental lithosphere and their isostatic consequences. Regional tectonic processes that alter these lithospheric characteristics include rifting, collision, subduction, transpression and transtension.

  8. Studies on the neuronal Golgi apparatus-complex. I. Quantitative ultrastructural autoradiographic analysis of the endocytosis into the Golgi complex of wheat germ agglutinin by cultured murine neuroblastoma cells. II. Identification of a 160 Kd polypeptide of the medial cisterns of the Golgi complex

    SciTech Connect

    Mezitis, S.G.E.

    1987-01-01

    An ultrastructural autoradiographic method is presented which quantitates the sequential endocytosis of tritiated wheat germ agglutinin (N-(acetyl-/sup 3/H)-WGA) into the Golgi complex and lysosomes of cultured murine neuroblastoma cells. Cells were incubated with /sup 3/H-WGA for one hour at 4/sup 0/C, washed and incubated in complete medium without ligand at 37/sup 0/C for 5, 15, 30, and 120 minutes. At 15 minutes, the optimized sources/..mu..m/sup 2/ of neuroblastoma cell area, which represented the grain density of each compartment, were: Golgi associated vesicles, i.e. clusters of vesicles within a one micron radius of the Golgi cisterns, (1.41 + -0.28), Golgi cisterns (0.73 + -0.41), lysosomes (0.1 + -0.09); at two hours, Golgi associated vesicles exhibited some labeling ((0.71 + -0.1), while lysosomes were heavily labeled (2.17 + -0.22). These results are consistent with the hypotheses that either the Golgi complex (cisterns and associated vesicles) is an early and intermediate step of the endocytosis of /sup 3/H-WGA into lysosomes, or that it constitutes part of a separate and quantitatively significant pathway of endocytosis of this ligand.

  9. Quantitative ultrastructural evidence of alterations in prolactin secretion related to external salinity in a teleost fish (Poecilia latipinna).

    PubMed

    Batten, T F; Ball, J N

    1977-11-30

    Quantitative ultrastructural morphometric studies were made on the prolactin cells of Poecilia latipinna adapted to freshwater (FW), one-third seawater (1/3 SW) and full-strength seawater (SW), and at various times after transfers between 1/3 SW and FW. In fully-adapted fish the rates of prolactin (PRL) synthesis and PRL release are inversely related to environmental salinity. During adaptation to a new salinity the two rates are temporarily uncoordinated, with release increasing or decreasing more readily than synthesis. Synthesis appears to take 30 h or longer to come into balance with the increased release rate following transfer from 1/3 SW to FW, and 72 h or longer to adjust to the reduction in release rate that follows the reverse transfer. The excess PRL granules that accumulate in the latter situation appear to be removed by lysosomal digestion. As in other teleosts, in fish adapted to the external medium the size of the stored PRL granules is inversely related to external salinity, but this relationship breaks down during adaptation to a new salinity. The stellate cells which penetrate between the PRL cells are more prominent, more extensively ramified, and appear more metabolically active in FW-adapted fish than in the other groups. These cells seem to be closely related in function to the secretory activity of the PRL cells.

  10. Ultrastructural analysis of megakaryocytes in GPV knockout mice.

    PubMed

    Poujol, C; Ramakrishnan, V; DeGuzman, F; Nurden, A T; Phillips, D R; Nurden, P

    2000-08-01

    Lesions in the genes for GPIb alpha, GPIb beta or GPIX result in a bleeding diathesis, the Bernard-Soulier syndrome (BSS), which associates a platelet adhesion defect with thrombocytopenia, giant platelets and abnormal megakaryocytes (MK). The role of GPV, also absent in BSS, was recently addressed by gene targeting in mice. While a negative modulator function for GPV on thrombin-induced platelet responses was found in one model, the absence of GP V had no effect on GPIb-IX expression or platelet adhesion. Our study extends previous results and reports that electron microscopy of bone marrow from the GPV knockout mice revealed a normal MK ultrastructure and development of the demarcation membrane system (DMS). There was a usual presence of MK fragments in the bone marrow vascular sinus. Immunogold labelling of MK from the knockout mice showed a normal distribution of GPIb-IX in the DMS and on the cell surface. The distribution of fibrinogen, vWF and P-selectin was unchanged with, interestingly, P-selectin also localised within the DMS in both situations. Thus GPV is not crucial to MK development and platelet production, consistent with the fact that no mutation in the GPV gene has as yet been described in BSS.

  11. Effect of thyroparathyroidectomy (TPX) on the zona reticularis: a quantitative ultrastructural study.

    PubMed

    Conran, R M; Nickerson, P A

    1979-07-01

    Atrophy of zona reticularis cells was observed two weeks after surgical thyroparathyroidectomy (TPX). Quantitative morphological techniques for electron microscopy showed significant decreases in the volume of cytoplasm, nucleus, mitochondria, smooth endoplasmic reticulum and lipid droplets in the zona reticularis of TPX rats. In addition, many mitochnodria contained lipid droplets, some of which occupied virtually the entire matrix of mitochondria. The volume per cell of mitochondria with these inclusions increased significantly after TPX. The lipid droplets may well arise from cytoplasmic droplets by increased transport or reduced metabolism of cholesterol, or by direct incorporation of droplets into the mitochondrial matrix. The serum corticosterone level of TPX rats sacrificed under quiescent conditions did not differ significantly from that of controls. Hypothyroidism induced a significant increase in the volume of peroxisomes per cell in TPX animals which may be related to changes in lipid metabolism or transport.

  12. Ultrastructural analysis of adult mouse neocortex comparing aldehyde perfusion with cryo fixation

    PubMed Central

    Korogod, Natalya; Petersen, Carl CH; Knott, Graham W

    2015-01-01

    Analysis of brain ultrastructure using electron microscopy typically relies on chemical fixation. However, this is known to cause significant tissue distortion including a reduction in the extracellular space. Cryo fixation is thought to give a truer representation of biological structures, and here we use rapid, high-pressure freezing on adult mouse neocortex to quantify the extent to which these two fixation methods differ in terms of their preservation of the different cellular compartments, and the arrangement of membranes at the synapse and around blood vessels. As well as preserving a physiological extracellular space, cryo fixation reveals larger numbers of docked synaptic vesicles, a smaller glial volume, and a less intimate glial coverage of synapses and blood vessels compared to chemical fixation. The ultrastructure of mouse neocortex therefore differs significantly comparing cryo and chemical fixation conditions. DOI: http://dx.doi.org/10.7554/eLife.05793.001 PMID:26259873

  13. Ultrastructural analysis of cell component distribution in the apical cell of Ceratodon protonemata

    NASA Technical Reports Server (NTRS)

    Walker, L. M.; Sack, F. D.

    1995-01-01

    A distinctive feature of tip-growing plant cells is that cell components are distributed differentially along the length of the cell, although most ultrastructural analyses have been qualitative. The longtitudinal distribution of cell components was studied both qualitatively and quantitatively in the apical cell of dark-grown protonemata of the moss Ceratodon. The first 35 micrometers of the apical cell was analyzed stereologically using transmission electron microscopy. There were four types of distributions along the cell's axis, three of them differential: (1) tubular endoplasmic reticulum was evenly distributed, (2) cisternal endoplasmic reticulum and Golgi vesicles were distributed in a tip-to-base gradient, (3) plastids, vacuoles, and Golgi stacks were enriched in specific areas, although the locations of the enrichments varied, and (4) mitochondria were excluded in the tip-most 5 micrometers and evenly distributed throughout the remaining 30 micrometers. This study provides one of the most comprehensive quantitative, ultrastructural analyses of the distribution of cell components in the apex of any tip-growing plant cell. The finding that almost every component had its own spatial arrangement demonstrates the complexity of the organization and regulation of the distribution of components in tip-growing cells.

  14. Ultrastructural analysis of cell component distribution in the apical cell of Ceratodon protonemata

    NASA Technical Reports Server (NTRS)

    Walker, L. M.; Sack, F. D.

    1995-01-01

    A distinctive feature of tip-growing plant cells is that cell components are distributed differentially along the length of the cell, although most ultrastructural analyses have been qualitative. The longtitudinal distribution of cell components was studied both qualitatively and quantitatively in the apical cell of dark-grown protonemata of the moss Ceratodon. The first 35 micrometers of the apical cell was analyzed stereologically using transmission electron microscopy. There were four types of distributions along the cell's axis, three of them differential: (1) tubular endoplasmic reticulum was evenly distributed, (2) cisternal endoplasmic reticulum and Golgi vesicles were distributed in a tip-to-base gradient, (3) plastids, vacuoles, and Golgi stacks were enriched in specific areas, although the locations of the enrichments varied, and (4) mitochondria were excluded in the tip-most 5 micrometers and evenly distributed throughout the remaining 30 micrometers. This study provides one of the most comprehensive quantitative, ultrastructural analyses of the distribution of cell components in the apex of any tip-growing plant cell. The finding that almost every component had its own spatial arrangement demonstrates the complexity of the organization and regulation of the distribution of components in tip-growing cells.

  15. Software for quantitative trait analysis.

    PubMed

    Almasy, Laura; Warren, Diane M

    2005-09-01

    This paper provides a brief overview of software currently available for the genetic analysis of quantitative traits in humans. Programs that implement variance components, Markov Chain Monte Carlo (MCMC), Haseman-Elston (H-E) and penetrance model-based linkage analyses are discussed, as are programs for measured genotype association analyses and quantitative trait transmission disequilibrium tests. The software compared includes LINKAGE, FASTLINK, PAP, SOLAR, SEGPATH, ACT, Mx, MERLIN, GENEHUNTER, Loki, Mendel, SAGE, QTDT and FBAT. Where possible, the paper provides URLs for acquiring these programs through the internet, details of the platforms for which the software is available and the types of analyses performed.

  16. Software for quantitative trait analysis

    PubMed Central

    2005-01-01

    This paper provides a brief overview of software currently available for the genetic analysis of quantitative traits in humans. Programs that implement variance components, Markov Chain Monte Carlo (MCMC), Haseman-Elston (H-E) and penetrance model-based linkage analyses are discussed, as are programs for measured genotype association analyses and quantitative trait transmission disequilibrium tests. The software compared includes LINKAGE, FASTLINK, PAP, SOLAR, SEGPATH, ACT, Mx, MERLIN, GENEHUNTER, Loki, Mendel, SAGE, QTDT and FBAT. Where possible, the paper provides URLs for acquiring these programs through the internet, details of the platforms for which the software is available and the types of analyses performed. PMID:16197737

  17. In vivo MRI analysis of depth-dependent ultrastructure in human knee cartilage at 7 T.

    PubMed

    Garnov, Nikita; Gründer, Wilfried; Thörmer, Gregor; Trampel, Robert; Turner, Robert; Kahn, Thomas; Busse, Harald

    2013-11-01

    Signal intensities of T2-weighted magnetic resonance images depend on the local fiber arrangement in hyaline cartilage. The aims of this study were to determine whether angle-sensitive MRI at 7 T can be used to quantify the cartilage ultrastructure of the knee in vivo and to assess potential differences with age. Ten younger (21-30) and ten older (55-76 years old) healthy volunteers were imaged with a T2-weighted spin-echo sequence in a 7 T whole-body MRI. A "fascicle" model was assumed to describe the depth-dependent fiber arrangement of cartilage. The R/T boundary positions between radial and transitional zones were assessed from intensity profiles in small regions of interest in the femur and tibia, and normalized to cartilage thickness using logistic curve fits. The quality of our highly resolved (0.3 × 0.3 × 1.0 mm(3)) MR cartilage images were high enough for quantitative analysis (goodness of fit R(2) = 0.91 ± 0.09). Between younger and older subjects, normalized positions of the R/T boundary, with value 0 at the bone-cartilage interface and 1 at the cartilage surface, were significantly (p < 0.05) different in femoral (0.51 ± 0.12 versus 0.41 ± 0.10), but not in tibial cartilage (0.65 ± 0.11 versus 0.57 ± 0.09, p = 0.119). Within both age groups, differences between femoral and tibial R/T boundaries were significant. Using a fascicle model and angle-sensitive MRI, the depth-dependent anisotropic fiber arrangement of knee cartilage could be assessed in vivo from a single 7 T MR image. The derived quantitative parameter, thickness of the radial zone, may serve as an indicator of the structural integrity of cartilage. This method may potentially be suitable to detect and monitor early osteoarthritis because the progressive disintegration of the anisotropic network is also indicative of arthritic changes in cartilage. Copyright © 2013 John Wiley & Sons, Ltd.

  18. Ultrastructural Analysis of Leishmania infantum chagasi Promastigotes Forms Treated In Vitro with Usnic Acid

    PubMed Central

    da Luz, João S. B.; de Oliveira, Erwelly B.; Martins, Monica C. B.; da Silva, Nicácio H.; Alves, Luiz C.; dos Santos, Fábio A. B.; da Silva, Luiz L. S.; Silva, Eliete C.; de Medeiros, Paloma L.

    2015-01-01

    Leishmaniasis is considered by the World Health Organization as one of the infectious parasitic diseases endemic of great relevance and a global public health problem. Pentavalent antimonials used for treatment of this disease are limited and new phytochemicals emerge as an alternative to existing treatments, due to the low toxicity and cost reduction. Usnic acid is uniquely found in lichens and is especially abundant in genera such as Alectoria, Cladonia, Evernia, Lecanora, Ramalina, and Usnea. Usnic acid has been shown to exhibit antiviral, antiprotozoal, antiproliferative, anti-inflammatory, and analgesic activity. The aim of this study was to evaluate the antileishmanial activity of usnic acid on Leishmania infantum chagasi promastigotes and the occurrence of drug-induced ultrastructural damage in the parasite. Usnic acid was effective against the promastigote forms (IC50 = 18.30 ± 2.00 µg/mL). Structural and ultrastructural aspects of parasite were analyzed. Morphological alterations were observed as blebs in cell membrane and shapes given off, increasing the number of cytoplasmic vacuoles, and cellular and mitochondrial swelling, with loss of cell polarity. We concluded that the usnic acid presented antileishmanial activity against promastigote forms of Leishmania infantum chagasi and structural and ultrastructural analysis reinforces its cytotoxicity. Further, in vitro studies are warranted to further evaluate this potential. PMID:25767824

  19. Ultrastructural analysis of microfilariae of Wuchereria bancrofti obtained from persistent carriers after repeated courses of diethylcarbamazine.

    PubMed

    Alves, L C; Cavalcanti, M G S; Araújo, H R C; Silva, G M; Veras, D L; Paiva, M H S; Brayner, F A

    2009-01-01

    Single dose of diethylcarbamazine (DEC) used in control programs is effective in breaking the transmission of filariasis. In order to investigate the effect of aggressive therapy on Wuchereria bancrofti (Wb) microfilariae, DEC was given to 29 patients who were positive for the circulating filarial antigen (CFA) assay but did not have clinical manifestations of filariasis, at 6 mg/kg/day for 12 days and again six months later using the same dosing regimen. For each patient, microfilarial density and serum CFA were followed up for two years. Ultrastructural analyses on Wb microfilariae obtained after repeated treatment with DEC were also performed. Microfilaremia and antigenemia decreased significantly after 12 months but returned to the initial levels after 24 months. This could indicate, as shown by other authors, that aggressive repeated therapy with DEC alone is ineffective in eradicating adult W. bancrofti, particularly in infected but asymptomatic individuals. The objective of the present study was to analyze the microfilaremic and antigenemic behavior and ultrastructural changes caused by different DEC concentrations in vitro in Wb microfilariae obtained from individuals who were sensitive and refractory to treatment. After in vitro treatment of the microfilariae using 5 and 10 microg/ml of DEC for 1h, ultrastructural analysis revealed low levels of cell damage compared with embryos obtained from individuals from a different area who had never received DEC treatment before. The results obtained suggest that microfilariae from patients who receive repeated aggressive therapy are less sensitive to DEC in vitro.

  20. Qualitative and quantitative ultrastructural observations on retinal ganglion cell layer of rat after intraorbital optic nerve crush.

    PubMed

    Barron, K D; Dentinger, M P; Krohel, G; Easton, S K; Mankes, R

    1986-06-01

    Rat retinal ganglion cell layer (GCL) was examined ultrastructurally 1-180 days after intraorbital crushing of one optic nerve. It was confirmed quantitatively that axotomized ganglion cells lost cisternal membranes of the rough endoplasmic reticulum (RER) and showed disintegration of Nissl bodies and ribosomal rosettes 3 days postoperatively. Between 60 and 180 days after neurotomy there was partial reversion of the RER towards normal. At postoperative intervals of 14-60 days, chromatin aggregation became conspicuous and some nuclei were prominently furrowed and contained electron-dense inclusions. Concurrently, profiles of dead ganglion cells were encountered. Mean mitochondrial area increased in axotomized neurons but mitochondrial density declined, while the Golgi apparatus, lamellar specializations of the RER and the size of nuclei did not change significantly. Cytoplasmic atrophy was profound, however. Small nerve cells of the GCL appeared morphologically distinct from ganglion cells and did not undergo appreciable alteration. A decline in neuronal density, approximating 35%, occurred between the third and seventh postoperative day and progressed slowly thereafter. Neuronal density was 32% of normal 180 days postoperatively. A temporary increase in glial density 3-28 days after operation was due to microglial hyperplasia. Müller cell and astrocytic processes hypertrophied, infiltrated nerve fibre bundles, and surrounded and intruded into neuronal somata. Bundles of unmyelinated small axons, invested by astrocytes and basal lamina, were present within the necrotic cavity of the lesioned nerve 28-90 days postoperatively and had cytologic features of regenerative axonal sprouts. We conclude that intraorbital optic nerve crush is followed by a noteworthy degree of regenerative axonal sprouting which occurs and persists against a background of slow but relentless decline in the retinal ganglion cell population. This slow decline follows a rapidly-sustained loss

  1. Quantitative analysis of glycated proteins.

    PubMed

    Priego-Capote, Feliciano; Ramírez-Boo, María; Finamore, Francesco; Gluck, Florent; Sanchez, Jean-Charles

    2014-02-07

    The proposed protocol presents a comprehensive approach for large-scale qualitative and quantitative analysis of glycated proteins (GP) in complex biological samples including biological fluids and cell lysates such as plasma and red blood cells. The method, named glycation isotopic labeling (GIL), is based on the differential labeling of proteins with isotopic [(13)C6]-glucose, which supports quantitation of the resulting glycated peptides after enzymatic digestion with endoproteinase Glu-C. The key principle of the GIL approach is the detection of doublet signals for each glycated peptide in MS precursor scanning (glycated peptide with in vivo [(12)C6]- and in vitro [(13)C6]-glucose). The mass shift of the doublet signals is +6, +3 or +2 Da depending on the peptide charge state and the number of glycation sites. The intensity ratio between doublet signals generates quantitative information of glycated proteins that can be related to the glycemic state of the studied samples. Tandem mass spectrometry with high-energy collisional dissociation (HCD-MS2) and data-dependent methods with collision-induced dissociation (CID-MS3 neutral loss scan) are used for qualitative analysis.

  2. Bioimaging for quantitative phenotype analysis.

    PubMed

    Chen, Weiyang; Xia, Xian; Huang, Yi; Chen, Xingwei; Han, Jing-Dong J

    2016-06-01

    With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses.

  3. Identification of focal viral infections by confocal microscopy for subsequent ultrastructural analysis.

    PubMed

    Miller, S E; Levenson, R M; Aldridge, C; Hester, S; Kenan, D J; Howell, D N

    1997-01-01

    A correlative microscopy method for the ultrastructural analysis of focal viral tissue infections is presented. Using a confocal scanning laser microscope, foci of infection are identified in tissue sections prior to embedment; a variety of techniques can be employed for viral detection, including staining with standard histochemical reagents and fluorescently labeled antibodies. Areas of infection identified using confocal microscopy are excised from the tissue sections, embedded, and examined by transmission electron microscopy. Applications of this technique in both diagnostic and basic research settings are described.

  4. Intraoral Laser Welding (ILW): ultrastructural and mechanical analysis

    NASA Astrophysics Data System (ADS)

    Fornaini, Carlo; Passaretti, Francesca; Villa, Elena; Nammour, Samir

    2010-05-01

    Nd:YAG, currently used since 1970 in dental laboratories to weld metals on dental prostheses has some limits such great dimensions, high costs and fixed delivery system. Recently it was proposed the possibility to use the Nd:YAG laser device commonly utilised in dental office, to repair broken fixed, removable and orthodontic prostheses and to weld metals directly into the mouth. The aim of this work is to value, through SEM (Scanning Electron Microscope), EDS (Energy Dispersive X-Ray Spectroscopy) and DMA (Dynamic Mechanical Analysis), quality and mechanical strength of the welding process comparing a device normally used in dental lab and a device normally used in dental office for oral surgery. Sixteen CoCrMo metal plates and twenty steel orthodontic wires were divided in four groups: one was welded without metal apposition by laboratory laser, one was welded with metal apposition by laboratory laser, one was welded without metal apposition by office laser and one was welded with metal apposition by office laser. The welding process was analysed by SEM, EDS and DMA to compare the differences between the different samples. By SEM analysis it was seen that the plates welded by office laser without apposition metal showed a greater number of fissurations compared with the other samples. By EDS analysis it was seen a homogeneous composition of the metals in all the samples. The mechanical tests showed a similar elastic behaviour of the samples, with minimal differences between the two devices. No wire broke even under the maximum strength by the Analyser. This study seems to demonstrate that the welding process by office Nd:YAG laser device and the welding process by laboratory Nd:YAG laser device, analysed by SEM, EDS and DMA, showed minimal and not significant differences even if these data will be confirmed by a greater number of samples.

  5. Ultrastructural and biochemical analysis of fibrinogen receptors on activated thrombocytes

    SciTech Connect

    O'Toole, E.T.

    1989-01-01

    The present studies have been concerned with the role of fibrinogen and its receptor, GP IIb/IIIa, during the activation and early aggregation of pigeon thrombocytes. Thrombocytes were surface labeled with {sup 125}I then separated on SDS-PAGE. Analysis by gel autoradiography revealed major bands at MW 145 kd and 98 kd, which corresponded to human GPIIb and GPIIIa. Immunologic similarity of the pigeon and human receptor components was established by dot blot analysis using polyclonal antibodies directed against human GPIIb and GPIIIa. Pigeon fibrinogen, isolated by plasma precipitation with PEG-1000 and purified over Sepharose 4B, was used to study receptor-ligand interaction. Separation of pigeon fibrinogen on SDS-PAGE resulted in three peptides having apparent MW of 62kd, 55kd, and 47kd which are comparable to human fibrinogen. Further similarity of human and pigeon fibrinogen was verified by immonodiffusion against an antibody specific for the human protein. The role of fibrinogen and its receptor in thrombocyte function was established by turbidimetric aggregation using thrombin as an agonist under conditions requiring Ca++ and fibrinogen.

  6. Bone impairment in oxalosis: An ultrastructural bone analysis.

    PubMed

    Bacchetta, Justine; Farlay, Delphine; Abelin-Genevois, Kariman; Lebourg, Ludivine; Cochat, Pierre; Boivin, Georges

    2015-12-01

    Deposition of calcium oxalate crystals in the kidney and bone is a hallmark of systemic oxalosis. Since the bone compartment can store massive amounts of oxalate, patients present with recurrent low-trauma fractures, bone deformations, severe bone pains and specific oxalate osteopathy on plain X-ray. Bone biopsy from the iliac crest displays specific features such as oxalate crystals surrounded by a granulomatous reaction due to an invasion of bone surface by macrophages. We present data obtained in 10 samples from 8 patients with oxalosis (16-68 years) who underwent iliac crest bone biopsy and bone quality analysis using modern methods (microradiography, microindentation, Fourier Transform InfraRed Microspectroscopy, transmission electron microscopy) in addition to histomorphometry. Disseminated calcium oxalate deposits (whewellite) were found in the bone marrow space (with a granulomatous reaction) but not in the bone matrix. Calcium oxalate deposits were totally surrounded by macrophages and multinucleated giant cells, and a phagocytosis activity was sometimes observed. Very few calcium oxalate crystals were directly in close contact with the mineral substance of the bone. Bone mineralization was not modified by the presence of calcium oxalate even in close vicinity. Bone quality analysis also revealed a harder bone than normal, perhaps in relationship with decreased carbonate content in the mineral. This increase in bone hardness could explain a more "brittle" bone. In patients with oxalosis, the formation and growth of calcium oxalate crystals in the bone appeared independent of apatite. The mechanisms leading to nucleation and growth of oxalate deposits are still unclear and deserve further studies.

  7. Ultrastructural, Elemental and Mineralogical Analysis of Vascular Calcification in Atherosclerosis.

    PubMed

    Perrotta, Ida; Perri, Edoardo

    2017-09-06

    Over the past few decades, remarkable progress has been achieved in terms of understanding the molecular and cellular mechanisms of atherosclerotic vascular calcification and the important role of matrix vesicles in initiating and propagating pathologic tissue mineralization has been widely recognized. Despite these recent advances, however, no definitive data are currently available regarding the texture and composition of the minerals that grow in the vessel wall during the course of the disease. Using different electron microscopy imaging and analysis, we demonstrate that vascular cells can produce and secrete more than one type of matrix vesicles which act as sites for initial mineral deposition independently of their structural features. Our results reveal that apatite formation in the atherosclerotic lesions of the human aorta occur through the deposition of amorphous calcium phosphate that matures over time, transforms into crystalline hydroxyapatite, and radiates towards the lumen of the vesicles, finally forming the calcified spherules. Elemental and mineralogical analyses also demonstrate that the presence of mature and stable amorphous calcium phosphate deposits in the affected tissues is linked to the incorporation of magnesium, which probably delay the conversion to the crystalline phase. Though more rarely, the presence of calcium oxalate crystals has been also documented.

  8. Ultrastructural and biochemical analysis of the effects of alendronate on salivary glands of young rats.

    PubMed

    Oliveira, Taís C; Bradaschia-Correa, Vivian; Castro, Juliana R; Simões, Alyne; Arana-Chavez, Victor E

    2014-12-01

    The bisphosphonates are drugs known by their antiresorptive potency and are widely prescribed for treating and preventing osteoporosis. In the past years the employment of this class of drugs had spread to other pathologies, and it is being prescribed to patients in a wide range of ages. Some adverse effects of bisphosphonate treatment have been highlighted recently, however, little is known about its potential side effects in salivary glands. Newborn rats received daily doses of 2.5mg/kg/day of sodium alendronate during 30 days. On the thirtieth day the animals were stimulated with pilocarpine and their parotid and submandibular glands were collected, fixed and embedded for histological and ultrastructural analysis. Some glands were collected for analysis of protein content and amylase activity. At light microscopy, the alendronate-treated animals presented an accumulation of secretion granules in their cytoplasm, which was confirmed by the ultrastructural examination. Biochemical analysis revealed an increase in total protein content and decreased amylase levels of both glands in the alendronate-treated animals in relation to the control. Based on the current findings, alendronate is probably interfering in secretory pathways of parotid and submandibular glands. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Analysis of the changes in the basal cell region of oral lichen planus: An ultrastructural study

    PubMed Central

    Paul, Mayura; Shetty, Devi Charan

    2013-01-01

    Context: Oral lichen planus (OLP) affects 0.5-1% of the total world's population. The histological features of oral lichen planus were first described by Dubreuill in 1906. Despite the advent of various techniques, the etiology of lichen planus remains obscure, although many theories for the etiology have been proposed. Aims: By studying OLP electron microscopically, we shall be emphasizing on the cells and its interactions in specific/altered surroundings which would help us in hypothesizing the effects of its specific cell-to-cell interactions. Materials and Methods: A total of 20 cases of oral lichen planus were selected and categorized into erosive and nonerosive forms based upon clinical pattern and confirmed as lichen planus by histopathological analysis. Tissue specimens thus obtained were cut into two halves and fixed in appropriate fixatives, i.e., neutral buffered formalin for paraffin-embedded hematoxylin and eosin stained sections and 2.5% glutaraldehyde and 2% paraformaldehyde for electron microscopic purpose respectively. Results: Ultrastructural comparison among the two forms showed significant differences between them. The basal layer showed cytoplasmic processes, intercellular spaces, desmosomes, nuclei, and signs of degeneration. The erosive form showed elongated, narrow or irregular cytoplasmic projections whereas the nonerosive showed short and broad based projections. Conclusions: The present study confirms the ultrastructural findings of basal cells in OLP with previous authors findings. Besides this, the categorization of the ultrastructural differences between erosive and nonerosive has raised the question of difference in the probable cellular and molecular mechanism between erosive and nonerosive forms. PMID:23798823

  10. Structural and Ultrastructural Analysis of the Cervical Discs of Young and Elderly Humans.

    PubMed

    Fontes, Ricardo Braganca de Vasconcellos; Baptista, Josemberg Silva; Rabbani, Said Rahnamaye; Traynelis, Vincent C; Liberti, Edson Aparecido

    2015-01-01

    Several studies describing the ultrastructure and extracellular matrix (ECM) of intervertebral discs (IVDs) involve animal models and specimens obtained from symptomatic individuals during surgery for degenerative disease or scoliosis, which may not necessarily correlate to changes secondary to normal aging in humans. These changes may also be segment-specific based on different load patterns throughout life. Our objective was to describe the ECM and collagen profile of cervical IVDs in young (G1 - <35 years) and elderly (G2 - >65 years) presumably-asymptomatic individuals. Thirty cervical discs per group were obtained during autopsies of presumably-asymptomatic individuals. IVDs were analyzed with MRI, a morphological grading scale, light microscopy, scanning electron microscopy (SEM) and immunohistochemistry (IHC) for collagen types I, II, III, IV, V, VI, IX and X. Macroscopic degenerative features such as loss of annulus-nucleus distinction and fissures were found in both groups and significantly more severe in G2 as expected. MRI could not detect all morphological changes when compared even with simple morphological inspection. The loose fibrocartilaginous G1 matrix was replaced by a denser ECM in G2 with predominantly cartilaginous characteristics, chondrocyte clusters and absent elastic fibers. SEM demonstrated persistence of an identifiable nucleus and Sharpey-type insertion of cervical annulus fibers even in highly-degenerated G2 specimens. All collagen types were detected in every disc sector except for collagen X, with the largest area stained by collagens II and IV. Collagen detection was significantly decreased in G2: although significant intradiscal differences were rare, changes may occur faster or earlier in the posterior annulus. These results demonstrate an extensive modification of the ECM with maintenance of basic ultrastructural features despite severe macroscopic degeneration. Collagen analysis supports there is not a "pathologic" collagen type

  11. Quantitative analysis of retinal OCT.

    PubMed

    Sonka, Milan; Abràmoff, Michael D

    2016-10-01

    Clinical acceptance of 3-D OCT retinal imaging brought rapid development of quantitative 3-D analysis of retinal layers, vasculature, retinal lesions as well as facilitated new research in retinal diseases. One of the cornerstones of many such analyses is segmentation and thickness quantification of retinal layers and the choroid, with an inherently 3-D simultaneous multi-layer LOGISMOS (Layered Optimal Graph Image Segmentation for Multiple Objects and Surfaces) segmentation approach being extremely well suited for the task. Once retinal layers are segmented, regional thickness, brightness, or texture-based indices of individual layers can be easily determined and thus contribute to our understanding of retinal or optic nerve head (ONH) disease processes and can be employed for determination of disease status, treatment responses, visual function, etc. Out of many applications, examples provided in this paper focus on image-guided therapy and outcome prediction in age-related macular degeneration and on assessing visual function from retinal layer structure in glaucoma.

  12. Ultrastructural analysis of rat articular cartilage following treatment with dexamethasone and glycosaminoglycan-peptide complex.

    PubMed

    Annefeld, M; Erne, B; Rasser, Y

    1990-01-01

    This ultrastructural study describes a stereological analysis of rat articular cartilage, with and without exposure to dexamethasone and a chondroprotective drug used in the treatment of osteoarthritis. Normal rat cartilage was found to contain 27.6 x 10(4) chondrocytes/mm3 which occupied approximately 10% of the cartilage tissue, and the organelle content of each chondrocyte was calculated to be about 20% of the cytoplasmic volume. After 3 weeks of treatment with dexamethasone the chondrocytic volume was increased by 23% with a proportionate increase in the cellular volume of the whole cartilage, and in addition the organelle content was significantly reduced to about half that of the control chondrocytes. By contrast the administration of GP-C (RUMALON) to dexamethasone-treated animals reduced these steroid effects. No significant change was seen in the total chondrocyte numbers with either of the treatments. Whereas dexamethasone inhibits chondrocyte metabolism and produces concomitant ultrastructural changes, GP-C was found to counteract these effects, a result which supports the contention that GP-C helps to preserve chondrocyte function.

  13. A quantitative ultrastructural comparison of alpha and gamma motoneurons in the thoracic region of the spinal cord of the adult cat.

    PubMed

    Johnson, I P

    1986-08-01

    The cell bodies of motoneurons supplying both the levator costae and external intercostal muscles were identified after retrograde labelling with horseradish peroxidase. A quantitative ultrastructural comparison of cell bodies of large (greater than 40 microns) and small (less than 30 microns) diameter revealed that the intracellular appearance of large and small motoneurons was similar. However, small motoneurons had less than half the synaptic terminal frequency or cover of large motoneurons. Furthermore, only synapses of the S- and F-type were seen on small motoneurons, while S- T- F- and C-type terminals were consistently seen on large motoneurons. The variation between individual small motoneurons for various aspects of their synaptic features was more than twice that found for large motoneurons. No correlation between small motoneuronal ultrastructure and cell body diameter was found, although scatter diagrams of synaptic terminal cover against cell body size indicated the presence of two groups of small motoneurons: one with relatively high values for synaptic cover and the other with relatively low values. On the basis of the similarity of their cell body diameters to those of electrophysiologically identified alpha and gamma motoneurons, it is concluded that the large and small motoneurons examined in the present study are alpha and gamma motoneurons respectively. The synaptic difference found between alpha and gamma motoneurons is discussed in relation to both their different functional properties and the different natures of their respective peripheral targets.

  14. Quantitative analysis of endogenous compounds.

    PubMed

    Thakare, Rhishikesh; Chhonker, Yashpal S; Gautam, Nagsen; Alamoudi, Jawaher Abdullah; Alnouti, Yazen

    2016-09-05

    Accurate quantitative analysis of endogenous analytes is essential for several clinical and non-clinical applications. LC-MS/MS is the technique of choice for quantitative analyses. Absolute quantification by LC/MS requires preparing standard curves in the same matrix as the study samples so that the matrix effect and the extraction efficiency for analytes are the same in both the standard and study samples. However, by definition, analyte-free biological matrices do not exist for endogenous compounds. To address the lack of blank matrices for the quantification of endogenous compounds by LC-MS/MS, four approaches are used including the standard addition, the background subtraction, the surrogate matrix, and the surrogate analyte methods. This review article presents an overview these approaches, cite and summarize their applications, and compare their advantages and disadvantages. In addition, we discuss in details, validation requirements and compatibility with FDA guidelines to ensure method reliability in quantifying endogenous compounds. The standard addition, background subtraction, and the surrogate analyte approaches allow the use of the same matrix for the calibration curve as the one to be analyzed in the test samples. However, in the surrogate matrix approach, various matrices such as artificial, stripped, and neat matrices are used as surrogate matrices for the actual matrix of study samples. For the surrogate analyte approach, it is required to demonstrate similarity in matrix effect and recovery between surrogate and authentic endogenous analytes. Similarly, for the surrogate matrix approach, it is required to demonstrate similar matrix effect and extraction recovery in both the surrogate and original matrices. All these methods represent indirect approaches to quantify endogenous compounds and regardless of what approach is followed, it has to be shown that none of the validation criteria have been compromised due to the indirect analyses.

  15. Three-dimensional ultrastructural analysis of cells in the periodontal ligament using focused ion beam/scanning electron microscope tomography.

    PubMed

    Hirashima, Shingo; Ohta, Keisuke; Kanazawa, Tomonoshin; Okayama, Satoko; Togo, Akinobu; Uchimura, Naohisa; Kusukawa, Jingo; Nakamura, Kei-Ichiro

    2016-12-20

    The accurate comprehension of normal tissue provides essential data to analyse abnormalities such as disease and regenerative processes. In addition, understanding the proper structure of the target tissue and its microenvironment may facilitate successful novel treatment strategies. Many studies have examined the nature and structure of periodontal ligaments (PDLs); however, the three-dimensional (3D) structure of cells in normal PDLs remains poorly understood. In this study, we used focused ion beam/scanning electron microscope tomography to investigate the whole 3D ultrastructure of PDL cells along with quantitatively analysing their structural properties and ascertaining their orientation to the direction of the collagen fibre. PDL cells were shown to be in contact with each other, forming a widespread mesh-like network between the cementum and the alveolar bone. The volume of the cells in the horizontal fibre area was significantly larger than in other areas, whereas the anisotropy of these cells was lower than in other areas. Furthermore, the orientation of cells to the PDL fibres was not parallel to the PDL fibres in each area. As similar evaluations are recognized as being challenging using conventional two-dimensional methods, these novel 3D findings may contribute necessary knowledge for the comprehensive understanding and analysis of PDLs.

  16. Three-dimensional ultrastructural analysis of cells in the periodontal ligament using focused ion beam/scanning electron microscope tomography

    PubMed Central

    Hirashima, Shingo; Ohta, Keisuke; Kanazawa, Tomonoshin; Okayama, Satoko; Togo, Akinobu; Uchimura, Naohisa; Kusukawa, Jingo; Nakamura, Kei-ichiro

    2016-01-01

    The accurate comprehension of normal tissue provides essential data to analyse abnormalities such as disease and regenerative processes. In addition, understanding the proper structure of the target tissue and its microenvironment may facilitate successful novel treatment strategies. Many studies have examined the nature and structure of periodontal ligaments (PDLs); however, the three-dimensional (3D) structure of cells in normal PDLs remains poorly understood. In this study, we used focused ion beam/scanning electron microscope tomography to investigate the whole 3D ultrastructure of PDL cells along with quantitatively analysing their structural properties and ascertaining their orientation to the direction of the collagen fibre. PDL cells were shown to be in contact with each other, forming a widespread mesh-like network between the cementum and the alveolar bone. The volume of the cells in the horizontal fibre area was significantly larger than in other areas, whereas the anisotropy of these cells was lower than in other areas. Furthermore, the orientation of cells to the PDL fibres was not parallel to the PDL fibres in each area. As similar evaluations are recognized as being challenging using conventional two-dimensional methods, these novel 3D findings may contribute necessary knowledge for the comprehensive understanding and analysis of PDLs. PMID:27995978

  17. Quantitative ultrastructural anatomy of esophagus in different regions in the horse: effects of alternate methods of tissue processing.

    PubMed

    Slocombe, R F; Todhunter, R J; Stick, J A

    1982-07-01

    A qualitative and quantitative study was made of 2 adult horses to determine the effect of specimen preparation and the influence of anatomically separate regions on the microscopic structure of the esophagus. The effects of 3 fixative solutions (formalin, Bouin's fixative and Karnovsky's fixative) and 4 histologic staining procedures (hematoxylin and eosin, Gomori's trichrome, Laidlow's reticulum, and orcein-elastin) were compared. Density-dependent image analysis was used to compare the relative contributions of elastic and reticular fibers in esophageal connective tissue for each region. Cross-sectional dimensions of the tissue layers which comprise the esophageal wall were obtained by light microscopic measurement and were compared for each region. The mucosal surface structure was examined by scanning electron microscopy. Our results indicate that specimen preparation has significant effects on the structural integrity of esophageal tissues. Bouin's fixative was inferior to the other fixatives in this regard. Furthermore, there are extensive regional differences in esophageal microstructure. Formalin-fixed tissues stained with either hematoxylin and eosin or Gomori's trichrome appear the most suitable for routine quantitative morphologic studies of the equine esophagus.

  18. Ultrastructure and elemental analysis of Hypoxis hemerocallidea: a multipurpose medicinal plant.

    PubMed

    Afolayan, Anthony J; Otunola, Gloria A

    2014-01-01

    Herbal medicine is a popular means of medical management in some parts of the world especially in Africa. Hypoxis hemerocallidea Fisch.C.A.Mey. & Avé-Lall, also known as African potato of the Hypoxidaecae family, is one of the medicinal plants that have enjoyed long usage as an herbal medicine in South Africa. In this study, the morphology and elemental constituents of H. hemerocallidea leaf was investigated to correlate the functional role of the ultrastructure in the production of therapeutic compounds. Fresh leaves of H. hemerocallidea were prepared for analysis using standard methods. The ultrastructure and crystal deposits of the plant were assessed using scanning electron microscopy (SEM), and energy dispersive x-ray (EDX). It was observed that the leaves were characterised by multicelullar glandular and non glandular trichomes which are sparsely distributed over the entire surfaces. The glandular trichomes (GTs) in H. hemerocallidea leaf have boulbous heads which are probably filled with secretions, while the non glandular trichomes were long, fibrous and sparse. EDX-SEM of Hypoxis hemerocallidea leaf revealed that carbon, oxygen, nitrogen and silicon are the major components of the deposits, while other elements such as iron, sulphur, sodium, calcium, magnesium, potassium, manganese, iodine, chromium and iodine were present in small but variable amounts. The presence of these elements which are crucial to maintaining good health, in addition to other bioactive constituents might be accountable for the multipurpose therapeutic uses of Hypoxis hemerocallidea in the treatment of cancers, HIV/AIDS related diseases, urinary tract infections, cardiovascular disorders, diabetes and other chronic ailments of humans.

  19. Vascular innervation in human skeletal muscle with and without neuromuscular disease. A quantitative ultrastructural study with references to the effects of age and different blood pressure.

    PubMed

    Case, C P; Girling, A J

    1988-01-01

    A quantitative ultrastructural study has been made of the innervation of 461 arterioles in 114 skeletal muscle biopsies of patients with or without neuromuscular disease excluding diabetes and autonomic neuropathy. In 18 controls the number of nerves and Schwann cells around each vessel was related to the size of the vessel, whether the vessel was within a muscle fascicle or between muscle fascicles. The innervation of arterioles increased with increased diastolic blood pressure. There was no statistically significant change in innervation with increased systolic blood pressure or with age, from 4 to 85 years. In 96 cases of neuromuscular disease and especially in motor neurone disease, axonal varicosities in cross section tended to be larger, more often contained no vesicles or only a few and had altered satellite cell cover depending on the location of the arteriole. Whilst the numerical density of Schwann cells did not change with disease, fewer varicosities were identified within Schwann cells in motor neurone disease, metabolic myopathy and neuropathy and myopathy due to toxins or vascular disease. Preterminal axons in nerve fascicles adjacent to arterioles were lost in polymyositis and muscle disease due to toxins or vascular disease. In polymyositis, metabolic myopathy and motor neurone disease there was some evidence of compensatory nerve sprouting, either in the nerve fascicles or in the adventitia of the arterioles. These structural changes may be related to the changes in blood flow or vascular reactivity described by others in motor neurone disease, polymyositis and metabolic myopathy. It is concluded that the ultrastructure of the vascular innervation of human skeletal muscle is similar to that in other mammals and is changed more with increased diastolic blood pressure and neuromuscular disease than with age.

  20. Characterization of human mesenchymal stem cell-engineered cartilage: analysis of its ultrastructure, cell density and chondrocyte phenotype compared to native adult and fetal cartilage.

    PubMed

    Hillel, Alexander T; Taube, Janis M; Cornish, Toby C; Sharma, Blanka; Halushka, Marc; McCarthy, Edward F; Hutchins, Grover M; Elisseeff, Jennifer H

    2010-01-01

    The production of engineered cartilage from mesenchymal stem cells is a rapidly developing field. Potential applications include the treatment of degenerative joint disease as well as the treatment of traumatic and surgical bone injury. Prior to clinical application, however, further characterization of the morphology, ultrastructure, biocompatibility, and performance of the engineered tissue is warranted. To achieve this, human mesenchymal stem cells (hMSCs) were grown in vitro in pellet culture for 3 weeks in chondrogenic medium conditions. The resultant engineered cartilage was compared to native adult and fetal tissue. Routine histology, special stains, and ultrastructural and quantitative histomorphometric analyses were performed. The engineered tissue demonstrated a similar chondrocyte phenotype, collagen fibril appearance, and matrix distribution when compared to native cartilage. By histomorphometric analysis, the cell density of the engineered cartilage was between that of native fetal and adult cartilage. The cell-to-matrix ratio and cellular area fraction of engineered cartilage samples was significantly greater than in adult samples, but indistinguishable from fetal cartilage samples, supporting the hypothesis that hMSC-engineered cartilage regeneration may mimic fetal cartilage development.

  1. Aging effects on the mongolian gerbil female prostate (Skene's paraurethral glands): structural, ultrastructural, quantitative, and hormonal evaluations.

    PubMed

    Custodio, Ana Maria G; Santos, Fernanda C A; Campos, Silvana G P; Vilamaior, Patricia S L; Góes, Rejane M; Taboga, Sebastião R

    2008-04-01

    Different from the classic view, the prostate is not a gland exclusive to the male, also being an organ of the female genital system presenting morphofunctional similarity between human and rodent. Thus structural, ultrastructural, morphometric-stereological features of the female prostate (Skene's paraurethral gland) and steroid serological levels were evaluated during young, adult, and senile ages in the Mongolian gerbil. The morphofunctional precocity of the female gland in comparison with the male gland occurring in young gland is probably associated with the female circulating steroid levels. The hormonal imbalance in senesce coincides with its susceptibility to histopathological lesions, such as epithelial hypertrophy, metaplasia, and intraepithelial neoplasia. Differently than that of males, the aging degeneration of the female gland involves the accumulation of lipofuscin granules. However, the alterations in senile prostate did not damage its functionality. These analyses reinforce the use of this experimental model for the comprehension of glandular morphofunctional aspects with special attention to senescence. Thus, the appreciation of this organ becomes relevant to avoid future discomfort to women's health. 2008 Wiley-Liss, Inc

  2. Distribution and content of microtubules in relation to the transport of lipid. An ultrastructural quantitative study of the absorptive cell of the small intestine

    PubMed Central

    1977-01-01

    To determine whether microtubules are linked to intracellular transport in absorptive cells of the proximal intestine, quantitative ultrastructural studies were carried out in which microtubule distribution and content were determined in cells from fasting and fed animals. Rats were given a 1-h meal of standard chow, and tissue was taken from the mid-jejunum before, 1/2 h, and 6 h after the meal. The microtubule content of apical, Golgi, and basal regions of cells was quantitated by point-counting stereology. The results show) that microtubules are localized in intracellular regions of enterocytes (apical and Golgi areas) previously shown to be associated with lipid transport, and that the microtubule content within apical and Golgi regions is significantly (P less than 0.01) reduced during transport of foodstuffs. To determine the effect of inhibition of microtubule assembly on transport, colchicine or vinblastine sulfate was administered to postabsorptive rats, and the lipid and microtubule content of enterocytes determined 1 and 3 h later. After treatment with these agents, lipid was found to accumulate in apical regions of the cells; this event was associated with a significant reduction in microtubule content. In conclusion, the regional distribution of microtubules in enterocytes, the decrease in assembled microtubules after a fat-containing meal, and the accumulation of lipid after the administration of antimicrotubule agents suggest that microtubules are related to lipid transport in enterocytes. PMID:264123

  3. Quantitative analysis of glycoprotein glycans.

    PubMed

    Orlando, Ron

    2013-01-01

    The ability to quantitatively determine changes in the N- and O-linked glycans is an essential component of comparative glycomics. Multiple strategies are available to by which this can be accomplished, including; both label free approaches and isotopic labeling strategies. The focus of this chapter is to describe each of these approaches while providing insight into their strengths and weaknesses, so that glycomic investigators can make an educated choice of the strategy that is best suited for their particular application.

  4. Observation on the ultrastructure morphology of HeLa cells treated with ethanol: Statistical analysis.

    PubMed

    Al-Bagdadi, Fakhri; Young, Matthew J; Geaghan, James P; Yao, Shaomian; Barona, Humberto M; Martinez-Ceballos, Eduardo; Yoshimura, Masami

    2016-01-01

    It is estimated that 5.9% of all human deaths are attributable to alcohol consumption and that the harmful use of ethanol ranks among the top five risk factors for causing disease, disability, and death worldwide. Ethanol is known to disrupt phospholipid packing and promote membrane hemifusion at lipid bilayers. With the exception of mitochondria involved in hormone synthesis, the sterol content of mitochondrial membranes is low. As membranes that are low in cholesterol have increased membrane fluidity and are the most easily disordered by ethanol, we hypothesize that mitochondria are sensitive targets for ethanol damage. HeLa cells were exposed to 50 mM ethanol and the direct effects of ethanol on cellular ultrastructure were examined utilizing transmission electron microscopy. Our ultramicroscopic analysis revealed that cells exposed to ethanol harbor fewer incidence of apoptotic morphology; however, significant alterations to mitochondria and to nuclei occurred. We observed statistical increases in the amount of irregular cells and cells with multiple nuclei, nuclei harboring indentations, and nuclei with multiple nucleolus-like bodies. Indeed, our analysis revealed that mitochondrial damage is the most extensive type of cellular damage. Rupturing of cristae was the most prominent damage followed by mitochondrial swelling. Ethanol exposure also resulted in increased amounts of mitochondrial rupturing, organelles with linked membranes, and mitochondria localizing to indentations of nuclear membranes. We theorize that these alterations could contribute to cellular defects in oxidative phosphorylation and, by extension, the inability to generate regular levels of cellular adenosine triphosphate.

  5. The response of the macaque tracheobronchial epithelium to acute ozone injury. A quantitative ultrastructural and autoradiographic study

    SciTech Connect

    Wilson, D.W.; Plopper, C.G.; Dungworth, D.L.

    1984-08-01

    The purpose of this study was to evaluate the response of the tracheal epithelium to cytotoxic injury in a primate species that may have an epithelium more representative of that in man than smaller laboratory species. This study evaluated changes in the light-microscopic, surface, and ultrastructural appearance of the tracheobronchial epithelium of bonnet monkeys exposed for 3 or 7 days to 0.64 ppm ozone. Population densities, epithelial volumetric densities, and thymidine labeling indexes were determined for cells from posterior membranous and anterior cartilaginous trachea and mainstem bronchus. Ozone-induced epithelial changes were characterized by decreased numbers of ciliated cells, loss of cilia, and necrosis of ciliated cells. Regional differences in lesion distribution were demonstrated by scanning electron microscopy. Longitudinal streaks of ciliary loss were evident in posterior membranous trachea, but ciliary loss in the ventral trachea was most prominent over the posterior border of the cartilaginous rings. The thymidine labeling index and numbers of necrotic ciliated cells were greater after 3 days than after 7 days of continuous exposure. Foci of stratification were often associated with increased numbers of labeled nuclei in the suprabasal region of the epithelium. The results of this study suggest that small mucous granule cells and intermediate cells are important participants in the repair of chemically injured airway epithelium; stratification and increased amounts of cytoplasmic filament bundles and desmosomal attachments, rather than being evidence of squamous metaplasia or dysplastic change, might be stereotypic responses of airway epithelium to injury; and the ciliated cell population becomes less susceptible to ozone-induced necrosis with continuing exposure.

  6. Chemical, ultrastructural and supramolecular analysis of tension wood in Populus tremula x alba as a model substrate for reduced recalcitrance

    SciTech Connect

    Foston, Marcus B; Hubbell, Christopher A; Samuel, Reichel; Jung, Seung-Yong; Ding, Shi-You; Zeng, Yining; Jawdy, Sara; Sykes, Virginia R; Tuskan, Gerald A; Kalluri, Udaya C; Ragauskas, Arthur J

    2011-01-01

    Biomass is one of the most abundant potential sustainable sources for fuel and material production, however to fully realize this potential an improved understanding of lignocellulosic recalcitrance must be developed. In an effort to appreciate the underlying phenotypic, biochemical and morphological properties associated with the reduced recalcitrance observed in tension stress-induced reaction wood, we report the increased enzymatic sugar yield and corresponding chemical and ultrastructural properties of Populus tension wood. Populus tremula x alba (PTA) was grown under tension and stem segments containing three different wood types: normal wood (NW), tension wood (TW) from the elongated stem side and opposite wood (OW) from the compressed stem side were collected. A variety of analytical techniques were used to describe changes occurring as a result of the tension stress-induced formation of a gelatinous cell wall layer (G-layer). For example, gel permeation chromatography (GPC) and 13C solid-state nuclear magnetic resonance (NMR) revealed that the molecular weight and crystallinity of cellulose in TW is greater than that of cellulose acquired from NW. Whole cell ionic liquid and other solid-state NMR analysis detailed the structure of lignin and hemicellulose in the samples, detecting the presence of variations in lignin and hemicellulose sub-units, linkages and semi-quantitatively estimating the relative amounts of syringyl (S), guaiacyl (G) and p-hydroxybenzoate (PB) monolignol units. It was confirmed that TW displayed an increase in PB or H-like lignin and S to G ratio from 1.25 to 1.50 when compared to the NW sample. Scanning electron microscopy (SEM) and coherent anti-Stokes Raman scattering (CARS) were also used to evaluate the morphology and corresponding spatial distribution of the major lignocellulosic components. We found changes in a combination of cell wall properties appear to influence recalcitrance more than any single factor alone.

  7. Quantitative Analysis of Face Symmetry.

    PubMed

    Tamir, Abraham

    2015-06-01

    The major objective of this article was to report quantitatively the degree of human face symmetry for reported images taken from the Internet. From the original image of a certain person that appears in the center of each triplet, 2 symmetric combinations were constructed that are based on the left part of the image and its mirror image (left-left) and on the right part of the image and its mirror image (right-right). By applying a computer software that enables to determine length, surface area, and perimeter of any geometric shape, the following measurements were obtained for each triplet: face perimeter and area; distance between the pupils; mouth length; its perimeter and area; nose length and face length, usually below the ears; as well as the area and perimeter of the pupils. Then, for each of the above measurements, the value C, which characterizes the degree of symmetry of the real image with respect to the combinations right-right and left-left, was calculated. C appears on the right-hand side below each image. A high value of C indicates a low symmetry, and as the value is decreasing, the symmetry is increasing. The magnitude on the left relates to the pupils and compares the difference between the area and perimeter of the 2 pupils. The major conclusion arrived at here is that the human face is asymmetric to some degree; the degree of asymmetry is reported quantitatively under each portrait.

  8. Histomorphometric and ultrastructural analysis of the tendon-bone interface after rotator cuff repair in a rat model

    PubMed Central

    Kanazawa, Tomonoshin; Gotoh, Masafumi; Ohta, Keisuke; Honda, Hirokazu; Ohzono, Hiroki; Shimokobe, Hisao; Shiba, Naoto; Nakamura, Kei-ichiro

    2016-01-01

    Successful rotator cuff repair requires biological anchoring of the repaired tendon to the bone. However, the histological structure of the repaired tendon-bone interface differs from that of a normal tendon insertion. We analysed differences between the normal tendon insertion and the repaired tendon-bone interface after surgery in the mechanical properties, histomorphometric analysis, and 3-dimensional ultrastructure of the cells using a rat rotator cuff repair model. Twenty-four adult Sprague-Dawley (SD) rats underwent complete cuff tear and subsequent repair of the supraspinatus tendon. The repaired tendon-bone interface was evaluated at 4, 8, and 12 weeks after surgery. At each time point, shoulders underwent micro-computed tomography scanning and biomechanical testing (N = 6), conventional histology and histomorphometric analysis (N = 6), and ultrastructural analysis with focused ion beam/scanning electron microscope (FIB/SEM) tomography (N = 4). We demonstrated that the cellular distribution between the repaired tendon and bone at 12 weeks after surgery bore similarities to the normal tendon insertion. However, the ultrastructure of the cells at any time point had a different morphology than those of the normal tendon insertion. These morphological differences affect the healing process, partly contributing to re-tearing at the repair site. These results may facilitate future studies of the regeneration of a normal tendon insertion. PMID:27647121

  9. Development of a rapid matrix digestion technique for ultrastructural analysis of elastic fibers in the intervertebral disc.

    PubMed

    Tavakoli, Javad; Costi, John J

    2017-07-01

    Collagen and elastic fibers are two major fibrous constituents of the annulus fibrosus (AF) in the disc that contribute to its mechanical and viscoelastic properties. It was thought that elastic fibers play no substantial role in the function and properties of the disc as these fibers were irregularly distributed. Studies that have revealed highly organized elastic fibers with different regional orientation and distribution, while being strongly crosslinked with matrix, suggesting their contribution to disc structure-function properties. These studies that were performed by light microscopic analysis of histologically prepared samples, have not been able to reveal the fine-scale architectural details of the elastic fiber network. Since elastic fibers are intermingled with other fibrous components of the disc and mostly obscured by the extracellular matrix, it is difficult to demonstrate their ultra-structural organization using scanning electron microscopy (SEM). Therefore the aim of this study was to develop a rapid matrix digestion technique for ultrastructural analysis of the disc elastic fibers. This study provides a new method for fundamental visualization of elastic fibers and their architecture in the disc. Through the ultra-structural analysis, the relationship between structure and function, as well as the role of elastic fibers on AF mechanical properties can be studied. This method may be used to develop a three-dimensional map of elastic fibers distribution within the disc, which would provide valuable information for designing tissue engineered scaffolds for AF repair and replacement. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Quantitative analysis of qualitative images

    NASA Astrophysics Data System (ADS)

    Hockney, David; Falco, Charles M.

    2005-03-01

    We show optical evidence that demonstrates artists as early as Jan van Eyck and Robert Campin (c1425) used optical projections as aids for producing their paintings. We also have found optical evidence within works by later artists, including Bermejo (c1475), Lotto (c1525), Caravaggio (c1600), de la Tour (c1650), Chardin (c1750) and Ingres (c1825), demonstrating a continuum in the use of optical projections by artists, along with an evolution in the sophistication of that use. However, even for paintings where we have been able to extract unambiguous, quantitative evidence of the direct use of optical projections for producing certain of the features, this does not mean that paintings are effectively photographs. Because the hand and mind of the artist are intimately involved in the creation process, understanding these complex images requires more than can be obtained from only applying the equations of geometrical optics.

  11. Ultrastructural analysis of guided nerve regeneration using progesterone- and pregnenolone-loaded chitosan prostheses.

    PubMed

    Chávez-Delgado, M E; Gomez-Pinedo, U; Feria-Velasco, A; Huerta-Viera, M; Castañeda, S Castro; Toral, F A López-Dellamary; Parducz, A; Anda, S Luquín-De; Mora-Galindo, J; García-Estrada, J

    2005-07-01

    Recently, numerous guide chambers for the treatment of injured nerves made up of different biomaterials have been designed, capable of hosting living cells or carrying neurotrophic or neuroactive substances to be directly released to the injured tissue. In this study, chitosan prostheses containing neurosteroids (progesterone and pregnenolone) were used for bridging a 10-mm gap in the rabbit facial nerve. Gas chromatography was used to quantify neurosteroid content in the prostheses prior to and after subcutaneous implantation at different periods of up to 60 days. The regeneration of the nerve fibers were evaluated at 15 and 45 days after axotomy by means of ultrastructural morphometric analysis. Different nerve fibers regenerative patterns were seen depending the groups studied and the analyzed stages. At 15 days after axotomy, the newly regenerating tissue revealed Schwann cells holding nonmyelinated nerve fiber bundles in an incipient and organized regenerative pattern. At 45 days, the regenerating tissue showed myelinated nerve fibers of different sizes, shapes, and myelin sheath thickness. Although the regeneration of the nerve fibers under neurosteroid treatment showed statistically significant differences in comparison with vehicle regenerated tissue, progesterone-loaded chitosan prostheses produced the best guided nerve regeneration response. These findings indicate that chitosan prostheses allowed regeneration of nerve fibers in their lumen, and when containing neurosteroids produced a faster guided nerve regeneration acting as a long-lasting release delivery vehicle.

  12. Neurogenesis, gliogenesis and the developing chicken optic tectum: an immunohistochemical and ultrastructural analysis.

    PubMed

    Lever, Mael; Brand-Saberi, Beate; Theiss, Carsten

    2014-05-01

    We present the first comprehensive analysis of avian optic tectum development, including proliferation, migration and maturation of both neuronal and glial cells. The distribution of doublecortin, Tuj-1, vimentin and GFAP was characterized by immunohistochemistry between E3 and E20, and correlated with the electron microscopic structure in the chicken optic tectum. The immunohistological markers used in our study are known to be critical for distinct steps of neurogenesis and gliogenesis. We demonstrate that neurogenesis within the optic tectum starts at E3 with prominent doublecortin and moderate Tuj-1 expression. With the aid of electron microscopy, we also show that most of the cells are still undifferentiated at E4. Starting from E6, all postmitotic Tuj-1-positive neurons have left the ventricular zone and concurrently, with the end of proliferation around E12, doublecortin disappears from this region. Before hatching, doublecortin expression totally ceases, indicating that now all neurons have matured, this was also confirmed by ultrastructural investigations. Furthermore, vimentin expression starts around E4, prior to the appearance of the first radial glial cells at E6. Astrocytes can be detected by GFAP expression at E12. As radial glial cells (RGC) transform into astrocytes between E12 and E20, the vimentin signal is progressively replaced by the GFAP signal. We could also show that vimentin-positive RGCs do express doublecortin between E4 and E6, the time-point of prominent neurogenesis, reflecting their bipotent character.

  13. Ultrastructural analysis of bone tissue irradiated by Er:YAG Laser.

    PubMed

    Sasaki, Katia M; Aoki, Akira; Ichinose, Shizuko; Ishikawa, Isao

    2002-01-01

    The use of erbium:yttrium aluminum garnet (Er:YAG) laser has been suggested for bone ablation, however, little is known about the nature of the tissue after irradiation. This study was aimed to analyze the ultrastructure of bone tissue treated with Er:YAG laser, as compared to those treated with CO(2) laser and bur drilling. Parietal bones of Wistar rats were treated and analyzed by light microscopy, transmission electron microscopy (TEM), electron diffraction analysis and energy dispersive X-ray spectroscopy (SEM-EDX). This study demonstrated that Er:YAG laser irradiation resulted in a very thin changed layer of approximately 30 microm thickness, which consisted of two distinct sub-layers: a superficial, greatly altered layer and a deep, less affected layer. The major changes found on bone surface after Er:YAG laser irradiation consisted of micro-cracking, disorganization, and slight recrystallization of the original apatites and reduction of surrounding organic matrix. Copyright 2002 Wiley-Liss, Inc.

  14. Sensitivity analysis in quantitative microbial risk assessment.

    PubMed

    Zwieterin, M H; van Gerwen, S J

    2000-07-15

    The occurrence of foodborne disease remains a widespread problem in both the developing and the developed world. A systematic and quantitative evaluation of food safety is important to control the risk of foodborne diseases. World-wide, many initiatives are being taken to develop quantitative risk analysis. However, the quantitative evaluation of food safety in all its aspects is very complex, especially since in many cases specific parameter values are not available. Often many variables have large statistical variability while the quantitative effect of various phenomena is unknown. Therefore, sensitivity analysis can be a useful tool to determine the main risk-determining phenomena, as well as the aspects that mainly determine the inaccuracy in the risk estimate. This paper presents three stages of sensitivity analysis. First, deterministic analysis selects the most relevant determinants for risk. Overlooking of exceptional, but relevant cases is prevented by a second, worst-case analysis. This analysis finds relevant process steps in worst-case situations, and shows the relevance of variations of factors for risk. The third, stochastic analysis, studies the effects of variations of factors for the variability of risk estimates. Care must be taken that the assumptions made as well as the results are clearly communicated. Stochastic risk estimates are, like deterministic ones, just as good (or bad) as the available data, and the stochastic analysis must not be used to mask lack of information. Sensitivity analysis is a valuable tool in quantitative risk assessment by determining critical aspects and effects of variations.

  15. [Tooth macromorphological and ultrastructural analysis of osteological material from the medieval locality of St. Panteleimon Church in Nis].

    PubMed

    Mitić, Nadica; Mitić, Aleksandar; Mitić, Vladimir; Savić, Vojin; Nikolić, Marija

    2010-01-01

    Analysis of macromorphological and ultrastructural tooth characteristics of osteological material from the medieval site of St. Pantaleimon Church in Nis provides us with insight on the life, nutrition and habits of medieval population, as well as the structure and composition of their teeth. The aim of this research, based on the tooth inspection of skeletal remains from the medieval site of St. Pantaleimon Church in Nis, was to analyze macromorphological characteristics, ultrastructure of the dental tissue of maxillary and mandibular molars, canines and incisors, as well as their chemical composition. Macromorphological and ultrastructural analysis of the dental tissue of osteological material dating from the 12th century included 1312 teeth with advanced abrasion. Macromorphological changes were detected by using a dental mirror, probe and radiography. After irrigation, the teeth were prepared using the standard procedure and analyzed by scanning electronic microscopy (JEOL-JSM-5300). Chemical analysis was done by expanded downscaling (EDS) method for Mg, P, Ca. The analysis detected second degree abrasions of all teeth in individuals aged 20-25 years. Third and fourth degree abrasions of teeth were detected in individuals aged over 40 years. Ultrastructural analysis showed a complete obliteration of dentin tubules and pulp of the lower incisors, the apposition of intratubular dentin inside the tubules, as well as extensive deformity and loss of dentin structure on molars with preserved pulp volume and nerve fiber calcification. The calcification of nerve fibers showed that the formation of intratubular dentin was proportional with the biological potential of pulp and the degree of abrasion, and inversely proportional with the size of dentin surface. Chemical analysis showed that in the analyzed teeth Ca composition was slightly lower than that in the control group, P composition was almost identical, while Mg composition was multiply increased in comparison to

  16. The response of the macaque tracheobronchial epithelium to acute ozone injury. A quantitative ultrastructural and autoradiographic study.

    PubMed Central

    Wilson, D. W.; Plopper, C. G.; Dungworth, D. L.

    1984-01-01

    The tracheal epithelium of a variety of laboratory species is widely used as a model system in studies of epithelial biology and respiratory carcinogenesis. The purpose of this study was to evaluate the response of the tracheal epithelium to cytotoxic injury in a primate species that may have an epithelium more representative of that in man than smaller laboratory species. This study evaluated changes in the light-microscopic, surface, and ultrastructural appearance of the tracheobronchial epithelium of bonnet monkeys exposed for 3 or 7 days to 0.64 ppm ozone. Population densities, epithelial volumetric densities, and thymidine labeling indexes were determined for cells from posterior membranous and anterior cartilaginous trachea and mainstem bronchus. Ozone-induced epithelial changes were characterized by decreased numbers of ciliated cells, loss of cilia, and necrosis of ciliated cells. There were alterations in mucous (goblet) cell granules. There was an increase in extracellular space and focal epithelial stratification that was associated with increased numbers of small mucous granule cells and the presence of an epithelial cell type not seen in control animals (intermediate cells). There was an increase in cytoplasmic filaments and desmosomal attachments in basal cells, small mucous granule cells, and intermediate cells. Regional differences in lesion distribution were demonstrated by scanning electron microscopy. Longitudinal streaks of ciliary loss were evident in posterior membranous trachea, but ciliary loss in the ventral trachea was most prominent over the posterior border of the cartilaginous rings. The thymidine labeling index and numbers of necrotic ciliated cells were greater after 3 days than after 7 days of continuous exposure. Foci of stratification were often associated with increased numbers of labeled nuclei in the suprabasal region of the epithelium. The results of this study suggest that small mucous granule cells and intermediate cells are

  17. Carcinosarcoma of the colon: report of a case with morphological, ultrastructural and molecular analysis

    PubMed Central

    Ambrosini-Spaltro, Andrea; Vaira, Valentina; Braidotti, Paola; Rovati, Marco PL; Ferrero, Stefano; Bosari, Silvano

    2006-01-01

    Background Carcinosarcoma of the colon is a rare histopathological entity with uncertain histogenesis, that shows both epithelial and mesenchymal malignant differentiation. Carcinosarcoma rarely affects the gastrointestinal tract and only few cases are reported in the colon. Herein we describe a carcinosarcoma of the ascending colon, with morphological, ultrastructural and molecular analysis. Case presentation An 81-year-old man was hospitalised for asthenia, weight loss and iron-deficiency anaemia. The patient underwent colonoscopy and adenocarcinoma was diagnosed by endoscopic biopsy. A right hemicolectomy was performed and, during surgical operation, liver metastases were detected. Histological examination of the surgical specimen revealed areas of both carcinomatous and sarcomatous differentiation, completely separated by fibrous septae. The sarcomatous component exhibited areas of smooth muscle and osteoblastic differentiation, with focal osteoid material deposition. Molecular analysis conducted separately on the epithelial and mesenchymal components revealed the same p53 gene mutation (R282W in exon 8) and identical polymorphisms in p53 exon 4, in EGFR exons 20 and 21, and in c-kit exon 17. Microsatellite markers analysis revealed a common loss of heterozygosis on 18q. Overall, the data are consistent with a common origin of the two tumor components. The patient was treated with 8 cycles of oral capecitabine (1250 mg/m2 twice a day for 14 days repeated every 28 days) and two years after surgery is alive with liver metastases. Conclusion Carcinosarcoma of the colon is a rare tumour with both epithelial and sarcomatous components. Molecular analysis of the current case suggests the histogenesis from a common cell progenitor. PMID:16836749

  18. A quantitative ultrastructural study of microtubule content and secretory granule accumulation in parathyroid glands of phosphate- and colchicine-treated rats.

    PubMed Central

    Reaven, E P; Reaven, G M

    1975-01-01

    Microtubule involvement in secretory events of the parathyroid gland was investigated in rats treated with colchicine and/or phosphorus, agents which have been shown to modify parathyroid secretion. Quantitative ultrastructural techniques were used in an effort to assess the cytoplasmic microtubule and secretory granule content of chief cells 3 h after treatment, when hypocalcemia was well established. After cochicine administration, the chief cells appeared to have lost all assembled microtubules and accumulated greater than normal amounts of cytoplasmic secretory granules. On the other hand, phosphorus treatment was associated with increased microtubule content although the cytoplasmic content of secretory granules remained unchanged. When colchicine and phosphorus were given concomitantly, microtubules were again absent, but the secretory granule content of the cells was markedly increased. These data provide direct evidence that colchicine disrupts assembled microtubules in chief cells of rat parathyroids; the consequence of this effect appears to be a blockage of hormone release which is reflected in the accumulation of secretory granules in the cell. The fact that microtubules also show a significant increase in content when hormone release from chief cells is presumed to increase, suggests that microtubules may participate in the physiological control of parathyroid hormone secretion. Images PMID:1141440

  19. Three-dimensional analysis of abnormal ultrastructural alteration in mitochondria of hippocampus of APP/PSEN1 transgenic mouse.

    PubMed

    Choi, Ki Ju; Kim, Mi Jeong; Je, A Reum; Jun, Sangmi; Lee, Chulhyun; Lee, Eunji; Jo, Mijung; Huh, Yang Hoon; Kweon, Hee-Seok

    2014-03-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disorder. The deterioration of subcellular organelles, including the mitochondria, is another major ultrastructural characteristic of AD pathogenesis, in addition to amyloid plaque deposition. However, the three-dimensional (3-D) study of mitochondrial structural alteration in AD remains poorly understood. Therefore, ultrastructural analysis, 3-D electron tomography, and immunogold electron microscopy were performed in the present study to clarify the abnormal structural alterations in mitochondria caused by the progression of AD in APP/PSEN1 transgenic mice, expressing human amyloid precursor protein, as a model for AD. Amyloid beta (A beta) plaques accumulated and dystrophic neurites (DN) developed in the hippocampus of transgenic AD mouse brains. We also identified the loss of peroxiredoxin 3, an endogenous cytoprotective antioxidant enzyme and the accumulation of A beta in the hippocampal mitochondria of transgenic mice, which differs from those in age-matched wild-type mice. The mitochondria in A beta plaque-detected regions were severely disrupted, and the patterns of ultrastructural abnormalities were classified into three groups: disappearance of cristae, swelling of cristae, and bulging of the outer membrane. These results demonstrated that morpho-functional alterations of mitochondria and AD progression are closely associated and may be beneficial in investigating the function of mitochondria in AD pathogenesis.

  20. Quantitative histogram analysis of images

    NASA Astrophysics Data System (ADS)

    Holub, Oliver; Ferreira, Sérgio T.

    2006-11-01

    A routine for histogram analysis of images has been written in the object-oriented, graphical development environment LabVIEW. The program converts an RGB bitmap image into an intensity-linear greyscale image according to selectable conversion coefficients. This greyscale image is subsequently analysed by plots of the intensity histogram and probability distribution of brightness, and by calculation of various parameters, including average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of the histogram and the median of the probability distribution. The program allows interactive selection of specific regions of interest (ROI) in the image and definition of lower and upper threshold levels (e.g., to permit the removal of a constant background signal). The results of the analysis of multiple images can be conveniently saved and exported for plotting in other programs, which allows fast analysis of relatively large sets of image data. The program file accompanies this manuscript together with a detailed description of two application examples: The analysis of fluorescence microscopy images, specifically of tau-immunofluorescence in primary cultures of rat cortical and hippocampal neurons, and the quantification of protein bands by Western-blot. The possibilities and limitations of this kind of analysis are discussed. Program summaryTitle of program: HAWGC Catalogue identifier: ADXG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXG_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Mobile Intel Pentium III, AMD Duron Installations: No installation necessary—Executable file together with necessary files for LabVIEW Run-time engine Operating systems or monitors under which the program has been tested: WindowsME/2000/XP Programming language used: LabVIEW 7.0 Memory required to execute with typical data:˜16MB for starting and ˜160MB used for

  1. Ultrastructural analysis of bone nodules formed in vitro by isolated fetal rat calvaria cells

    SciTech Connect

    Bhargava, U.; Bar-Lev, M.; Bellows, C.G.; Aubin, J.E.

    1988-01-01

    When cells enzymatically digested from 21 d fetal rat calvaria are grown in ascorbic acid and Na beta-glycerophosphate, they form discrete three-dimensional nodular structures with the histological and immunohistochemical appearance of woven bone. The present investigation was undertaken to verify that bone-like features were identifiable at the ultrastructural level. The nodules formed on top of a fibroblast-like multilayer of cells. The upper surface of the nodules was lined by a continuous layer of cuboidal osteoblastic cells often seen to be joined by adherens junctions. Numerous microvilli, membrane protrusions, and coated pits could be seen on the upper surface of these cells, their cytoplasm contained prominent RER and Golgi membranes, and processes extended from their lower surfaces into a dense, highly organized collagenous matrix. Some osteocyte-like cells were completely embedded within this matrix; they also displayed RER and prominent processes which extended through the matrix and often made both adherens and gap junctional contacts with the processes of other cells. The fibroblastic cells not participating in nodule formation were surrounded by a less dense collagenous matrix and, in contrast to the matrix of the nodules, it did not mineralize. An unmineralized osteoid-like layer was seen directly below the cuboidal top layer of cells. A mineralization front was detectable below this in which small, discrete structures resembling matrix vesicles and feathery mineral crystals were evident and frequently associated with the collagen fibrils. More heavily mineralized areas were seen further into the nodule. Electron microprobe and electron and X-ray diffraction analysis confirmed the mineral to be hydroxyapatite.

  2. Genetic architecture dissection by genome-wide association analysis reveals avian eggshell ultrastructure traits

    PubMed Central

    Duan, Zhongyi; Sun, Congjiao; Shen, ManMan; Wang, Kehua; Yang, Ning; Zheng, Jiangxia; Xu, Guiyun

    2016-01-01

    The ultrastructure of an eggshell is considered the major determinant of eggshell quality, which has biological and economic significance for the avian and poultry industries. However, the interrelationships and genome-wide architecture of eggshell ultrastructure remain to be elucidated. Herein, we measured eggshell thickness (EST), effective layer thickness (ET), mammillary layer thickness (MT), and mammillary density (MD) and conducted genome-wide association studies in 927 F2 hens. The SNP-based heritabilities of eggshell ultrastructure traits were estimated to be 0.39, 0.36, 0.17 and 0.19 for EST, ET, MT and MD, respectively, and a total of 719, 784, 1 and 10 genome-wide significant SNPs were associated with EST, ET, MT and MD, respectively. ABCC9, ITPR2, KCNJ8 and WNK1, which are involved in ion transport, were suggested to be the key genes regulating EST and ET. ITM2C and KNDC1 likely affect MT and MD, respectively. Additionally, there were linear relationships between the chromosome lengths and the variance explained per chromosome for EST (R2 = 0.57) and ET (R2 = 0.67). In conclusion, the interrelationships and genetic architecture of eggshell ultrastructure traits revealed in this study are valuable for our understanding of the avian eggshell and contribute to research on a variety of other calcified shells. PMID:27456605

  3. Tendon's ultrastructure.

    PubMed

    Tresoldi, Ilaria; Oliva, Francesco; Benvenuto, Monica; Fantini, Massimo; Masuelli, Laura; Bei, Roberto; Modesti, Andrea

    2013-01-01

    The structure of a tendon is an important example of complexity of ECM three-dimensional organization. The extracellular matrix (ECM) is a macromolecular network with both structural and regulatory functions. ECM components belong to four major types of macromolecules: the collagens, elastin, proteoglycans, and noncollagenous glycoproteins. Tendons are made by a fibrous, compact connective tissue that connect muscle to bone designed to transmit forces and withstand tension during muscle contraction. Here we show the ultrastructural features of tendon's components.

  4. Quantitative 3D Ultrastructure of Thalamocortical Synapses from the "Lemniscal" Ventral Posteromedial Nucleus in Mouse Barrel Cortex.

    PubMed

    Rodriguez-Moreno, Javier; Rollenhagen, Astrid; Arlandis, Jaime; Santuy, Andrea; Merchan-Pérez, Angel; DeFelipe, Javier; Lübke, Joachim H R; Clasca, Francisco

    2017-07-28

    Thalamocortical synapses from "lemniscal" neurons of the dorsomedial portion of the rodent ventral posteromedial nucleus (VPMdm) are able to induce with remarkable efficacy, despite their relative low numbers, the firing of primary somatosensory cortex (S1) layer 4 (L4) neurons. To which extent this high efficacy depends on structural synaptic features remains unclear. Using both serial transmission (TEM) and focused ion beam milling scanning electron microscopy (FIB/SEM), we 3D-reconstructed and quantitatively analyzed anterogradely labeled VPMdm axons in L4 of adult mouse S1. All VPMdm synapses are asymmetric. Virtually all are established by axonal boutons, 53% of which contact multiple (2-4) elements (overall synapse/bouton ratio = 1.6). Most boutons are large (mean 0.47 μm3), and contain 1-3 mitochondria. Vesicle pools and postsynaptic density (PSD) surface areas are large compared to others in rodent cortex. Most PSDs are complex. Most synapses (83%) are established on dendritic spine heads. Furthermore, 15% of the postsynaptic spines receive a second, symmetric synapse. In addition, 13% of the spine heads have a large protrusion inserted into a membrane pouch of the VPMdm bouton. The unusual combination of structural features in VPMdm synapses is likely to contribute significantly to the high efficacy, strength, and plasticity of these thalamocortical synapses. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Mobile app-based quantitative scanometric analysis.

    PubMed

    Wong, Jessica X H; Liu, Frank S F; Yu, Hua-Zhong

    2014-12-16

    The feasibility of using smartphones and other mobile devices as the detection platform for quantitative scanometric assays is demonstrated. The different scanning modes (color, grayscale, black/white) and grayscale converting protocols (average, weighted average/luminosity, and software specific) have been compared in determining the optical darkness ratio (ODR) values, a conventional quantitation measure for scanometric assays. A mobile app was developed to image and analyze scanometric assays, as demonstrated by paper-printed tests and a biotin-streptavidin assay on a plastic substrate. Primarily for ODR analysis, the app has been shown to perform as well as a traditional desktop scanner, augmenting that smartphones (and other mobile devices) promise to be a practical platform for accurate, quantitative chemical analysis and medical diagnostics.

  6. Quantitative WDS analysis using electron probe microanalyzer

    SciTech Connect

    Ul-Hamid, Anwar . E-mail: anwar@kfupm.edu.sa; Tawancy, Hani M.; Mohammed, Abdul-Rashid I.; Al-Jaroudi, Said S.; Abbas, Nureddin M.

    2006-04-15

    In this paper, the procedure for conducting quantitative elemental analysis by ZAF correction method using wavelength dispersive X-ray spectroscopy (WDS) in an electron probe microanalyzer (EPMA) is elaborated. Analysis of a thermal barrier coating (TBC) system formed on a Ni-based single crystal superalloy is presented as an example to illustrate the analysis of samples consisting of a large number of major and minor elements. The analysis was performed by known standards and measured peak-to-background intensity ratios. The procedure for using separate set of acquisition conditions for major and minor element analysis is explained and its importance is stressed.

  7. Seniors' Online Communities: A Quantitative Content Analysis

    ERIC Educational Resources Information Center

    Nimrod, Galit

    2010-01-01

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

  8. Seniors' Online Communities: A Quantitative Content Analysis

    ERIC Educational Resources Information Center

    Nimrod, Galit

    2010-01-01

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

  9. Quantitative analysis of arm movement smoothness

    NASA Astrophysics Data System (ADS)

    Szczesna, Agnieszka; Błaszczyszyn, Monika

    2017-07-01

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

  10. Ultrastructural Analysis of the Prostate Gland under the Effect of Factors of Chemical Industry.

    PubMed

    Nepomnyashchikh, L M; Lapiy, G A; Nikityuk, D B; Neimark, A I; Kiptilov, A V; Molodykh, O P

    2015-04-01

    We analyzed ultrastruciture of the cell populations in the prostate gland in chronic nonbacterial prostatitis in a chemical industry worker. It was shown that ultrastructural reorganization of the epithelium consisted in reduction of the secretory compartment of the cytoplasm and dystrophic-degenerative changes in cell organelles. Endothelial cells of the capillaries showed signs of significant degeneration and low intensity of micropinocytosis. Most of the smooth muscle cells underwent dystrophic-degenerative modifications of ultrastructural elements. The dominance of degenerative cell changes in the epithelial and stromal cell populations along with intensification of collagen formation in the absence of inflammatory elements allows us to interpret this pathological condition of the prostate gland as prostate pathology of occupational or mixed genesis.

  11. Method and apparatus for chromatographic quantitative analysis

    DOEpatents

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

    1981-06-09

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

  12. Quantitative ADF STEM: acquisition, analysis and interpretation

    NASA Astrophysics Data System (ADS)

    Jones, L.

    2016-01-01

    Quantitative annular dark-field in the scanning transmission electron microscope (ADF STEM), where image intensities are used to provide composition and thickness measurements, has enjoyed a renaissance during the last decade. Now in a post aberration-correction era many aspects of the technique are being revisited. Here the recent progress and emerging best-practice for such aberration corrected quantitative ADF STEM is discussed including issues relating to proper acquisition of experimental data and its calibration, approaches for data analysis, the utility of such data, its interpretation and limitations.

  13. Quantitative analysis of blood vessel geometry

    NASA Astrophysics Data System (ADS)

    Fuhrman, Michael G.; Abdul-Karim, Othman; Shah, Sujal; Gilbert, Steven G.; Van Bibber, Richard

    2001-07-01

    Re-narrowing or restenosis of a human coronary artery occurs within six months in one third of balloon angioplasty procedures. Accurate and repeatable quantitative analysis of vessel shape is important to characterize the progression and type of restenosis, and to evaluate effects new therapies might have. A combination of complicated geometry and image variability, and the need for high resolution and large image size makes visual/manual analysis slow, difficult, and prone to error. The image processing and analysis described here was developed to automate feature extraction of the lumen, internal elastic lamina, neointima, external elastic lamina, and tunica adventitia and to enable an objective, quantitative definition of blood vessel geometry. The quantitative geometrical analysis enables the measurement of several features including perimeter, area, and other metrics of vessel damage. Automation of feature extraction creates a high throughput capability that enables analysis of serial sections for more accurate measurement of restenosis dimensions. Measurement results are input into a relational database where they can be statistically analyzed compared across studies. As part of the integrated process, results are also imprinted on the images themselves to facilitate auditing of the results. The analysis is fast, repeatable and accurate while allowing the pathologist to control the measurement process.

  14. Comparative ultrastructure analysis of radiation-induced radioresistant laryngeal cancer hep-2 cell line.

    PubMed

    Yang, Bo; Tang, Fuqiu; Zhang, Bicheng; Zhao, Yong; Ding, Shifang; Rao, Zhiguo

    2014-08-01

    Radioresistance is one of the main reasons for the failure of radiotherapy in laryngeal cancer. However, the mechanisms of radioresistance of tumor cells have remained elusive. This study was conducted to identify the ultrastructural changes of radiation-induced radioresistant laryngeal cancer hep-2 cell line. First, a radioresistant hep-2R cell line was generated after prolonged exposure to γ-rays for 60 Gy (6 Gy/day, 2 days/week) and was confirmed by clonogenic assay. Next, the ultrastructural differences between hep-2R cells and hep-2 cells were compared by transmission electron microscopy. Finally, the results showed that hep-2R cells showed significant resistance to radiation compared with parental hep-2 cells. Increased cell nucleus atypia, more rough endoplasmic reticulum and less mitochondria were observed in hep-2R cells. The amount of microvilli of hep-2R was similar to hep-2 cell. In summary, these ultrastructural differences revealed the morphological mechanism that hep-2R cells had stronger radioresistance than hep-2 cells.

  15. Ultrastructural analysis of testicular tissue and sperm by transmission and scanning electron microscopy.

    PubMed

    Chemes, Hector E

    2013-01-01

    Transmission electron microscopy (TEM) studies have provided the basis for an in-depth understanding of the cell biology and normal functioning of the testis and male gametes and have opened the way to characterize the functional role played by specific organelles in spermatogenesis and sperm function. The development of the scanning electron microscope (SEM) extended these boundaries to the recognition of cell and organ surface features and the architectural array of cells and tissues. The merging of immunocytochemical and histochemical approaches with electron microscopy has completed a series of technical improvements that integrate structural and functional features to provide a broad understanding of cell biology in health and disease. With these advances the detailed study of the intricate structural and molecular organization as well as the chemical composition of cellular organelles is now possible. Immunocytochemistry is used to identify proteins or other components and localize them in specific cells or organelles with high specificity and sensitivity, and histochemistry can be used to understand their function (i.e., enzyme activity). When these techniques are used in conjunction with electron microscopy their resolving power is further increased to subcellular levels. In the present chapter we will describe in detail various ultrastructural techniques that are now available for basic or translational research in reproductive biology and reproductive medicine. These include TEM, ultrastructural immunocytochemistry, ultrastructural histochemistry, and SEM.

  16. Pomology observations, morphometric analysis, ultrastructural study and allelic profiles of "olivastra Seggianese" endocarps from ancient olive trees (Olea europaea L.).

    PubMed

    Milanesi, Claudio; Sorbi, Andrea; Paolucci, Elisa; Antonucci, Francesca; Menesatti, Paolo; Costa, Corrado; Pallottino, Federico; Vignani, Rita; Cimato, Antonio; Ciacci, Andrea; Cresti, Mauro

    2011-01-01

    Preliminary studies of historical sources and remote sensing were used to identify ancient olive trees near archaeological sites and heritage buildings in the Orcia Valley (Siena, Italy). Distinctive characters were assessed by traditional pomological observation. Trees with similar characters were selected on the basis of the features of endocarps, the only structure that survives aerobic deterioration and conserves useful botanical information for centuries. Non-invasive morphometric analysis of endocarp size and shape established morphological variations in individuals of different populations. Plastid organization in the endocarp and location of DNA in the endocarp tegument were detected by morphological and ultrastructural observations using light and electron microscopy. Cytoplasmic markers with high polymorphism were used to test similarity of endocarp and leaf DNA within individuals and to confirm low variability and minimal divergence between individuals. The ancient trees studied showed the same allelic profiles and therefore belonged to a distinct cultivar. The traditional pomological descriptions of the trees, leaves and fruits, morphometric analysis of size, and shape elliptic Fourier analysis of endocarp outline, ultrastructural observations and allelic profiles of endocarp tegument delineated the general species-specific qualities of the cultivar "olivastra Seggianese" of the Orcia Valley.

  17. Comprehensive Quantitative Analysis on Privacy Leak Behavior

    PubMed Central

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

    2013-01-01

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

  18. Comprehensive quantitative analysis on privacy leak behavior.

    PubMed

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

    2013-01-01

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

  19. High-energy PIXE: quantitative analysis

    NASA Astrophysics Data System (ADS)

    Denker, A.; Opitz-Coutureau, J.; Campbell, J. L.; Maxwell, J. A.; Hopman, T.

    2004-06-01

    In recent years, high-energy PIXE was applied successfully for qualitative analysis on art and archaeological objects, e.g. coins, bronzes, sculptures, brooches. However, in the absence of software for quantitative analysis the full benefit inherent in the PIXE technique was not obtained. For example, a bronze could easily be distinguished from a brass, but the concentrations could not be rigorously compared within a set of bronzes. In this paper, the first quantitative analysis by high-energy PIXE is presented. The Guelph PIXE Software Package GUPIX has been extended to proton energies up to 100 MeV, so that high-energy PIXE spectra can be evaluated and concentrations derived. Measurements on metal and alloy standards at two different proton energies have been performed and the obtained compositions were compared to the certified values. The results will be presented and deviations discussed.

  20. Quantitative analysis of colony morphology in yeast.

    PubMed

    Ruusuvuori, Pekka; Lin, Jake; Scott, Adrian C; Tan, Zhihao; Sorsa, Saija; Kallio, Aleksi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Dudley, Aimée M

    2014-01-01

    Microorganisms often form multicellular structures such as biofilms and structured colonies that can influence the organism's virulence, drug resistance, and adherence to medical devices. Phenotypic classification of these structures has traditionally relied on qualitative scoring systems that limit detailed phenotypic comparisons between strains. Automated imaging and quantitative analysis have the potential to improve the speed and accuracy of experiments designed to study the genetic and molecular networks underlying different morphological traits. For this reason, we have developed a platform that uses automated image analysis and pattern recognition to quantify phenotypic signatures of yeast colonies. Our strategy enables quantitative analysis of individual colonies, measured at a single time point or over a series of time-lapse images, as well as the classification of distinct colony shapes based on image-derived features. Phenotypic changes in colony morphology can be expressed as changes in feature space trajectories over time, thereby enabling the visualization and quantitative analysis of morphological development. To facilitate data exploration, results are plotted dynamically through an interactive Yeast Image Analysis web application (YIMAA; http://yimaa.cs.tut.fi) that integrates the raw and processed images across all time points, allowing exploration of the image-based features and principal components associated with morphological development.

  1. Good practices for quantitative bias analysis.

    PubMed

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

    2014-12-01

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

  2. Quantitative analysis to guide orphan drug development.

    PubMed

    Lesko, L J

    2012-08-01

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

  3. The closer we look the more we see? Quantitative microscopic analysis of the pulmonary surfactant system.

    PubMed

    Ochs, Matthias

    2010-01-01

    The surfactant system of the lung has essential biophysical and immunomodulatory functions. Only at the electron microscopic level does surfactant reveal its morphological complexity--and beauty. Therefore, morphological tools are indispensible to characterize the surfactant system in health and disease. Stereology provides the gold standard for obtaining quantitative (morphometric) data in microscopy. The combination of microscopy and stereology allows for qualitative and quantitative analysis of the intraalveolar as well as the intracellular surfactant pool, both in its preserved microorganization and localization within the lung. Surfactant-producing alveolar epithelial type II cells can be counted and sampled for size estimation with physical disectors at a high magnification light microscopic level. The number of their surfactant storing lamellar bodies can be estimated using physical disectors at the electron microscopic level. Electron tomography allows for high resolution 3D visualization of lamellar body fusion pores. Intraalveolar surfactant subtypes can be quantitated in situ, thus reflecting the functional state of the intraalveolar surfactant pool. By immunoelectron microscopy, surfactant protein distribution can be analyzed. These methods allow for a comprehensive quantitative analysis of surfactant (ultra-)structure. Here, we give an overview on the analysis of the normal and disordered surfactant system by electron microscopy and stereology.

  4. Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

    NASA Technical Reports Server (NTRS)

    Shortle, J. F.; Allocco, M.

    2005-01-01

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

  5. Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

    NASA Technical Reports Server (NTRS)

    Shortle, J. F.; Allocco, M.

    2005-01-01

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

  6. Ultrastructural Analysis of In Vivo Hypoglycemiant Effect of Two Polyoxometalates in Rats with Streptozotocin-Induced Diabetes.

    PubMed

    Bâlici, Ştefana; Wankeu-Nya, Modeste; Rusu, Dan; Nicula, Gheorghe Z; Rusu, Mariana; Florea, Adrian; Matei, Horea

    2015-10-01

    Two polyoxometalates (POMs), synthesized through a self-assembling method, were used in the treatment of streptozotocin (STZ)-induced diabetic rats. One of these nanocompounds [tris(vanadyl)-substituted tungsto-antimonate(III)-anions—POM1] was previously described in the literature, whereas the second [tris-butyltin-21-tungsto-9-antimonate(III)-anions—POM2], was prepared by us based on our original formula. In rats with STZ-induced diabetes treated with POMs (up to a cumulative dose of 4 mg/kg bodyweight at the end of the treatments), statistically significant reduced levels of blood glucose were measured after 3 weeks, as compared with the diabetic control groups (DCGs). Ultrastructural analysis of pancreatic β-cells (including the mean diameter of secretory vesicles and of their insulin granules) in the treated diabetic rats proved the POMs contribute to limitation of cellular degeneration triggered by STZ, as well as to the presence of increased amounts of insulin-containing vesicles as compared with the DCG. The two POMs also showed hepatoprotective properties when ultrastructural aspects of hepatocytes in the experimental groups of rats were studied. Based on our in vivo studies, we concluded that the two POMs tested achieved hypoglycemiant effects by preventing STZ-triggered apoptosis of pancreatic β-cells and stimulation of insulin synthesis.

  7. Influence analysis in quantitative trait loci detection

    PubMed Central

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

    2014-01-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods—the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. PMID:24740424

  8. Influence analysis in quantitative trait loci detection.

    PubMed

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

    2014-07-01

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

  9. Ultrastructural analysis and identification of membrane proteins in the free-living amoeba Difflugia corona.

    PubMed

    Silva-Briano, Marcelo; Martínez-Hernández, Sandra Luz; Adabache-Ortíz, Araceli; Ventura-Juárez, Javier; Salinas, Eva; Quintanar, J Luis

    2007-08-01

    Syntaxin-1 and 25-kDa Synaptosome-associated Protein (SNAP-25) are present in the plasma membrane of several different secretory cell types and are involved in the exocytosis process. In this work, the free-living amoeba Difflugia corona was studied in relation to ultrastructure, structural membrane proteins, and proteins such as Syntaxin-1 and SNAP-25. Our results obtained by scanning electron microscopy in the amoeba without its theca, showed many membrane projections and several pore-like structures. Using immunocytochemistry, we found structural proteins Syntaxin-1 and SNAP-25.

  10. Acute Exposure of Medaka to Carcinogens: An Ultrastructural, Cytochemical and Morphometric Analysis of Liver and Kidney

    DTIC Science & Technology

    1991-02-24

    were incubated for 1 hour at 37 degrees C in a solution comprised of 1.25% sodium glycerophosphate , 2% magnesium chloride, 0.2M Tris/maleate buffer (pH...peroxidase and magnesium dependent, adenosine triphosphatase are being investigated ultrastructurally by means of electron-dense visual 4 markers. Pre...were incubated for 1 hour at 37 degrees C in a solution consisting of 3mM ATP, 3mM magnesium sulfate, 3mM lead nitrate and 0.2M Tris/maleate (pH 7.4

  11. An ultrastructural analysis of platelets, erythrocytes, white blood cells, and fibrin network in systemic lupus erythematosus.

    PubMed

    Pretorius, Etheresia; du Plooy, Jenny; Soma, Prashilla; Gasparyan, Armen Yuri

    2014-07-01

    The study suggests that patients with systemic lupus erythematosus (SLE) present with distinct inflammatory ultrastructural changes such as platelets blebbing, generation of platelet-derived microparticles, spontaneous formation of massive fibrin network and fusion of the erythrocytes membranes. Lupoid platelets actively interact with other inflammatory cells, particularly with white blood cells (WBCs), and the massive fibrin network facilitates such an interaction. It is possible that the concerted actions of platelets, erythrocytes and WBC, caught in the inflammatory fibrin network, predispose to pro-thrombotic states in patients with SLE.

  12. [Experimental studies on possible biological effects of ultrasonic diagnosis: ultrastructural analysis of rat embryo].

    PubMed

    Cardinale, A; Lagalla, R; De Maria, M; Valentino, B; Laconi, A

    1985-01-01

    Within the limits of a systematic research on the biological effects of the ultrasounds, the authors refer on their personal experience on rat's embrions treated, for 120 seconds, with a ultrasonic beam having the common characteristics used in diagnostic investigations. The ultra-structural studies on the hepatic parenchyma substantially confirm the previous results obtained in the adult cavy, exposed for the same period of time, i.e. a diffuse cytoplasmic vacuolization and an unstable mitochondrial damage. Various suggestions are advanced on the particular sensibility that the mitocondria show because of the ultrasonic action. The authors explain the limits of their experimentation in this specific sector of the scientific research.

  13. Quantitative resilience analysis through control design.

    SciTech Connect

    Sunderland, Daniel; Vugrin, Eric D.; Camphouse, Russell Chris

    2009-09-01

    Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently assessing all aspects of critical infrastructure resilience. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the development of quantitative resilience through application of control design methods. Specifically, we conducted a survey of infrastructure models to assess what types of control design might be applicable for critical infrastructure resilience assessment. As a result of this survey, we developed a decision process that directs the resilience analyst to the control method that is most likely applicable to the system under consideration. Furthermore, we developed optimal control strategies for two sets of representative infrastructure systems to demonstrate how control methods could be used to assess the resilience of the systems to catastrophic disruptions. We present recommendations for future work to continue the development of quantitative resilience analysis methods.

  14. Ultrastructure and morphometric analysis of hypertrophic nucleoli in non-Hodgkin's lymphoma and phytohemagglutinin-stimulated lymphocytes.

    PubMed

    Shapiro, S H; Chang, L Y; Wessely, Z; Klavins, J V

    1982-01-01

    The ultrastructure of hypertrophic nucleoli in large cells from each of 5 successive cases of non-Hodgkin's lymphoma (regardless of predominant cell type) showed irregularly rounded or ovoid, mostly compact forms with few scattered light spaces. Occasional nucleolonemal forms were noted. Few ring forms or transitional forms between ring and compact or nucleolonemal types were present. Granular components occupied 78.5 +/- 1.0% of the mean total area of 132 lymphoma large cell nucleoli of all configurations studied. Hypertrophic nucleoli in 27 phytohemagglutinin (PHA)-stimulated lymphocytes were predominantly nucleolonemal with 74.2 +/- 10.6% granular composition. The qualitative and quantitative distribution of nucleolar granular moieties did not vary significantly between individual cases of lymphoma nor quantitatively between these and nucleoli in PHA-stimulated lymphocytes. These observations lend further credence to the suggestion of the lymphocyte as a common progenitor cell type for the large B and T cell of malignant lymphomas. Some functional similarity of their nucleoli and those of PHA-stimulated lymphocytes in their participation in ribonucleic acid synthesis is implied. Generally compact nucleoli of lymphomas in contrast to nucleolonemal forms of PHA-stimulated lymphocytes may be pathognomonic for large lymphocytic cells undergoing neoplasia.

  15. Iron-enhanced coagulation is attenuated by chelation: thrombelastographic and ultrastructural analysis.

    PubMed

    Nielsen, Vance G; Pretorius, Etheresia

    2014-12-01

    Increased circulating ferritin and free iron have been found in a variety of disease states associated with thrombophilia. When blood or plasma is exposed to iron addition, characteristic changes in thrombus formation are observed by scanning electron microscopy, which include fusion of fibrin polymers, matting, and even sheeting of fibrin. A primary mechanism posited to explain iron-mediated hypercoagulability is hydroxyl radical formation and modification of fibrinogen; however, iron has also been demonstrated to bind to fibrinogen. We have recently demonstrated that iron enhances coagulation, manifested as a decrease in the time of onset of coagulation. Using clinically encountered concentrations of iron created by addition of FeCl3 to human plasma, we demonstrated that iron-mediated changes in reaction time determined by thrombelastography or changes in thrombus ultrastructure were significantly, but not completely, reversed by iron chelation with deferoxamine. Thus, reversible iron binding to fibrinogen mechanistically explains a significant portion of coagulation kinetic and ultrastructural hypercoagulability. Further investigation is needed to determine whether residual iron binding or other iron-mediated effects is responsible for hypercoagulability observed after chelation.

  16. Ultrastructural analysis of the ovary and oogenesis in Spinicaudata and Laevicaudata (Branchiopoda) and its phylogenetic implications.

    PubMed

    Jaglarz, Mariusz K; Kubrakiewicz, Janusz; Jędrzejowska, Izabela; Gołdyn, Bartłomiej; Biliński, Szczepan M

    2014-06-01

    Recent molecular studies have indicated a close relationship between Crustacea and Hexapoda and postulated their unification into the Pancrustacea/Tetraconata clade. Certain molecular analyses have also suggested that the crustacean lineage, which includes the Branchiopoda, might be the sister group of Hexapoda. We test this hypothesis by analyzing the structure of the ovary and the ultrastructural features of oogenesis in two branchiopod species, Cyzicus tetracerus and Lynceus brachyurus, representing two separate orders, Spinicaudata and Laevicaudata, respectively. The female gonads of these species have not been investigated before. Here, we demonstrate that in both studied species the ovarian follicles develop inside characteristic ovarian protrusions and comprise a germline cyst surrounded by a simple somatic (follicular) epithelium, supported by a thin basal lamina. Each germline cyst consists of one oocyte and three supporting nurse cells, and the oocyte differentiates relatively late during ovarian follicle development. The synthesis of oocyte reserve materials involves rough endoplasmic reticulum and Golgi complexes. The follicular cells are penetrated by a complex canal system and there is no external epithelial sheath covering the ovarian follicles. The structure of the ovary and the ultrastructural characteristics of oogenesis are not only remarkably similar in both Cyzicus and Lynceus, but also share morphological similarities with Notostraca as well as the basal hexapods Campodeina and Collembola. Possible phylogenetic implications of these findings are discussed.

  17. Ultrastructural and immunohistochemical analysis of the 8-20 week human fetal pancreas

    PubMed Central

    Riopel, Matthew; Li, Jinming; Fellows, George F; Goodyer, Cynthia G; Wang, Rennian

    2014-01-01

    Development of the human pancreas is well-known to involve tightly controlled differentiation of pancreatic precursors to mature cells that express endocrine- or exocrine-specific protein products. However, details of human pancreatic development at the ultrastructural level are limited. The present study analyzed 8–20 week fetal age human pancreata using scanning and transmission electron microscopy (TEM), TEM immunogold and double or triple immunofluorescence staining. Primary organization of islets and acini occurred during the developmental period examined. Differentiating endocrine and exocrine cells developed from the ductal tubules and subsequently formed isolated small clusters. Extracellular matrix fibers and proteins accumulated around newly differentiated cells during their migration and cluster formation. Glycogen expression was robust in ductal cells of the pancreas from 8–15 weeks of fetal age; however, this became markedly reduced at 20 weeks, with a concomitant increase in acinar cell glycogen content. Insulin secretory granules transformed from being dense and round at 8 weeks to distinct geometric (multilobular, crystalline) structures by 14–20 weeks. Initially many of the differentiating endocrine cells were multihormonal and contained polyhormonal granules; by 20 weeks, monohormonal cells were in the majority. Interestingly, certain secretory granules in the early human fetal pancreatic cells showed positivity for both exocrine (amylase) and endocrine proteins. This combined ultrastructural and immunohistochemical study showed that, during early developmental stages, the human pancreas contains differentiating epithelial cells that associate closely with the extracellular matrix, have dynamic glycogen expression patterns and contain polyhormonal as well as mixed endocrine/exocrine granules. PMID:25425025

  18. Nanoparticles as Alternative Strategies for Drug Delivery to the Alzheimer Brain: Electron Microscopy Ultrastructural Analysis.

    PubMed

    Aliev, Gjumrakch; Daza, Jesús; Herrera, Arturo Solís; del Carmen Arias Esparza, María; Morales, Ludis; Echeverria, Valentina; Bachurin, Sergey Olegovich; Barreto, George Emilio

    2015-01-01

    One of the biggest problems and challenges for the development of new drugs and treatment strategies against Alzheimer Disease (AD) is the crossing of target drugs into the blood brain barrier. The use of nanoparticles in drug delivery therapy holds much promise in targeting remote tissues, and as a result many studies have attempted to study the ultrastructural localization of nanoparticles in various tissues. However, there are currently no in vivo studies demonstrating the ultrastructural distribution of nanoparticles in the brain. The aim of this study was to address how intraperitoneal injection of silver nanoparticles in the brain leads to leaking on the inter-endothelial contact and luminal plasma membrane, thus elucidating the possibility of penetrating into the most affected areas in the Alzheimer brain (vascular endothelium, perivascular, neuronal and glial cells). Our results show that the silver nanoparticles reached the brain and were found in hippocampal areas, indicating that they can be conjugated and used to deliver the drugs into the cell cytoplasm of the damaged brain cells. The present study can be useful for the development of novel drug delivering therapy and useful in understanding the delivery, distribution and effects of silver nanoparticles in AD brain tissue at cellular and subcellular level.

  19. Ultrastructural and immunohistochemical analysis of the 8-20 week human fetal pancreas.

    PubMed

    Riopel, Matthew; Li, Jinming; Fellows, George F; Goodyer, Cynthia G; Wang, Rennian

    2014-01-01

    Development of the human pancreas is well-known to involve tightly controlled differentiation of pancreatic precursors to mature cells that express endocrine- or exocrine-specific protein products. However, details of human pancreatic development at the ultrastructural level are limited. The present study analyzed 8-20 week fetal age human pancreata using scanning and transmission electron microscopy (TEM), TEM immunogold and double or triple immunofluorescence staining. Primary organization of islets and acini occurred during the developmental period examined. Differentiating endocrine and exocrine cells developed from the ductal tubules and subsequently formed isolated small clusters. Extracellular matrix fibers and proteins accumulated around newly differentiated cells during their migration and cluster formation. Glycogen expression was robust in ductal cells of the pancreas from 8-15 weeks of fetal age; however, this became markedly reduced at 20 weeks, with a concomitant increase in acinar cell glycogen content. Insulin secretory granules transformed from being dense and round at 8 weeks to distinct geometric (multilobular, crystalline) structures by 14-20 weeks. Initially many of the differentiating endocrine cells were multihormonal and contained polyhormonal granules; by 20 weeks, monohormonal cells were in the majority. Interestingly, certain secretory granules in the early human fetal pancreatic cells showed positivity for both exocrine (amylase) and endocrine proteins. This combined ultrastructural and immunohistochemical study showed that, during early developmental stages, the human pancreas contains differentiating epithelial cells that associate closely with the extracellular matrix, have dynamic glycogen expression patterns and contain polyhormonal as well as mixed endocrine/exocrine granules.

  20. Ultrastructural analysis of Vitis vinifera leaf tissues showing atypical symptoms of Plasmopara viticola.

    PubMed

    Musetti, R; Stringher, L; Borselli, S; Vecchione, A; Zulini, L; Pertot, I

    2005-01-01

    In an abandoned farm in Tuscany a year by year regression of downy mildew disease on grapevines was observed and a decrease in virulence as well as vigor and fertility of the causal fungus, Plasmopara viticola. Anomalous spots of the fungus (i.e. atypical coloration of leaves or mosaic) on leaf tissues of a sensitive Vitis vinifera grapevine were observed. The anomalous symptoms were often associated with the typical 'oil spots' and were present under environmental conditions favourable for a normal development of the disease. An ultrastructural study was carried out on leaf tissues of grapevine plants aimed at clarifying the cause of this phenomenon and detecting whether there were alterations in P. viticola mycelium and endophytes present. ELISA was also performed to check the presence of grapevine viruses in the plants. TEM results demonstrated that characteristic P. viticola was present in leaf samples showing oil spots, while, both the fungus and the host tissues showed cytological alterations in leaves with mosaic symptoms. Finally, hyphae were absent in leaf tissues without downy mildew spots, but showing severe ultrastructural modifications. Several plant virus infections were found in these grapevines. Literature reports that the development and sporulation of some phytopathogenic fungi inside their hosts can be limited by virus infections. Further experimental approaches are required to determine if resistance to P. viticola can be induced by viral infections in grapevines.

  1. Developmental and Ultrastructural Characterization and Phylogenetic Analysis of Trypanosoma herthameyeri n. sp. of Brazilian Leptodactilydae Frogs.

    PubMed

    Attias, Márcia; Sato, Lyslaine H; Ferreira, Robson C; Takata, Carmen S A; Campaner, Marta; Camargo, Erney P; Teixeira, Marta M G; de Souza, Wanderley

    2016-09-01

    We described the phylogenetic affiliation, development in cultures and ultrastructural features of a trypanosome of Leptodacylus chaquensis from the Pantanal biome of Brazil. In the inferred phylogeny, this trypanosome nested into the Anura clade of the basal Aquatic clade of Trypanosoma, but was separate from all known species within this clade. This finding enabled us to describe it as Trypanosoma herthameyeri n. sp., which also infects other Leptodacylus species from the Pantanal and Caatinga biomes. Trypanosoma herthameyeri multiplies as small rounded forms clumped together and evolving into multiple-fission forms and rosettes of epimastigotes released as long forms with long flagella; scarce trypomastigotes and glove-like forms are common in stationary-phase cultures. For the first time, a trypanosome from an amphibian was observed by field emission scanning electron microscopy, revealing a cytostome opening, well-developed flagellar lamella, and many grooves in pumpkin-like forms. Transmission electron microscopy showed highly developed Golgi complexes, relaxed catenation of KDNA, and a rich set of spongiome tubules in a regular parallel arrangement to the flagellar pocket as confirmed by electron tomography. Considering the basal position in the phylogenetic tree, developmental and ultrastructural data of T. herthameyeri are valuable for evolutionary studies of trypanosome architecture and cell biology. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  2. Quantitative chemical analysis of ocular melanosomes in stained and non-stained tissues.

    PubMed

    Biesemeier, Antje; Schraermeyer, Ulrich; Eibl, Oliver

    2011-07-01

    Energy-filtered Analytical Electron Microscopy (AEM) was used to image the ultrastructure and determine quantitatively the chemical composition of rat melanosomes of the choroid and the Retinal Pigment Epithelium (RPE). For the first time, the effect of staining in elemental analysis of melanosomes was investigated. Detection limits and accuracies of the applied methods were determined. Compared to previous work applying only quantitative Energy Dispersive X-ray microanalysis (EDX) in the TEM (Eibl, O., et al., 2006. Micron 37, 262), here we present a combined quantitative EDX and Electron Energy Loss Spectroscopy (EELS) analysis, including N. This yields the fraction of eumelanin and pheomelanin in melanosomes by the S/N mole fraction ratio. Melanosomes of the sepia ink sac, used as eumelanin standard, showed an S/N mole fraction ratio of <0.004. Thus, they consist primarily of eumelanin as reported by degradation analysis. In contrast, melanosomes of the rats contained mixed melanin with significant amounts of pheomelanin (S/N 0.02) in the RPE and the choroid. Consistent with the previous publication, it was shown that oxygen mole fractions are especially large in melanosomes (7-10 at.%) compared to other cell compartments, e.g. 2-4 at.% oxygen in the cytoplasm. In the melanosomes of non-stained tissue, the oxygen mole fraction clearly correlated with the Ca mole fraction. EDX spectra used for quantitative analysis had about 15,000 net counts under the oxygen peak, which is necessary to obtain (i) a small statistical error for oxygen and (ii) optimum minimum detectable mole fractions for S, Ca and transition metals. The precise determination of the oxygen mole fraction in melanosomes is important for understanding metabolism. Therefore, a detailed analysis was carried out on the possible errors affecting quantification. While O, S, and N mole fractions yielded similar results in stained and non-stained ocular melanosomes of rats, transition metals can only be

  3. Replication of Bacteriophage Ribonucleic Acid: Analysis of the Ultrastructure of the Replicative Form and the Replicative Intermediate of Bacteriophage R17

    PubMed Central

    Granboulan, Nicole; Franklin, Richard M.

    1968-01-01

    A detailed qualitative and quantitative comparison was made of the ultrastructure of single-stranded ribonucleic acid (RNA) from bacteriophage R17 and double-stranded replicative form (RF) and replicative intermediate (RI) from cells infected with this bacteriophage. The nucleic acids were prepared for electron microscopy by the protein monolayer spreading technique of Kleinschmidt. Single-stranded RNA aggregated during spreading in the absence of urea, whereas RF and RI did not. On the other hand, RF and RI appeared to be susceptible to shear during spreading, whereas R17 RNA was not. From the maximal length of RF, a base translation of 3.14 A was calculated. This value favors a 10-fold helix model of double-stranded RNA. The same base translation was found for R17 RNA, indicating a stacked base structure for single-stranded RNA spread in the presence of urea. RI is a branched structure and the branches are removed by ribonuclease treatment. The branches are believed to be nascent single-stranded viral RNA. The contour length of the branch was equal to the contour length of the main chain up to the branch point, as predicted from theoretical analysis of the replication of viral RNA. The structure of RF and the main chain of RI was also analyzed by plotting the log (end-to-end distance squared) versus log (contour length). This demonstrated structures intermediate in stiffness between a random coil and a rigid rod. Images PMID:5742034

  4. Quantitative petrostructure analysis. Technical summary report

    SciTech Connect

    Warren, N.

    1980-09-01

    The establishment of quantitative techniques would lead to the development of predictive tools which would be of obvious importance in applied geophysics and engineering. In rock physics, it would help establish laws for averaging the effects of finite densities of real cracks and pores. It would also help in elucidating the relation between observed complex crack structures and various models for the mechanical properties of single cracks. The petrostructure study is addressed to this problem. The purpose of the effort is to quantitatively characterize the mineral and crack texture of granitic rock samples. The rock structures are to be characterized in such a way that the results can be used (1) to constrain the modelling of the effect of cracks on the physical properties of rocks, and (2) to test the possibility of establishing quantitative and predictive relations between petrographic observables and whole rock properties. Statistical techniques are being developed and being applied to the problem of parameterizing complex texture and crack patterns of rock, and of measuring correlation of these parameters to other measurable variables. The study is an application in factor analysis.

  5. Quantitative textural analysis of phenocryst zoning patterns

    NASA Astrophysics Data System (ADS)

    Niespolo, E.; Andrews, B. J.

    2011-12-01

    The textural complexity of phenocrysts has made quantitative analysis of large populations of crystals a challenging study. Because each phenocryst expresses a unique localized event in the volcanic interior, no single crystal necessarily records the complete pre-eruptive history of the magmatic system as a whole. Synthesizing the textural and compositional records of many crystals, however, should provide a more complete understanding of conditions prior to eruption. In this research, we present new techniques for quantitative analysis of individual crystals and across populations of crystals. We apply those techniques to back-scattered electron images of complexly zoned plagioclase from El Chichón volcano, Mexico. Analysis begins with Gaussian filtering to remove noise from the images and create more qualitatively distinct zoning patterns. Because pixel intensity is directly correlated with Anorthite content, compositional anisotropy is then calculated throughout each image by determining the distance from a grid point at which variation in pixel intensity exceeds a pre-determined standard deviation; both regular and adaptive grid spacings are used, and length scales are calculated in 8 directions. The resulting textural maps are analogous to a vector field and quantify 2-dimensional variation in texture. With both types of grid spacing, changes in magnitude and orientation of textural anisotropy and length scale indicate different crystal zones. The adaptive grid spacing, however, describes non-uniform textural variation more completely and has a higher measurement density in regions of high-frequency variation. In general, textural regions commonly described as clean or smooth show longer length scales and aligned anisotropies, whereas shorter length scales with variable anisotropies identify areas commonly described as patchy, dusty, or rough. The comparison and correlation of textural and compositional zoning help determine how different crystals record the

  6. Quantitative NIR Raman analysis in liquid mixtures.

    PubMed

    Sato-Berrú, R Ysacc; Medina-Valtierra, Jorge; Medina-Gutiérrez, Cirilo; Frausto-Reyes, Claudio

    2004-08-01

    The capability to obtain quantitative information of a simple way from Raman spectra is a subject of considerable interest. In this work, this is demonstrated for mixtures of ethanol with water and rhodamine-6G (R-6G) with methanol, which were analyzed directly in glass vessel. The Raman intensities and a simple mathematical model have been used and applied for the analysis of liquid samples. It is starting point to generate a general expression, from the experimental spectra, as the sum of the particular expression for each pure compound allow us to obtain an expression for the mixtures which can be used for determining concentrations, from the Raman spectrum, of the mixture.

  7. Quantitative analysis of non-Hodgkin's lymphoma.

    PubMed Central

    Abbott, C R; Blewitt, R W; Bird, C C

    1982-01-01

    A preliminary attempt has been made to characterise a small series of non-Hodgkin's lymphomas (NHL) by morphometric means using the Quantimet 720 Kontron MOP/AMO3 image analysis systems. In most cases it was found that the distribution of nuclear area and correlation between mean nuclear area and frequency per unit field, corresponded closely with tumour classification determined by light microscopy. These results suggest that it may be possible to devise an objective and reproducible grading system for NHL using quantitative morphometric techniques. PMID:7040479

  8. Structural and Ultrastructural Analysis of Cerebral Cortex, Cerebellum, and Hypothalamus from Diabetic Rats

    PubMed Central

    Hernández-Fonseca, Juan P.; Rincón, Jaimar; Pedreañez, Adriana; Viera, Ninoska; Arcaya, José L.; Carrizo, Edgardo; Mosquera, Jesús

    2009-01-01

    Autonomic and peripheral neuropathies are well-described complications in diabetes. Diabetes mellitus is also associated to central nervous system damage. This little-known complication is characterized by impairment of brain functions and electrophysiological changes associated with neurochemical and structural abnormalities. The purpose of this study was to investigate brain structural and ultrastructural changes in rats with streptozotocin-induced diabetes. Cerebral cortex, hypothalamus, and cerebellum were obtained from controls and 8 weeks diabetic rats. Light and electron microscope studies showed degenerative changes of neurons and glia, perivascular and mitochondrial swelling, disarrangement of myelin sheath, increased area of myelinated axons, presynaptic vesicle dispersion in swollen axonal boutoms, fragmentation of neurofilaments, and oligodendrocyte abnormalities. In addition, depressive mood was observed in diabetic animals. The brain morphological alterations observed in diabetic animals could be related to brain pathologic process leading to abnormal function, cellular death, and depressive behavioral. PMID:19812703

  9. Ultrastructural analysis and polymorphisms in Coarazuphium caatinga (Coleoptera: Carabidae: Zuphiini), a new Brazilian troglobitic beetle.

    PubMed

    Pellegrini, Thais Giovannini; Ferreira, Rodrigo Lopes

    2014-02-21

    Coarazuphium caatinga sp. n. occurs in limestone caves located in Campo Formoso municipality, in the Brazilian Caatinga (Bahia, Brazil). The new species is close to C. formoso although they are morphologically distinct by the elytra sinuosity, which is more pronounced in C. caatinga; the aedeagus is more tapered at the tip in this last species. Important traits found in C. caatinga are the variable size presented by the eyes, and the remarkable variability of body pigmentation among specimens; both traits do not seem to be correlated. Coarazuphium Gnaspini, P., Vanin, S.A. & Godoy, N.M., 1998, species exhibit advanced troglomorphic characters in comparison to other Brazilian cave beetles, as are increased extra-optic sensory structures, presence of particular sensilla, and sensory and gustatory receptors. These characters are not detected under routine microscopy and thus require ultrastructural methods for their study.

  10. Light and electron microscopic study of mature spermatozoa from White Pekin duck (Anas platyrhynchos): an ultrastructural and molecular analysis.

    PubMed

    Majhi, Rakesh Kumar; Kumar, Ashutosh; Yadav, Manoj; Kumar, Pradeep; Maity, Apratim; Giri, Sunil C; Goswami, Chandan

    2016-03-01

    The morphology, ultrastructure, and functions of mature avian spermatozoa have been of immense commercial and scientific interest for several reasons. This is mainly important in case of birds in poultry production, conservation, and in the use of sperm morphometry as phylogenetic evidence. Avian spermatozoa share complex or no correlation of sperm morphometry with respect to testis and/or body size as described before. In this work, we have isolated mature spermatozoa from White Pekin duck (Anas platyrhynchos) by non-invasive methods and performed several immunostaining analysis as well as cytochemical analysis using electron and light microscopes. Here, we report the presence of different post-translationally modified tubulin such as tyrosinated-, detyrosinated-, acetylated-, polyglutamylated-, and glycylated-tubulin in specific regions of the mature spermatozoa. By using field-emission scanning electron microscope, we confirm the presence of acrosome-like structure at the tip of the sperm head. However, this structure remains non-reactive to common lectins such as Peanut Agglutinin (PNA) and cholesterol-sensitive dyes such as Filipin. We report that this acrosomal structure is primarily made of lipid-based structures and is resistant to 0.1% Triton X100. Confocal microscopy and super resolution structured illumination microscopy study indicates that the nucleus is bifurcated at the tip region. By using specific markers, we report that the perforatorium structure present at the tip of the spermatozoa head contains specialized organelles that is similar to atypical mitochondria. We propose that these ultrastructural and molecular parameters can be used as species-specific features. The bifurcated nucleus and presence of atypical mitochondria within this structure may be relevant for the complex mitochondrial inheritance and mitochondrial heteroplasmy observed in case of avian population. © 2016 American Society of Andrology and European Academy of Andrology.

  11. Quantitative analysis of retinal changes in hypertension

    NASA Astrophysics Data System (ADS)

    Giansanti, Roberto; Boemi, Massimo; Fumelli, Paolo; Passerini, Giorgio; Zingaretti, Primo

    1995-05-01

    Arterial hypertension is a high prevalence disease in Western countries and it is associated with increased risk for cardiovascular accidents. Retinal vessel changes are common findings in patients suffering from long-standing hypertensive disease. Morphological evaluations of the fundus oculi represent a fundamental tool for the clinical approach to the patient with hypertension. A qualitative analysis of the retinal lesions is usually performed and this implies severe limitations both in the classification of the different degrees of the pathology and in the follow-up of the disease. A diagnostic system based on a quantitative analysis of the retinal changes could overcome these problems. Our computerized approach was intended for this scope. The paper concentrates on the results and the implications of a computerized approach to the automatic extraction of numerical indexes describing morphological details of the fundus oculi. A previously developed image processing and recognition system, documented elsewhere and briefly described here, was successfully tested in pre-clinical experiments and applied in the evaluation of normal as well as of pathological fundus. The software system was developed to extract indexes such as caliber and path of vessels, local tortuosity of arteries and arterioles, positions and angles of crossings between two vessels. The reliability of the results, justified by their low variability, makes feasible the standardization of quantitative parameters to be used both in the diagnosis and in the prognosis of hypertension, and also allows prospective studies based upon them.

  12. Quantitative architectural analysis of bronchial intraepithelial neoplasia

    NASA Astrophysics Data System (ADS)

    Guillaud, Martial; MacAulay, Calum E.; Le Riche, Jean C.; Dawe, Chris; Korbelik, Jagoda; Lam, Stephen

    2000-04-01

    Considerable variation exists among pathologist in the interpretation of intraepithelial neoplasia making it difficult to determine the natural history of these lesion and to establish management guidelines for chemoprevention. The aim of the study is to evaluate architectural features of pre-neoplastic progression in lung cancer, and to search for a correlation between architectural index and conventional pathology. Quantitative architectural analysis was performed on a series of normal lung biopsies and Carcinoma In Situ (CIS). Centers of gravity of the nuclei within a pre-defined region of interest were used as seeds to generate a Voronoi Diagram. About 30 features derived from the Voronoi diagram, its dual the Delaunay tessellation, and the Minimum Spanning Tree were extracted. A discriminant analysis was performed to separate between the two groups. The architectural Index was calculated for each of the bronchial biopsies that were interpreted as hyperplasia, metaplasia, mild, moderate or severe dysplasia by conventional histopathology criteria. As a group, lesions classified as CIS by conventional histopathology criteria could be distinguished from dysplasia using the architectural Index. Metaplasia was distinct from hyperplasia and hyperplasia from normal. There was overlap between severe and moderate dysplasia but mild dysplasia could be distinguished form moderate dysplasia. Bronchial intraepithelial neoplastic lesions can be degraded objectively by architectural features. Combination of architectural features and nuclear morphometric features may improve the quantitation of the changes occurring during the intra-epithelial neoplastic process.

  13. Quantitative interactome analysis reveals a chemoresistant edgotype

    PubMed Central

    Chavez, Juan D.; Schweppe, Devin K.; Eng, Jimmy K.; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E.

    2015-01-01

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for ‘edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype. PMID:26235782

  14. The method of quantitative automatic metallographic analysis

    NASA Astrophysics Data System (ADS)

    Martyushev, N. V.; Skeeba, V. Yu

    2017-01-01

    A brief analysis of the existing softwares for computer processing of microstructure photographs is presented. The descriptions of the the software package developed by the author are demonstrated. This software product is intended for quantitative metallographic analysis of digital photographs of the microstructure of materials. It allows calculating the volume fraction and the average size of particles of the structure by several hundred secants (depending on the photographs resolution) in one vision field. Besides, a special module is built in the software allowing assessing the degree of deviation of the shape of different particles and impurities from the spherical one. The article presents the main algorithms, used during the creation of the software product, and formulae according to which the software calculates the parameters of the microstructure. It is shown that the reliability of calculations depends on the quality of preparation of the microstructure.

  15. Quantitative laryngeal electromyography: turns and amplitude analysis.

    PubMed

    Statham, Melissa McCarty; Rosen, Clark A; Nandedkar, Sanjeev D; Munin, Michael C

    2010-10-01

    Laryngeal electromyography (LEMG) is primarily a qualitative examination, with no standardized approach to interpretation. The objectives of our study were to establish quantitative norms for motor unit recruitment in controls and to compare with interference pattern analysis in patients with unilateral vocal fold paralysis (VFP). Retrospective case-control study We performed LEMG of the thyroarytenoid-lateral cricoarytenoid muscle complex (TA-LCA) in 21 controls and 16 patients with unilateral VFP. Our standardized protocol used a concentric needle electrode with subjects performing variable force TA-LCA contraction. To quantify the interference pattern density, we measured turns and mean amplitude per turn for ≥10 epochs (each 500 milliseconds). Logarithmic regression analysis between amplitude and turns was used to calculate slope and intercept. Standard deviation was calculated to further define the confidence interval, enabling generation of a linear-scale graphical "cloud" of activity containing ≥90% of data points for controls and patients. Median age of controls and patients was similar (50.7 vs. 48.5 years). In controls, TA-LCA amplitude with variable contraction ranged from 145-1112 μV, and regression analysis comparing mean amplitude per turn to root-mean-square amplitude demonstrated high correlation (R = 0.82). In controls performing variable contraction, median turns per second was significantly higher compared to patients (450 vs. 290, P = .002). We first present interference pattern analysis in the TA-LCA in healthy adults and patients with unilateral VFP. Our findings indicate that motor unit recruitment can be quantitatively measured within the TA-LCA. Additionally, patients with unilateral VFP had significantly reduced turns when compared with controls.

  16. Automated quantitative image analysis of nanoparticle assembly

    NASA Astrophysics Data System (ADS)

    Murthy, Chaitanya R.; Gao, Bo; Tao, Andrea R.; Arya, Gaurav

    2015-05-01

    The ability to characterize higher-order structures formed by nanoparticle (NP) assembly is critical for predicting and engineering the properties of advanced nanocomposite materials. Here we develop a quantitative image analysis software to characterize key structural properties of NP clusters from experimental images of nanocomposites. This analysis can be carried out on images captured at intermittent times during assembly to monitor the time evolution of NP clusters in a highly automated manner. The software outputs averages and distributions in the size, radius of gyration, fractal dimension, backbone length, end-to-end distance, anisotropic ratio, and aspect ratio of NP clusters as a function of time along with bootstrapped error bounds for all calculated properties. The polydispersity in the NP building blocks and biases in the sampling of NP clusters are accounted for through the use of probabilistic weights. This software, named Particle Image Characterization Tool (PICT), has been made publicly available and could be an invaluable resource for researchers studying NP assembly. To demonstrate its practical utility, we used PICT to analyze scanning electron microscopy images taken during the assembly of surface-functionalized metal NPs of differing shapes and sizes within a polymer matrix. PICT is used to characterize and analyze the morphology of NP clusters, providing quantitative information that can be used to elucidate the physical mechanisms governing NP assembly.The ability to characterize higher-order structures formed by nanoparticle (NP) assembly is critical for predicting and engineering the properties of advanced nanocomposite materials. Here we develop a quantitative image analysis software to characterize key structural properties of NP clusters from experimental images of nanocomposites. This analysis can be carried out on images captured at intermittent times during assembly to monitor the time evolution of NP clusters in a highly automated

  17. Torpedo electromotor system development: a quantitative analysis of synaptogenesis.

    PubMed

    Fox, G Q; Kötting, D

    1984-04-10

    Synaptogenesis in the electric organ of Torpedo marmorato has been studied quantitatively at the ultrastructural level of observation. In addition to establishing the normal developmental time course for this event we were interested in determining whether a gradient of synaptogenesis might be present because the electric organ produces several morphologically recognizable spatiotemporal gradients during its early ontogeny. These gradients genesis of electrocyte columns, both gradients of which are operative for periods of weeks. No gradient of synaptogenesis was found, indicating this to be a synchronous process. The idea is advanced that synaptogenesis in the electric organ is modulated by extrinsic influences, many of which may originate from the target electrocytes which, by this time, have become synchronized in their development.

  18. Materials characterization through quantitative digital image analysis

    SciTech Connect

    J. Philliber; B. Antoun; B. Somerday; N. Yang

    2000-07-01

    A digital image analysis system has been developed to allow advanced quantitative measurement of microstructural features. This capability is maintained as part of the microscopy facility at Sandia, Livermore. The system records images digitally, eliminating the use of film. Images obtained from other sources may also be imported into the system. Subsequent digital image processing enhances image appearance through the contrast and brightness adjustments. The system measures a variety of user-defined microstructural features--including area fraction, particle size and spatial distributions, grain sizes and orientations of elongated particles. These measurements are made in a semi-automatic mode through the use of macro programs and a computer controlled translation stage. A routine has been developed to create large montages of 50+ separate images. Individual image frames are matched to the nearest pixel to create seamless montages. Results from three different studies are presented to illustrate the capabilities of the system.

  19. Near Real Time Quantitative Gas Analysis Techniques

    NASA Astrophysics Data System (ADS)

    Herget, William F.; Tromp, Marianne L.; Anderson, Charles R.

    1985-12-01

    A Fourier transform infrared (FT-IR) - based system has been developed and is undergoing evaluation for near real time multicomponent quantitative analysis of undiluted gaseous automotive exhaust emissions. The total system includes: (1) a gas conditioning system (GCS) for tracer gas injection, gas mixing, and temperature stabilization; and (2) an exhaust gas analyzer (EGA) consisting of a sample cell, an FT-IR system, and a computerized data processing system. Tests have shown that the system can monitor about 20 individual species (concentrations down to the 1-20 ppm range) with a time resolution of one second. Tests have been conducted on a chassis dynamometer system utilizing different autos, different fuels, and different driving cycles. Results were compared with those obtained using a standard constant volume sampling (CVS) system.

  20. Quantitative Analysis of Tremors in Welders

    PubMed Central

    Sanchez-Ramos, Juan; Reimer, Dacy; Zesiewicz, Theresa; Sullivan, Kelly; Nausieda, Paul A.

    2011-01-01

    Background: Workers chronically exposed to manganese in welding fumes may develop an extra-pyramidal syndrome with postural and action tremors. Objectives: To determine the utility of tremor analysis in distinguishing tremors among workers exposed to welding fumes, patients with Idiopathic Parkinson’s Disease (IPD) and Essential Tremor (ET). Methods: Retrospective study of recorded tremor in subjects from academic Movement Disorders Clinics and Welders. Quantitative tremor analysis was performed and associated with clinical status. Results: Postural tremor intensity was increased in Welders and ET and was associated with visibly greater amplitude of tremor with arms extended. Mean center frequencies (Cf) of welders and patients with ET were significantly higher than the mean Cf of PD subjects. Although both the welders and the ET group exhibited a higher Cf with arms extended, welders could be distinguished from the ET subjects by a significantly lower Cf of the rest tremor than that measured in ET subjects. Conclusions: In the context of an appropriate exposure history and neurological examination, tremor analysis may be useful in the diagnosis of manganese-related extra-pyramidal manifestations. PMID:21655131

  1. Nonlinear dynamics and quantitative EEG analysis.

    PubMed

    Jansen, B H

    1996-01-01

    Quantitative, computerized electroencephalogram (EEG) analysis appears to be based on a phenomenological approach to EEG interpretation, and is primarily rooted in linear systems theory. A fundamentally different approach to computerized EEG analysis, however, is making its way into the laboratories. The basic idea, inspired by recent advances in the area of nonlinear dynamics and chaos theory, is to view an EEG as the output of a deterministic system of relatively simple complexity, but containing nonlinearities. This suggests that studying the geometrical dynamics of EEGs, and the development of neurophysiologically realistic models of EEG generation may produce more successful automated EEG analysis techniques than the classical, stochastic methods. A review of the fundamentals of chaos theory is provided. Evidence supporting the nonlinear dynamics paradigm to EEG interpretation is presented, and the kind of new information that can be extracted from the EEG is discussed. A case is made that a nonlinear dynamic systems viewpoint to EEG generation will profoundly affect the way EEG interpretation is currently done.

  2. A comparative ultrastructural analysis of spermatozoa in Pleurodema (Anura, Leptodactylidae, Leiuperinae).

    PubMed

    Cruz, Julio C; Ferraro, Daiana P; Farías, Alejandro; Santos, Julio S; Recco-Pimentel, Shirlei M; Faivovich, Julián; Hermida, Gladys N

    2016-07-01

    This study describes the spermatozoa of 10 of the 15 species of the Neotropical frog genus Pleurodema through transmission electron microscopy. The diversity of oviposition modes coupled with a recent phylogenetic hypothesis of Pleurodema makes it an interesting group for the study of ultrastructural sperm evolution in relation to fertilization environment and egg-clutch structure. We found that Pleurodema has an unusual variability in sperm morphology. The more variable structures were the acrosomal complex, the midpiece, and the tail. The acrosomal complex has all the structures commonly reported in hyloid frogs but with different degree of development of the subacrosomal cone. Regarding the midpiece, the variability is given by the presence or absence of the mitochondrial collar. Finally, the tail is the most variable structure, ranging from single (only axoneme) to more complex (presence of paraxonemal rod, cytoplasmic sheath, and undulating membrane), with the absence of the typical axial fiber present in hyloid frogs, also shared with some other genera of Leiuperinae. J. Morphol. 277:957-977, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. An ultrastructural analysis of the prototype single-step adhesive applied on enamel and dentin surfaces.

    PubMed

    Han, Linlin; Cruz, Edward; Fukushima, Masayoshi; Okamoto, Akira; Okiji, Takashi

    2004-09-01

    A new type of self-etching agent, the single-step adhesive, was developed. The purpose of this study was to investigate the difference in the ultrastructural features of enamel and dentin surfaces following application of the prototype single-step adhesive (EXM618, 3M, MN, USA). Extracted caries-free human premolars were used in this study. Occlusal enamels of teeth--to be used as cut surface specimens--were removed perpendicular to the long axis of the specimens. The mesial and distal surfaces of these teeth, on the other hand, were used as uncut surface specimens in the test. In addition, Mega Bond (Kuraray Medical Inc., Tokyo, Japan) and Xeno CFII Bond (Dentsply Sankin, Tokyo, Japan) were used as controls. After covering half of the tooth surfaces with nail varnish (for control), the other half of each surface was treated with one of the three test adhesives--EXM618, Mega Bond, or Xeno CFII Bond--according to the manufacturer's recommendations. Conditioned enamel and dentin surfaces (i.e., decalcified depth and rugged surface) were observed with a scanning confocal laser microscope (SCLM 1100, Olympus, Tokyo, Japan; henceforth abbreviated as SCLM). Based on the findings of this study, the prototype single-step adhesive EXM618 appears to be suitable for use in dental clinics.

  4. Morphological and ultrastructural analysis of Turritopsis nutricula during life cycle reversal.

    PubMed

    Carla', E C; Pagliara, P; Piraino, S; Boero, F; Dini, L

    2003-06-01

    The hydrozoa life cycle is characterized, in normal conditions, by the alternation of a post-larval benthic polyp and an adult pelagic medusa; however, some species of Hydrozoa react to environmental stress by reverting their life cycle: i.e. an adult medusa goes back to the juvenile stage of polyp. This very uncommon life cycle could be considered as some sort of inverted metamorphosis. A morphological study of different stages during the reverted life cycle of Turritopsis nutricula led to the characterization of four different stages: healthy medusa, unhealthy medusa, four-leaf clover and cyst. The ultrastructural study of the cellular modifications (during the life cycle reversion of T. nutricula) showed the presence of both degenerative and apoptotic processes. Degeneration was prevalent during the unhealthy medusa and four-leaf clover stages, while the apoptotic rate was higher during the healthy medusa and cyst stages. The significant presence of degenerative and apoptotic processes could be related to the occurrence of a sort of metamorphosis when an adult medusa transforms itself into a polyp.

  5. Ultrastructural analysis of in vivo expanded corneal epithelium on amniotic membrane.

    PubMed

    Ha, Hyo Shin; Song, Kye Yong; Kim, Jae Chan

    2006-06-01

    The purpose of this study is to characterize and compare the ultrastructural changes occurring during the in vivo cultivation of corneal epithelium on amniotic membrane (AM) at several different time points. Corneal burn patients (n=7) with a corneal epithelial defect and severe limbal damage were selected. Initially, AM transplantation with limbal autograft was performed at the acute stage of corneal burn to reconstruct the damaged ocular surface. One to six (mean interval; 3.3+/-1.2) months later, the central part of AM containing an in vivo expanded corneal epithelium was excised and retransplanted in adjacent lesions. The excised epithelium with AM was examined by electron microscopy and immunohistochemical study. By electron microscopy, one and two months after expansion, cultivated epithelium on AM showed an undifferentiated epithelium and an incomplete basement membrane (BM). But, after three months, the cultivated epithelium began to differentiate into a multilayered epithelium with a continuous BM with increased hemidesmosomes. These findings were further confirmed by immunohistochemical study, that cytokeratin K3 was expressed in the cultivated corneal epithelium and newly formed BM was partially positive of collagen IV at three months. At least 3 months may be needed for the proliferation and differentiation of in vivo cultivated corneal epithelium on AM.

  6. An ultrastructural and carotenoid analysis of the red ventrum of the Japanese newt, Cynops pyrrhogaster.

    PubMed

    Matsui, Kumi; Marunouchi, Junsuke; Nakamura, Masahisa

    2002-08-01

    The ventral skin of the wild Japanese newt Cynops pyrrhogaster is creamy at metamorphosis, but turns red when mature. The color of the ventral skin of laboratory (lab)-reared newts stays yellow throughout their life. However, the mechanism for the red coloration of this animal still remains unknown. In this study, we have performed ultrastructural and carotenoid analyses of the red ventrum of wild and lab-reared Japanese newts. Using electron microscopy, we observed a number of xanthophores having ring carotenoid vesicles (rcv) and homogenous carotenoid granules (hcg) in the ventral red skin of the wild newt. In the skin, beta-carotene and five other kinds of carotenoids were detected by thin-layer chromatography (TLC). In the ventral yellow skin of lab-reared newts, however, only beta-carotene and three other kinds of carotenoids were found. The total amount of carotenoids in the red skin of the wild adult newt was six times more than that of the yellow skin of the lab-reared newt. Moreover, rcv were more abundant in xanthophores in red skin, but hcg were more abundant in yellow skin. These results, taken together, suggest that the presence of carotenoids in rcv in xanthophores is one of the critical factors for producing the red ventral coloration of the Japanese newt C. pyrrhogaster.

  7. Experimental white piedra: a robust approach to ultrastructural analysis, scanning electron microscopy and etiological discoveries.

    PubMed

    Inácio, Cicero P; Rocha, Ana Paula S; Barbosa, Renan do N; Oliveira, Neiva T; Silva, Josineide C; de Lima-Neto, Reginaldo G; Macêdo, Danielle Patrícia C; Neves, Rejane P

    2016-01-01

    White piedra is a fungal infection characterized by nodules comprised of Trichosporon species and restricted to the extrafollicular portion of the hair shaft. The diagnosis is based on clinical and mycological characteristics, and must be confirmed with a precise identification of the etiological agent. This research aimed to develop an in vitro infection model of white piedra and analyze its morphological and ultra-structural aspects. In the process, hair infection was induced using eight isolates of the genus Trichosporon maintained in the Culture Collection Micoteca URM. The ITS and IGS1 regions were sequenced for taxonomic confirmation. Scanning Electron Microscope (SEM) was performed at the Strategic Center for Northeast Technologies (CETENE). The scanning electron microscope was equipped with an Energy Dispersion Spectrometer (EDS). The Trichosporon isolates were identified as Trichosporon asahii (6) and Trichosporon montevideense (2) by internal transcript spacer (ITS) region and intergenic spacer 1 region (IGS1) sequencing. All eight strains were used to induce the in vitro hair infection, and nodules formed after the incubation period. Temperature variations and high humidity were not observed to be related to the development of this hair disease. The main chemical constituents detected in the nodules were carbon, nitrogen and oxygen, as well as a low level of sulfur. The absence of calcium, combined with the low level of sulfur, might explain the soft nature of the white piedra nodules. This study demonstrated that several Trichosporon species may be responsible for causing white piedra.

  8. Ultrastructural analysis of salivary glands in a phytophagous stink bug revealed the presence of unexpected muscles.

    PubMed

    Castellanos, Nathaly; Martínez, Luis C; Silva, Eder H; Teodoro, Adenir V; Serrão, José Eduardo; Oliveira, Eugênio E

    2017-01-01

    The exceptional abilities of stink bugs (Hemiptera: Pentatomidae) to colonize a diverse group of plants have been attributed to the feeding behaviors and the functions of the salivary complex of these insects. Here, we describe the ultrastructure of the salivary glands of the Neotropical brown stink bug, Euschistus heros, which is a major component of the pentatomid pest complex on soybeans, Glycine max, in the neotropics. Our results revealed a salivary gland complex consisting of two lobes (i.e., anterior and posterior), with a constriction between them (i.e., the hilum), in which the salivary and accessory gland ducts are inserted. The principal gland epithelium has a single layer of cells lining an enlarged lumen filled with saliva, and these cells are cuboidal, rich in rough endoplasmic reticulum and secretory vesicles, with well-developed nuclei, all of which are typical features of protein-secreting cells. We report, for the first time in insects, the presence of a layer of muscle cells surrounding the columnar hilum epithelium. The accessory salivary gland cells are cuboidal with nuclei containing condensed chromatin and cytoplasm rich in vacuoles and rough endoplasmic reticulum, indicating the potential involvement of these glands in water transport/secretion. The lumen content of each lobe of the principal gland suggests that the lobes produce different compounds. Thus, our results suggest that the E. heros salivary complex might have unconventional mechanisms to mix/release saliva, which might help explain the polyphagous abilities of these insects.

  9. The human myotendinous junction: an ultrastructural and 3D analysis study.

    PubMed

    Knudsen, A B; Larsen, M; Mackey, A L; Hjort, M; Hansen, K K; Qvortrup, K; Kjaer, M; Krogsgaard, M R

    2015-02-01

    The myotendinous junction (MTJ) is a specialized structure in the musculotendinous system, where force is transmitted from muscle to tendon. Animal models have shown that the MTJ takes form of tendon finger-like processes merging with muscle tissue. The human MTJ is largely unknown and has never been described in three dimensions (3D). The aim of this study was to describe the ultrastructure of the human MTJ and render 3D reconstructions. Fourteen subjects (age 25 ± 3 years) with isolated injury of the anterior cruciate ligament (ACL), scheduled for reconstruction with a semitendinosus/gracilis graft were included. Semitendinosus and gracilis tendons were stripped as grafts for the ACL reconstruction. The MTJ was isolated from the grafts and prepared for transmission electron microscopy (TEM) and focused ion beam/scanning electron microscopy. It was possible to isolate recognizable MTJ tissue from all 14 patients. TEM images displayed similarities to observations in animals: Sarcolemmal evaginations observed as finger-like processes from the tendon and endomysium surrounding the muscle fibers, with myofilaments extending from the final Z-line of the muscle fiber merging with the tendon tissue. The 3D reconstruction revealed that tendon made ridge-like protrusions, which interdigitiated with groove-like indentations in the muscle cell. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. New ultrastructural analysis of the invasive apparatus of the Plasmodium ookinete.

    PubMed

    Patra, Kailash P; Vinetz, Joseph M

    2012-09-01

    Invasion of the mosquito midgut by the Plasmodium ookinete determines the success of transmission of malaria parasites from humans to mosquitoes and therefore, is a potential target for molecular intervention. Here, we show higher-resolution ultrastructural details of developing and mature P. gallinaceum ookinetes than previously available. Improved fixation and processing methods yielded substantially improved transmission electron micrographs of ookinetes, particularly with regard to visualization of subcellular secretory and other organelles. These new images provide new insights into the synthesis and function of vital invasive machinery focused on the following features: apical membrane protrusions presumptively used for attachment and protein secretion, dark spherical bodies at the apical end of the mature ookinete, and the presence of a dense array of micronemes apposed to microtubules at the apical end of the ookinete involved in constitutive secretion. This work advances understanding of the molecular and cellular details of the Plasmodium ookinete and provides the basis of future, more detailed mechanistic experimentation on the biology of the Plasmodium ookinete.

  11. Ultrastructural Analysis of in vivo Expanded Corneal Epithelium on Amniotic Membrane

    PubMed Central

    Ha, Hyo Shin; Song, Kye Yong

    2006-01-01

    The purpose of this study is to characterize and compare the ultrastructural changes occurring during the in vivo cultivation of corneal epithelium on amniotic membrane (AM) at several different time points. Corneal burn patients (n=7) with a corneal epithelial defect and severe limbal damage were selected. Initially, AM transplantation with limbal autograft was performed at the acute stage of corneal burn to reconstruct the damaged ocular surface. One to six (mean interval; 3.3±1.2) months later, the central part of AM containing an in vivo expanded corneal epithelium was excised and retransplanted in adjacent lesions. The excised epithelium with AM was examined by electron microscopy and immunohistochemical study. By electron microscopy, one and two months after expansion, cultivated epithelium on AM showed an undifferentiated epithelium and an incomplete basement membrane (BM). But, after three months, the cultivated epithelium began to differentiate into a multilayered epithelium with a continuous BM with increased hemidesmosomes. These findings were further confirmed by immunohistochemical study, that cytokeratin K3 was expressed in the cultivated corneal epithelium and newly formed BM was partially positive of collagen IV at three months. At least 3 months may be needed for the proliferation and differentiation of in vivo cultivated corneal epithelium on AM. PMID:16778403

  12. Ultrastructural, physiological and proteomic analysis of Nostoc flagelliforme in response to dehydration and rehydration.

    PubMed

    Liang, Wenyu; Zhou, Youwen; Wang, Lingxia; You, Xiangrong; Zhang, Yaping; Cheng, Chi-Lien; Chen, Wei

    2012-10-22

    Nostoc flagelliforme must undergo a dehydration/rehydration cycle during its growth stages; the mechanisms underlying this constraint are examined. The novel insights into N. flagelliforme's response to desiccation and rehydration at ultrastructural, physiological and proteomic levels were offered. The structure of colonies and cells remained unchanged in response to dehydration and rehydration treatments except that the sheath appeared shrunken, and both the quantity and volume of vacuoles were decreased when dehydrated compared with rehydration. A significant increase in photosynthesis, respiration, total Rubisco activity, superoxide anion level, SOD, CAT, POD, nitrogenase and glutamine synthetase (GS) activities in response to rehydration was noted, whereas H(2)O(2), ammonium, proline and glutamate contents all registered a decrease. 32 differentially expressed proteins between dehydrated and rehydrated colonies were categorized according to their predicted functions into secretion, signaling, transcription and translation, antioxidative processes, nitrogen metabolism, energy metabolism, lipid metabolism and chaperonin. The dehydration is a quiescent state in which metabolism is down-regulated, upon rehydration, a metabolic shift occurs from quiescent to active. The specific metabolic and regulated mechanisms to accommodate the dehydration/rehydration cycle in N. flagelliforme is reported here.

  13. Quantitative Analysis of Triple Mutant Genetic Interactions

    PubMed Central

    Braberg, Hannes; Alexander, Richard; Shales, Michael; Xu, Jiewei; Franks-Skiba, Kathleen E.; Wu, Qiuqin; Haber, James E.; Krogan, Nevan J.

    2014-01-01

    The quantitative analysis of genetic interactions between pairs of gene mutations has proven effective for characterizing cellular functions but can miss important interactions for functionally redundant genes. To address this limitation, we have developed an approach termed Triple Mutant Analysis (TMA). The procedure relies on a query strain that contains two deletions in a pair of redundant or otherwise related genes, that is crossed against a panel of candidate deletion strains to isolate triple mutants and measure their growth. A central feature of TMA is to interrogate mutants that are synthetically sick when two other genes are deleted but interact minimally with either single deletion. This approach has been valuable for discovering genes that restore critical functions when the principle actors are deleted. TMA has also uncovered double mutant combinations that produce severe defects because a third protein becomes deregulated and acts in a deleterious fashion, and it has revealed functional differences between proteins presumed to act together. The protocol is optimized for Singer ROTOR pinning robots, takes 3 weeks to complete, and measures interactions for up to 30 double mutants against a library of 1536 single mutants. PMID:25010907

  14. Seniors' online communities: a quantitative content analysis.

    PubMed

    Nimrod, Galit

    2010-06-01

    To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. There was a constant increase in the daily activity level during the research period. Content analysis identified 13 main subjects discussed in the communities, including (in descending order) "Fun on line," "Retirement," "Family," "Health," "Work and Study," "Recreation" "Finance," "Religion and Spirituality," "Technology," "Aging," "Civic and Social," "Shopping," and "Travels." The overall tone was somewhat more positive than negative. The findings suggest that the utilities of Information and Communications Technologies for older adults that were identified in previous research are valid for seniors' online communities as well. However, the findings suggest several other possible benefits, which may be available only to online communities. The communities may provide social support, contribute to self-preservation, and serve as an opportunity for self-discovery and growth. Because they offer both leisure activity and an expanded social network, it is suggested that active participation in the communities may contribute to the well-being of older adults. Directions for future research and applied implications are further discussed.

  15. Quantitative analysis of protein turnover in plants.

    PubMed

    Nelson, Clark J; Li, Lei; Millar, A Harvey

    2014-03-01

    Proteins are constantly being synthesised and degraded as plant cells age and as plants grow, develop and adapt the proteome. Given that plants develop through a series of events from germination to fruiting and even undertake whole organ senescence, an understanding of protein turnover as a fundamental part of this process in plants is essential. Both synthesis and degradation processes are spatially separated in a cell across its compartmented structure. The majority of protein synthesis occurs in the cytosol, while synthesis of specific components occurs inside plastids and mitochondria. Degradation of proteins occurs in both the cytosol, through the action of the plant proteasome, and in organelles and lytic structures through different protease classes. Tracking the specific synthesis and degradation rate of individual proteins can be undertaken using stable isotope feeding and the ability of peptide MS to track labelled peptide fractions over time. Mathematical modelling can be used to follow the isotope signature of newly synthesised protein as it accumulates and natural abundance proteins as they are lost through degradation. Different technical and biological constraints govern the potential for the use of (13)C, (15)N, (2)H and (18)O for these experiments in complete labelling and partial labelling strategies. Future development of quantitative protein turnover analysis will involve analysis of protein populations in complexes and subcellular compartments, assessing the effect of PTMs and integrating turnover studies into wider system biology study of plants. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Shear bond strength and ultrastructural interface analysis of different adhesive systems to Er:YAG laser-prepared dentin.

    PubMed

    Guven, Yeliz; Aktoren, Oya

    2015-02-01

    The aim of this study was to evaluate the shear bond strength (SBS) of a microhybrid composite resin bonded with three different adhesive systems to Er:YAG laser- (EL) or bur-prepared dentin surfaces and to analyze the quality and ultrastructure of the adhesive-dentin interfaces by scanning electron microscopy (SEM). The specimens prepared for SBS test and SEM analysis were randomly assigned to eight groups (G1-G8): G1, EL (Fidelis PlusIII, Fotona) + Clearfil S3 Bond (C3S); G2, EL + AdperSE Plus (SE); G3, EL + laser etch + Adper Single Bond2 (SB2); G4, EL + acid etch + SB2; G5, EL + SB2 (no etching); G6, bur + acid etch + SB2; G7, bur + S3; G8, bur + SE. Laser was used in very short pulse mode at a setting of 200 mJ/20 Hz for dentin preparation and at 80 mJ/10 Hz for dentin etching. Bond strength test: 3.5 × 2.0 mm cylindrical molds were placed onto adhesives and filled with the composites. After 24 h in distilled water, SBS was tested at a crosshead speed of 0.5 mm/min. SEM analysis: The dentin-adhesive interfaces were evaluated for the ultrastructure of hybrid layer. Data of SBS (MPa) were statistically analyzed by ANOVA and Tukey HSD. ER:YAG laser-prepared dentin has demonstrated significantly more SBS (p < 0.01) for SE when compared to bur-prepared dentin. No significancies (p > 0.05) in SBS have been determined between the total-etch adhesive applied groups with regard to etching types. SEM analysis revealed that hybrid layers obtained in Er:YAG laser-irradiated dentin exhibited more irregular and non-homogeneous pattern than the conventionally prepared dentin. In conclusion, SE Bond demonstrated superior results in Er:YAG laser-ablated dentin compared to bur-prepared dentin.

  17. In vivo ultrastructural analysis of the intimate relationship between polymorphonuclear leukocytes and the chlamydial developmental cycle.

    PubMed

    Rank, Roger G; Whittimore, Judy; Bowlin, Anne K; Wyrick, Priscilla B

    2011-08-01

    We utilized a recently developed model of intracervical infection with Chlamydia muridarum in the mouse to elicit a relatively synchronous infection during the initial developmental cycle in order to examine at the ultrastructural level the development of both the chlamydial inclusion and the onset of the inflammatory response. At 18 h after infection, only a few elementary bodies attached to cells were visible, as were an occasional intracellular intermediate body and reticulate body. By 24 h, inclusions had 2 to 5 reticulate bodies and were beginning to fuse. A few polymorphonuclear leukocytes (PMNs) were already present in the epithelium in the vicinity of and directly adjacent to infected cells. By 30 h, the inclusions were larger and consisted solely of reticulate bodies, but by 36 to 42 h, they contained intermediate bodies and elementary bodies as well. Many PMNs were adjacent to or actually inside infected cells. Chlamydiae appeared to exit the cell either (i) through disintegration of the inclusion membrane and rupture of the cell, (ii) by dislodgement of the cell from the epithelium by PMNs, or (iii) by direct invasion of the infected cell by the PMNs. When PMNs were depleted, the number of released elementary bodies was significantly greater as determined both visually and by culture. Interestingly, depletion of PMNs revealed the presence of inclusions containing aberrant reticulate bodies, reminiscent of effects seen in vitro when chlamydiae are incubated with gamma interferon. In vivo evidence for the contact-dependent development hypothesis, a potential mechanism for triggering the conversion of reticulate bodies to elementary bodies, and for translocation of lipid droplets into the inclusion is also presented.

  18. Ultrastructural Analysis of Incinerated Teeth by Scanning Electron Microscope – A Short Study

    PubMed Central

    Swamy, Sugunakar Raju Godishala; Muddana, Keerthi

    2016-01-01

    Introduction In forensic context precise knowledge on physical and histological changes of teeth subjected to high temperatures is of great importance. Preserving fragile incinerated teeth for physical, histological and ultra structural examinations is essential in fire investigations involving the origin of fire, its cause as well as the identification of victims which relies on a thorough understanding of the structural changes in dental tissues subjected to heat. Aim The study was conducted to evaluate the physical and ultrastructural changes seen in freshly extracted teeth when subjected to gradual heating at different temperatures using Scanning Electron Microscope (SEM). Settings and Design Freshly extracted teeth collected from subjects of different age groups were subjected to different temperatures using laboratory furnace and findings were correlated to the temperature. Materials and Methods The study was conducted on 60 healthy freshly extracted teeth belonging to age group between 20-30 years. Group A comprised of control group which included teeth that were not subjected to heat whereas Group B, C and D comprised of teeth that were subjected to different temperatures i.e., 100oC, 300oC and 600oC respectively for a time of fifteen minutes in laboratory furnace, after which they were processed for SEM examination. Each group included 15 teeth; 5 anteriors, 5 premolars and 5 molars. Results Examination under SEM revealed definite ultra structural changes which were explicitly seen at particular temperatures (100oC, 300oC and 600oC). The samples showed cracks and charring of the tooth structure with ultra structural findings such as pebbles, granules, dots on enamel surface; and soap bubble pattern, honey comb pattern and snail track pattern on cementum surface. Conclusion Because of the consistency of morphological changes and the ultra structural patterns at various temperatures, evaluation of incinerated dental remains using SEM can provide additional

  19. [Ultrastructural observation on nymphal Armillifer sp. by scanning electron microscopy and phylogenetic analysis based on 18S rRNA].

    PubMed

    Li, Jian; Shi, Yun-Liang; Shi, Wei; Fang, Fang; Zhou, Qing-An; Li, Wen-Wen; He, Guo-Sheng; Huang, Wei-Yi

    2012-04-30

    To observe the ultrastructure of nymphal Armillifer sp. isolated from Macaca fascicularis by using scanning electron microscope (SEM), and analyze the phylogenetic relationships based on 18S rRNA gene sequences. The parasite samples stored in 70% alcohol were fixed by glutaraldehyde and osmium peroxide. Ultrastructural characters of those samples were observed under SEM. Amplification and sequencing of the 18S rRNA gene were performed following the extraction of total genome DNA. Sequence analysis was performed based on multiple alignment using ClustalX1.83, while phylogenetic analysis was made by Neighbor-Joining method using MEGA4.0. The nymphs were in cylindrical shape, the body slightly claviform tapering to posterior end. Abdominal annuli were gradually widened from anterior to posterior parts, the 12th-13th abdominal annuli of which were similar in width. The annuli ranged closer in the front half body, whereas in the latter part there were certain gaps between them. The circular-shaped mouth located in the middle of head ventrally. Folds were seen in inner margin of the mouth with a pair of curved hooks on both sides above it which practically disposed in a straight line. Two pairs of large sensory papillae were observed symmetrically over the last thoracic annulus of cephalothoraxs lying below the outer hook, and the first abdominal annulus was near the median ventral line. The number of abdominal annuli was 29, not including 2 incomplete terminal annuli. Rounded sensory papillae were fully distributed on the body surface, except the dorsal side of head and the ventral part of the terminal annulus. Agglomerate-like anus opening was observed at the end of ventral abdominal annuli and distinctly sub-terminal. These morphological features demonstrated that the nymphs were highly similar with that of Armillifer moniliformis Diesing, 1835. A fragment of 18SrRNA gene (1 836 bp) sequences was obtained by PCR combined with sequencing, and was registered to the Gene

  20. Applying Knowledge of Quantitative Design and Analysis

    ERIC Educational Resources Information Center

    Baskas, Richard S.

    2011-01-01

    This study compared and contrasted two quantitative scholarly articles in relation to their research designs. Their designs were analyzed by the comparison of research references and research specific vocabulary to describe how various research methods were used. When researching and analyzing quantitative scholarly articles, it is imperative to…

  1. Quantitative color analysis for capillaroscopy image segmentation.

    PubMed

    Goffredo, Michela; Schmid, Maurizio; Conforto, Silvia; Amorosi, Beatrice; D'Alessio, Tommaso; Palma, Claudio

    2012-06-01

    This communication introduces a novel approach for quantitatively evaluating the role of color space decomposition in digital nailfold capillaroscopy analysis. It is clinically recognized that any alterations of the capillary pattern, at the periungual skin region, are directly related to dermatologic and rheumatic diseases. The proposed algorithm for the segmentation of digital capillaroscopy images is optimized with respect to the choice of the color space and the contrast variation. Since the color space is a critical factor for segmenting low-contrast images, an exhaustive comparison between different color channels is conducted and a novel color channel combination is presented. Results from images of 15 healthy subjects are compared with annotated data, i.e. selected images approved by clinicians. By comparison, a set of figures of merit, which highlights the algorithm capability to correctly segment capillaries, their shape and their number, is extracted. Experimental tests depict that the optimized procedure for capillaries segmentation, based on a novel color channel combination, presents values of average accuracy higher than 0.8, and extracts capillaries whose shape and granularity are acceptable. The obtained results are particularly encouraging for future developments on the classification of capillary patterns with respect to dermatologic and rheumatic diseases.

  2. Ultrastructural analysis of oral exfoliated epithelial cells of tobacco smokers and betel nut chewers: A scanning electron microscopy study

    PubMed Central

    Khan, Sameera Shamim; Shreedhar, Balasundari; Kamboj, Mala

    2016-01-01

    Background: The study was undertaken to correlate epithelial surface pattern changes of oral exfoliated cells of tobacco smokers and betel nut chewers and also to compare them with patients of oral squamous cell carcinoma (OSCC) and healthy individuals. Materials and Methods: In this cross-sectional study, a total of fifty persons were included in the study, out of which thirty formed the study group (15 each tobacco smokers and betel nut chewers) and twenty formed the control group (ten each of OSCC patients – positive control and ten normal buccal mucosa – negative control). Their oral exfoliated cells were scraped, fixed, and studied under scanning electron microscope (SEM). The statistical analysis was determined using ANOVA, Tukey honestly significant difference, Chi-square test, and statistical SPASS software, P < 0.05. Results: OSCC, Individual cell modifications, intercellular relationships and surface characteristics observed by scanning electron microscopy between OSCC, tobacco smokers, betel nut chewers compared to normal oral mucosa have been tabulated. Conclusion: In normal oral mucosa, cell surface morphology depends on the state of keratinization of the tissue. Thus, it could prove helpful in detecting any carcinomatous change at its incipient stage and also give an insight into the ultra-structural details of cellular differentiations in epithelial tissues. PMID:28182055

  3. Ultrastructural analysis of the integument of a desert-adapted mammal, the one-humped camel (Camelus dromedarius).

    PubMed

    Pfeiffer, C J; Osman, A H K; Pfeiffer, D C

    2006-04-01

    In this study, we conducted a light microscopic and ultrastructural analysis of the integument of the one-humped camel (Camelus dromedarius). In general, the epidermal strata of the camel integument appeared typical of those found in non-desert mammals. Two cell populations were noted in the stratum basale: one with a flat, non-serrated base and the other with a highly serrated base. Typical fine structure was observed in keratinocytes of the stratum spinosum and stratum granulosum. The stratum corneum was six to 10 cells thick. Within the different strata, overall cell morphologies and the general distribution and relative abundance of cellular organelles appeared typical. Dermal features included the presence of myoepithelial cells surrounding apocrine tubular glands. Inter- or intracellular canaliculi within the secretory cells of the apocrine glands, reported to be present in certain other non-desert mammals, were not evident in the camel. Together, these data indicate that while the camel is clearly adapted for a desert lifestyle, these adaptations do not include significant specializations at the cellular or subcellular level in the integument.

  4. Ultrastructural and histochemical analysis reveals ethylene-induced responses underlying reduced peel collapse in detached citrus fruit.

    PubMed

    Cajuste, Jacques F; García-Breijo, Francisco J; Reig-Armiñana, José; Lafuente, María T

    2011-10-01

    Fruits from many citrus cultivars develop depressed areas in the flavedo (outer part of the peel) and albedo (inner part) following detachment. Although ultrastructural analysis may provide important information about multiple plant responses to stresses and external stimuli at the cell and tissue levels, and despite the proved efficacy of ethylene in reducing peel damage in citrus fruit, cytological responses of this horticultural crop to protective ethylene concentrations have not yet been reported. We show that applying high ethylene levels (2 μL L(-1) for 14 days) causes sublethal stress as it favored the alteration of cuticle, vacuole, middle lamella and primary wall, especially in the albedo cells, but reduced peel collapse in detached mature "Navelate" oranges (C. sinensis, L. Osbeck) held under nonstressful environmental conditions (22°C and 90-95% RH). Ethylene did not induce relevant changes in lignification but favored the deposition of pectic exudates and the release of sugars from degradation of cell polysaccharides including starch, cellulose, and pectins. In contrast, inhibiting ethylene perception by applying 1-methylcyclopropene (1-MCP) reduced these ethylene-related responses and favored degradation of cell membranes and peel damage. The overall results reflect that mature oranges tolerate high ethylene levels that might favor the activation of defense responses involving oxidative-stress related mechanisms and recycling of nutrients and carbon supply to enable cells to sustain respiration and cope with carbon deprivation stress caused by detachment.

  5. Application of a low-level laser therapy and the purified protein from natural latex (Hevea brasiliensis) in the controlled crush injury of the sciatic nerve of rats: a morphological, quantitative, and ultrastructural study.

    PubMed

    Dias, Fernando José; Issa, João Paulo Mardegan; Iyomasa, Mamie Mizusaki; Coutinho-Netto, Joaquim; Calzzani, Ricardo Alexandre Junqueria; Iyomasa, Daniela Mizusaki; Sousa, Luiz Gustavo; de Almeida, Sonia Regina Yokomizo; Cury, Diego Pulzatto; Watanabe, Ii-sei

    2013-01-01

    This study analyzed the effects of a low-level laser therapy (LLLT, 15 J/cm(2), 780 nm wavelength) and the natural latex protein (P1, 0.1%) in sciatic nerve after crush injury (15 Kgf, axonotmesis) in rats. Sixty rats (male, 250 g) were allocated into the 6 groups (n = 10): CG-control group; EG-nerve exposed; IG-injured nerve without treatment; LG-crushed nerve treated with LLLT; PG-injured nerve treated with P1; and LPG-injured nerve treated with LLLT and P1. After 4 or 8 weeks, the nerve samples were processed for morphological, histological quantification and ultrastructural analysis. After 4 weeks, the myelin density and morphological characteristics improved in groups LG, PG, and LPG compared to IG. After 8 weeks, PG, and LPG were similar to CG and the capillary density was higher in the LG, PG, and LPG. In the ultrastructural analysis the PG and LPG had characteristics that were similar to the CG. The application of LLLT and/or P1 improved the recovery from the nerve crush injury, and in the long term, the P1 protein was the better treatment used, since only the application of LLLT has not reached the same results, and these treatments applied together did not potentiate the recovery.

  6. Quantitative Analysis of Hypoperfusion in Acute Stroke

    PubMed Central

    Nael, Kambiz; Meshksar, Arash; Liebeskind, David S.; Coull, Bruce M.; Krupinski, Elizabeth A.; Villablanca, J. Pablo

    2014-01-01

    Background and Purpose This study compares the concordance between arterial spin labeling (ASL) and dynamic susceptibility contrast (DSC) for the identification of regional hypoperfusion and diffusion-perfusion mismatch tissue classification using a quantitative method. Methods The inclusion criteria for this retrospective study were as follows: patients with acute ischemic syndrome with symptom onset <24 hours and acquisition of both ASL and DSC MR perfusion. The volumes of infarction and hypoperfused lesions were calculated on ASL and DSC multi-parametric maps. Patients were classified into reperfused, matched, or mismatch groups using time to maximum >6 sec as the reference. In a subset of patients who were successfully recanalized, the identical analysis was performed and the infarction and hypoperfused lesion volumes were used for paired pre- and posttreatment comparisons. Results Forty-one patients met our inclusion criteria. Twenty patients underwent successful endovascular revascularization (TICI>2a), resulting in a total of 61 ASL-DSC data pairs for comparison. The hypoperfusion volume on ASL-cerebral blood flow best approximated the DSC-time to peak volume (r=0.83) in pretreatment group and time to maximum (r=0.46) after recanalization. Both ASL-cerebral blood flow and DSC-TTP overestimated the hypoperfusion volume compared with time to maximum volume in pretreatment (F=27.41, P<0.0001) and recanalized patients (F=8.78, P<0.0001). Conclusions ASL-cerebral blood flow overestimates the DSC time to maximum hypoperfusion volume and mismatch classification in patients with acute ischemic syndrome. Continued overestimation of hypoperfused volume after recanalization suggests flow pattern and velocity changes in addition to arterial transit delay can affects the performance of ASL. PMID:23988646

  7. Ultrastructural analysis of the decellularized cornea after interlamellar keratoplasty and microkeratome-assisted anterior lamellar keratoplasty in a rabbit model

    PubMed Central

    Hashimoto, Yoshihide; Hattori, Shinya; Sasaki, Shuji; Honda, Takako; Kimura, Tsuyoshi; Funamoto, Seiichi; Kobayashi, Hisatoshi; Kishida, Akio

    2016-01-01

    The decellularized cornea has received considerable attention for use as an artificial cornea. The decellularized cornea is free from cellular components and other immunogens, but maintains the integrity of the extracellular matrix. However, the ultrastructure of the decellularized cornea has yet to be demonstrated in detail. We investigated the influence of high hydrostatic pressure (HHP) on the decellularization of the corneal ultrastructure and its involvement in transparency, and assessed the in vivo behaviour of the decellularized cornea using two animal transplantation models, in relation to remodelling of collagen fibrils. Decellularized corneas were prepared by the HHP method. The decellularized corneas were executed by haematoxylin and eosin and Masson’s trichrome staining to demonstrate the complete removal of corneal cells. Transmission electron microscopy revealed that the ultrastructure of the decellularized cornea prepared by the HHP method was better maintained than that of the decellularized cornea prepared by the detergent method. The decellularized cornea after interlamellar keratoplasty and microkeratome-assisted anterior lamellar keratoplasty using a rabbit model was stable and remained transparent without ultrastructural alterations. We conclude that the superior properties of the decellularized cornea prepared by the HHP method were attributed to the preservation of the corneal ultrastructure. PMID:27291975

  8. Skeleton-based cerebrovascular quantitative analysis.

    PubMed

    Wang, Xingce; Liu, Enhui; Wu, Zhongke; Zhai, Feifei; Zhu, Yi-Cheng; Shui, Wuyang; Zhou, Mingquan

    2016-12-20

    Cerebrovascular disease is the most common cause of death worldwide, with millions of deaths annually. Interest is increasing toward understanding the geometric factors that influence cerebrovascular diseases, such as stroke. Cerebrovascular shape analyses are essential for the diagnosis and pathological identification of these conditions. The current study aimed to provide a stable and consistent methodology for quantitative Circle of Willis (CoW) analysis and to identify geometric changes in this structure. An entire pipeline was designed with emphasis on automating each step. The stochastic segmentation was improved and volumetric data were obtained. The L1 medial axis method was applied to vessel volumetric data, which yielded a discrete skeleton dataset. A B-spline curve was used to fit the skeleton, and geometric values were proposed for a one-dimensional skeleton and radius. The calculations used to derive these values were illustrated in detail. In one example(No. 47 in the open dataset) all values for different branches of CoW were calculated. The anterior communicating artery(ACo) was the shortest vessel, with a length of 2.6mm. The range of the curvature of all vessels was (0.3, 0.9) ± (0.1, 1.4). The range of the torsion was (-12.4,0.8) ± (0, 48.7). The mean radius value range was (3.1, 1.5) ± (0.1, 0.7) mm, and the mean angle value range was (2.2, 2.9) ± (0, 0.2) mm. In addition to the torsion variance values in a few vessels, the variance values of all vessel characteristics remained near 1. The distribution of the radii of symmetrical posterior cerebral artery(PCA) and angle values of the symmetrical posterior communicating arteries(PCo) demonstrated a certain correlation between the corresponding values of symmetrical vessels on the CoW. The data verified the stability of our methodology. Our method was appropriate for the analysis of large medical image datasets derived from the automated pipeline for populations. This method was applicable to

  9. Quantitative Data Analysis--In the Graduate Curriculum

    ERIC Educational Resources Information Center

    Albers, Michael J.

    2017-01-01

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

  10. Quantitative Auger analysis of Nb-Ge superconducting alloys

    SciTech Connect

    Buitrago, R.H.

    1980-01-01

    The feasibility of using Auger electron analysis for quantitative analysis was investigated by studying Nb/sub 3/Ge thin-film Auger data with different approaches. A method base on elemental standards gave consistent quantitative values with reported Nb-Ge data. Alloy sputter yields were also calculated and results were consistent with those for pure elements.

  11. Prognostic factors in oral and oropharyngeal cancer based on ultrastructural analysis and DNA methylation of the tumor and surgical margin.

    PubMed

    Mielcarek-Kuchta, Daniela; Paluszczak, Jarosław; Seget, Monika; Kiwerska, Katarzyna; Biczysko, Wiesława; Szyfter, Krzysztof; Szyfter, Witold

    2014-08-01

    Oral and oropharyngeal cancers are characterized by relatively low 5- year survival rates due to many factors, including local recurrence. The identification of new molecular markers may serve for the estimation of prognosis and thus augment treatment decisions and affect therapy outcome. The aim of this study was to describe the morphological characteristics and the DNA methylation status of the CDKN2A,CDH1, ATM, FHIT and RAR- genes in the central and peripheral part of the tumor and the surgical margin and evaluate their prognostic significance. 53 patients with oral and oropharyngeal cancer were enrolled to the prospective study, and had been primarily treated surgically. Correlations between morphological data, hypermethylation status and clinicopathological data, as well as prognosis, were assessed. Nuclei polymorphism highly correlated with T stage (p < 0.0001), N stage (p < 0.046), and metastases to the lymph nodes pN (p < 0.004 ). Also, the number of cells in irregular mitosis correlated with T stage (p < 0.004), and highly with pN (p < 0.009). The significance of CDKN2A hypermethylation as a good prognostic factor was also established in the Kaplan-Meir test. The ultrastructural analysis showed that none of the examined tumors had homogenous texture and that resection margin specimens clean in HE stained tissue samples frequently contained single tumor cells or few cells in groups surrounded by connective tissue. This indicates the superiority of electron microscopy over standard histopathological analysis. Thus, a combination of such morphological examination with epigenetic parameters described herein could result in the discovery of promising new prognostic markers of the disease.

  12. [Ultrastructural and element spectrometric analysis of distraction osteogenesis for reconstruction of cleft palate in rhesus macaque model].

    PubMed

    Chen, Gang; Liu, Yi; Liu, Yan-Shan; Shen, Dai; Wang, Zhi-Qi; Wang, Jian

    2010-07-01

    To study the ultrastructure and Ca/P element spectrometry of distraction osteogenesis (DO) for reconstruction of cleft palate (CP), so as to explore the osteogenesis and remodeling of new bone in situ. 23 rhesus macaques were operated to establish animal models of CP. 2 monkeys didn't received DO as controls. The other 21 monkeys in experimental group underwent DO to correct both bony and soft tissue defects in palate. The distraction was performed at a rate of 0.8 mm/d, twice a day until the cleft was closed. After fixation for 1, 2, 4, 6, 8, 12, 24 weeks, every 3 animals were sacrificed to get the specimens at the distraction gap. The scanning electron microscopic study and Ca, P elements spectrometric analysis were adopted. There were also two unoperated animals as sham group. After fixation for 1-2 weeks, the distraction gap was full of collagen fibers oriented along vector of distraction. Few trabeculae was seen at the margin area. After fixation for 4-6 weeks, active osteogenesis was presented with new formed bone trabeculae and abundant cellular component. After fixation for 8-12 weeks, the new formed bone became mature and couldn't distinguish from the normal bone. 24 weeks later, the bone between the distraction gap had a similar structure to the normal bone. Elements spectrometric analysis results indicated that in early stage of osteogenesis, the P and S peaks were relatively high while the Ca peak was much lower. During the late stage, the S peak was obviously decreased, and Ca/P ratio increased to normal level as in the empty control group. The CP can be corrected by DO. The new bone between the distraction gap is formed and remodeled through intramembraneous osteogenesis.

  13. Quantitative Analysis of Radar Returns from Insects

    NASA Technical Reports Server (NTRS)

    Riley, J. R.

    1979-01-01

    When a number of flying insects is low enough to permit their resolution as individual radar targets, quantitative estimates of their aerial density are developed. Accurate measurements of heading distribution using a rotating polarization radar to enhance the wingbeat frequency method of identification are presented.

  14. Some Epistemological Considerations Concerning Quantitative Analysis

    ERIC Educational Resources Information Center

    Dobrescu, Emilian

    2008-01-01

    This article presents the author's address at the 2007 "Journal of Applied Quantitative Methods" ("JAQM") prize awarding festivity. The festivity was included in the opening of the 4th International Conference on Applied Statistics, November 22, 2008, Bucharest, Romania. In the address, the author reflects on three theses that…

  15. Quantitative analysis of planetary reflectance spectra with principal components analysis

    NASA Technical Reports Server (NTRS)

    Johnson, P. E.; Smith, M. O.; Adams, J. B.

    1985-01-01

    A technique is presented for quantitative analysis of planetary reflectance spectra as mixtures of particles on microscopic and macroscopic scales using principal components analysis. This technique allows for determination of the endmembers being mixed, their abundance, and the scale of mixing, as well as other physical parameters. Eighteen lunar telescopic reflectance spectra of the Copernicus crater region, from 600 nm to 1800 nm in wavelength, are modeled in terms of five likely endmembers: mare basalt, mature mare soil, anorthosite, mature highland soil, and clinopyroxene. These endmembers were chosen from a similar analysis of 92 lunar soil and rock samples. The models fit the data to within 2 percent rms. It is found that the goodness of fit is marginally better for intimate mixing over macroscopic mixing.

  16. Quantitative analysis of planetary reflectance spectra with principal components analysis

    NASA Astrophysics Data System (ADS)

    Johnson, P. E.; Smith, M. O.; Adams, J. B.

    1985-02-01

    A technique is presented for quantitative analysis of planetary reflectance spectra as mixtures of particles on microscopic and macroscopic scales using principal components analysis. This technique allows for determination of the endmembers being mixed, their abundance, and the scale of mixing, as well as other physical parameters. Eighteen lunar telescopic reflectance spectra of the Copernicus crater region, from 600 nm to 1800 nm in wavelength, are modeled in terms of five likely endmembers: mare basalt, mature mare soil, anorthosite, mature highland soil, and clinopyroxene. These endmembers were chosen from a similar analysis of 92 lunar soil and rock samples. The models fit the data to within 2 percent rms. It is found that the goodness of fit is marginally better for intimate mixing over macroscopic mixing.

  17. Ultrastructural analysis of slime positive & slime negative Staphylococcus epidermidis isolates in infectious keratitis.

    PubMed

    Nayak, N; Nag, T C; Satpathy, G; Ray, S B

    2007-06-01

    Slime is a major determinant of Staphylococcus epidermidis adherence. The established methods of laboratory detection of slime production by this organism i.e., Christensen's tube method and congo red agar plate method, can both yield inconclusive and/or intermediate results. We, therefore tried to find out electronmicroscopically the localization of slime in relation to the bacterial cell wall and look for the effect, if any of the slime location on the staphylococcal adherence as well as on the quantum of slime production. A total of 132 coagulase negative staphylococci from cases of infectious keratitis were identified as S. epidermidis following the recommended protocol. Slime was detected both by Christensen's tube method and congo red agar plate method. Antibiotic sensitivity testing was performed by standardized disc diffusion method. Adherence of the organisms to artificial surfaces was determined by a quantitative method and transmission electron microscopy was carried out by the conventional techniques. Of the total 132 isolates, 57 (43.2%) were slime positive and 75 (56.8%) were slime negative. Twenty seven (47.4%) of the 57 slime producing organisms were multi drug resistant as compared to only 12 (16%) of 75 nonslime-producing organisms (P<0.001). A majority i.e., 45 (78.9%) of 57 adherent organisms were slime producers as against 12 (16%) of 75 nonadherent organisms. Electron microscopic study revealed a thick viscid layer of slime anchoring to the bacterial cell wall, especially in adherent organisms and those yielding positive slime test. Some of the organisms showed loose nonadherent slime and those were mostly nonadherent to artificial surfaces. Slime and multi drug resistance were the important virulence factors of S. epidermidis in bacterial keratitis. It was the adherent slime (i.e., slime in intimate association with the bacterial cell wall as shown by electron microscopy) only, which was responsible for resistance to multiple antibiotics and

  18. Analysis of Two Quantitative Ultrasound Approaches.

    PubMed

    Muleki-Seya, Pauline; Han, Aiguo; Andre, Michael P; Erdman, John W; O'Brien, William D

    2017-09-01

    There are two well-known ultrasonic approaches to extract sets of quantitative parameters: Lizzi-Feleppa (LF) parameters: slope, intercept, and midband; and quantitative ultrasound (QUS)-derived parameters: effective scatterer diameter (ESD) and effective acoustic concentration (EAC). In this study, the relation between the LF and QUS-derived parameters is studied theoretically and experimentally on ex vivo mouse livers. As expected from the theory, LF slope is correlated to ESD ([Formula: see text]), and from experimental data, LF midband is correlated to EAC ([Formula: see text]). However, LF intercept is not correlated to ESD ([Formula: see text]) nor EAC ([Formula: see text]). The unexpected correlation observed between LF slope and EAC ([Formula: see text]) results likely from the high correlation between ESD and EAC due to the inversion process. For a liver fat percentage estimation, an important potential medical application, the parameters presenting the better correlation are EAC ([Formula: see text]) and LF midband ([Formula: see text]).

  19. [Determination of the chemical composition of gallstones by roentgen ultrastructural analysis].

    PubMed

    Rauchfuss, E; Glaser, M; Keller, F

    1985-01-01

    The definition of the chemical composition of human gallstones is shown by means of X-ray fine structure analysis. The simple method allowed a prompt distinction in stones poor and rich in cholesterol and of other ingredients. The method needs smallest test quantities (2 mg) in regard for a conservative medicamentous therapy.

  20. Desmosomes: A light microscopic and ultrastructural analysis of desmosomes in odontogenic cysts

    PubMed Central

    Raju, Pratima; Wadhwan, Vijay; Chaudhary, Minal S.

    2014-01-01

    Introduction: Desmosomes together with adherens junctions represent the major adhesive cell–cell junctions of epithelial cells. Any damage to these junctions leads to loss of structural balance. Aim: The present study was designed to analyze the desmosomal junctions in different odontogenic cysts and compare them with their corresponding hematoxylin and eosin (H and E)   stained sections. Materials and Methods: Ten cases each of odontogenic keratocyst (OKC), dentigerous cysts (DCs), radicular cysts (RCs) and normal mucosa were stained with hematoxylin and eosin. Scanning electron microscopy (SEM) analysis of the sections was then carried out of all the sections. The area of interest on H and E stained section was marked and this marking was later superimposed onto the corresponding unstained sections and were subjected to SEM analysis. Results and Observations: OKC at ×1000 magnification showed many prominent desmosomes. However, an increase in the intercellular space was also noted. SEM analysis demonstrated similar findings with the presence of many desmosomes, though they were seen to be damaged and fragile. H and E stained DC under oil immersion did not show any prominent desmosomes. SEM analysis of the same confirmed the observation and very minimal number were seen with a very condense arrangement of the epithelial cells. RC at ×1000 magnification revealed plenty of desmosomes, which were again confirmed by SEM. Conclusion: The number and quality of desmosomal junctions in all the cysts has a role in the clinical behavior of the cyst. PMID:25948985

  1. Structural and quantitative analysis of Equisetum alkaloids.

    PubMed

    Cramer, Luise; Ernst, Ludger; Lubienski, Marcus; Papke, Uli; Schiebel, Hans-Martin; Jerz, Gerold; Beuerle, Till

    2015-08-01

    Equisetum palustre L. is known for its toxicity for livestock. Several studies in the past addressed the isolation and identification of the responsible alkaloids. So far, palustrine (1) and N(5)-formylpalustrine (2) are known alkaloids of E. palustre. A HPLC-ESI-MS/MS method in combination with simple sample work-up was developed to identify and quantitate Equisetum alkaloids. Besides the two known alkaloids six related alkaloids were detected in different Equisetum samples. The structure of the alkaloid palustridiene (3) was derived by comprehensive 1D and 2D NMR experiments. N(5)-Acetylpalustrine (4) was also thoroughly characterized by NMR for the first time. The structure of N(5)-formylpalustridiene (5) is proposed based on mass spectrometry results. Twenty-two E. palustre samples were screened by a HPLC-ESI-MS/MS method after development of a simple sample work-up and in most cases the set of all eight alkaloids were detected in all parts of the plant. A high variability of the alkaloid content and distribution was found depending on plant organ, plant origin and season ranging from 88 to 597mg/kg dried weight. However, palustrine (1) and the alkaloid palustridiene (3) always represented the main alkaloids. For the first time, a comprehensive identification, quantitation and distribution of Equisetum alkaloids was achieved.

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  4. Ultrastructural and biochemical analysis of epidermal xanthophores and dermal chromatophores of the teleost Sparus aurata.

    PubMed

    Ferrer, C; Solano, F; Zuasti, A

    1999-04-01

    We have studied the pigmentary system of the teleost Sparus aurata skin by electron microscopy and chromatographic analysis. Under electron microscopy, we found the dermis to contain the three major types of recognized chromatophores: melanophores, xanthophores and iridophores. Melanophores were more abundant in the dorsal region, whereas the iridophores were more abundant in the ventral region. The most important discovery was that of epidermal xanthophores. Epidermal xanthophores were the only chromatophores in the epidermis, something only found in S aurata and in a teleost species living in the Antartic sea. In contrast, the biochemical analysis did not establish any special characteristics: we found pteridine and flavin pigments located mostly in the pigmented dorsal region. Riboflavin and pterin were two of the most abundant coloured pigment types, but other colourless pigments such as xanthopterin and isoxanthopterin were also detected.

  5. Histological and Ultrastructure Analysis of Dentin Dysplasia Type I in Primary Teeth: A Case Report.

    PubMed

    Pintor, Andrea; Alexandria, Adilis; Marques, Andrea; Abrahao, Aline; Guedes, Fabio; Primo, Laura

    2015-01-01

    Dentin dysplasia type I (DD-I) is a rare human dentin disorder that may affect both the primary and permanent dentitions. The teeth present crowns with normal morphology but short or absent roots. Pulp chamber obliteration and early exfoliation of primary teeth are also observed. We describe herein the typical and atypical features of DD-I presented by a 6-year-old patient, the diagnostic rationale and assessment emphasizing the histological and scanning electron microscopic analysis and the therapeutic approach. The DD-I diagnosis in patients in the mixed dentition period is challenging, especially when only some teeth are affected.

  6. Molecular and ultrastructural analysis of forisome subunits reveals the principles of forisome assembly

    PubMed Central

    Müller, Boje; Groscurth, Sira; Menzel, Matthias; Rüping, Boris A.; Twyman, Richard M.; Prüfer, Dirk; Noll, Gundula A.

    2014-01-01

    Background and Aims Forisomes are specialized structural phloem proteins that mediate sieve element occlusion after wounding exclusively in papilionoid legumes, but most studies of forisome structure and function have focused on the Old World clade rather than the early lineages. A comprehensive phylogenetic, molecular, structural and functional analysis of forisomes from species covering a broad spectrum of the papilionoid legumes was therefore carried out, including the first analysis of Dipteryx panamensis forisomes, representing the earliest branch of the Papilionoideae lineage. The aim was to study the molecular, structural and functional conservation among forisomes from different tribes and to establish the roles of individual forisome subunits. Methods Sequence analysis and bioinformatics were combined with structural and functional analysis of native forisomes and artificial forisome-like protein bodies, the latter produced by expressing forisome genes from different legumes in a heterologous background. The structure of these bodies was analysed using a combination of confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and the function of individual subunits was examined by combinatorial expression, micromanipulation and light microscopy. Key Results Dipteryx panamensis native forisomes and homomeric protein bodies assembled from the single sieve element occlusion by forisome (SEO-F) subunit identified in this species were structurally and functionally similar to forisomes from the Old World clade. In contrast, homomeric protein bodies assembled from individual SEO-F subunits from Old World species yielded artificial forisomes differing in proportion to their native counterparts, suggesting that multiple SEO-F proteins are required for forisome assembly in these plants. Structural differences between Medicago truncatula native forisomes, homomeric protein bodies and heteromeric bodies

  7. Qualitative and quantitative analysis of endocytic recycling.

    PubMed

    Reineke, James B; Xie, Shuwei; Naslavsky, Naava; Caplan, Steve

    2015-01-01

    Endocytosis, which encompasses the internalization and sorting of plasma membrane (PM) lipids and proteins to distinct membrane-bound intracellular compartments, is a highly regulated and fundamental cellular process by which eukaryotic cells dynamically regulate their PM composition. Indeed, endocytosis is implicated in crucial cellular processes that include proliferation, migration, and cell division as well as maintenance of tissue homeostasis such as apical-basal polarity. Once PM constituents have been taken up into the cell, either via clathrin-dependent endocytosis (CDE) or clathrin-independent endocytosis (CIE), they typically have two fates: degradation through the late-endosomal/lysosomal pathway or returning to the PM via endocytic recycling pathways. In this review, we will detail experimental procedures that allow for both qualitative and quantitative assessment of endocytic recycling of transmembrane proteins internalized by CDE and CIE, using the HeLa cervical cancer cell line as a model system.

  8. Joint association analysis of bivariate quantitative and qualitative traits.

    PubMed

    Yuan, Mengdie; Diao, Guoqing

    2011-11-29

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a prespecified threshold determine the value of the qualitative trait. To jointly model the quantitative and qualitative traits, we assume that the quantitative trait and the latent variable follow a bivariate normal distribution. The latent variable is allowed to be correlated with the quantitative phenotype. Simultaneous modeling of the quantitative and qualitative traits allows us to make more precise inference on the pleiotropic genetic effects. We derive likelihood ratio tests for the testing of genetic effects. An application to the Genetic Analysis Workshop 17 data is provided. The new method yields reasonable power and meaningful results for the joint association analysis of the quantitative trait Q1 and the qualitative trait disease status at SNPs with not too small MAF.

  9. Ultrastructure of a magnetotactic spirillum.

    PubMed Central

    Balkwill, D L; Maratea, D; Blakemore, R P

    1980-01-01

    The ultrastructure of a magnetotactic bacterium (strain MS-1) was examined by transmission, scanning, and scanning-transmission electron microscopy. The organism resembled other spirilla in general cell morphology, although some differences were detected at the ultrastructural level. Electron-dense particles within magnetotactic cells were shown by energy-dispersive X-ray analysis to be localizations containing iron. A non-magnetotactic variant of strain MS-1 lacked these novel bacterial inclusion bodies. A chain of these particles traversed each magnetotactic cell in a specific arrangement that was consistent from cell to cell, seemingly associated with the inner surface of the cytoplasmic membrane. Each particle was surrounded by an electron-dense layer separated from the particle surface by an electron-transparent region. The term "magnetosome" is proposed for the electron-dense particles with their enveloping layer(s) as found in this and other magnetotactic bacteria. Images PMID:6245069

  10. Intraoral laser welding: ultrastructural and mechanical analysis to compare laboratory laser and dental laser.

    PubMed

    Fornaini, Carlo; Passaretti, Francesca; Villa, Elena; Rocca, Jean-Paul; Merigo, Elisabetta; Vescovi, Paolo; Meleti, Marco; Manfredi, Maddalena; Nammour, Samir

    2011-07-01

    The Nd:YAG laser has been used since 1970 in dental laboratories to weld metals on dental prostheses. Recently in several clinical cases, we have suggested that the Nd:YAG laser device commonly utilized in the dental office could be used to repair broken fixed, removable and orthodontic prostheses and to weld metals directly in the mouth. The aim of this work was to evaluate, using scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) and dynamic mechanical analysis (DMA), the quality of the weld and its mechanical strength, comparing a device normally used in dental laboratory and a device normally used in the dental office for oral surgery, the same as that described for intraoral welding. Metal plates of a Co-Cr-Mo dental alloy and steel orthodontic wires were subjected to four welding procedures: welding without filler metal using the laboratory laser, welding with filler metal using the laboratory laser, welding without filler metal using the office laser, and welding with filler metal using the office laser. The welded materials were then analysed by SEM, EDS and DMA. SEM analysis did not show significant differences between the samples although the plates welded using the office laser without filler metal showed a greater number of fissures than the other samples. EDS microanalysis of the welding zone showed a homogeneous composition of the metals. Mechanical tests showed similar elastic behaviours of the samples, with minimal differences between the samples welded with the two devices. No wire broke even under the maximum force applied by the analyser. This study seems to demonstrate that the welds produced using the office Nd:YAG laser device and the laboratory Nd:YAG laser device, as analysed by SEM, EDS and DMA, showed minimal and nonsignificant differences, although these findings need to be confirmed using a greater number of samples.

  11. Electron tomographic analysis reveals ultrastructural features of mitochondrial cristae architecture which reflect energetic state and aging

    PubMed Central

    Jiang, Yi-fan; Lin, Shao-syuan; Chen, Jing-min; Tsai, Han-zen; Hsieh, Tao-shih; Fu, Chi-yu

    2017-01-01

    Within mitochondria, the ability to produce energy relies upon the architectural hallmarks of double membranes and cristae invaginations. Herein, we describe novel features of mitochondrial cristae structure, which correspond to the energetic state of the organelle. In concordance with high-energy demand, mitochondria of Drosophila indirect flight muscle exhibited extensive intra-mitochondrial membrane switches between densely packed lamellar cristae that resulted in a spiral-like cristae network and allowed for bidirectional matrix confluency. This highly interconnected architecture is expected to allow rapid equilibration of membrane potential and biomolecules across integrated regions. In addition, mutant flies with mtDNA replication defect and an accelerated aging phenotype accumulated mitochondria that contained subsections of swirling membrane alongside normal cristae. The swirling membrane had impaired energy production capacity as measured by protein composition and function. Furthermore, mitochondrial fusion and fission dynamics were affected in the prematurely aged flies. Interestingly, the normal cristae that remained in the mitochondria with swirling membranes maintained acceptable function that camouflaged them from quality control elimination. Overall, structural features of mitochondrial cristae were described in three-dimension from serial section electron tomographic analysis which reflect energetic state and mtDNA-mediated aging. PMID:28358017

  12. Electron tomographic analysis reveals ultrastructural features of mitochondrial cristae architecture which reflect energetic state and aging.

    PubMed

    Jiang, Yi-Fan; Lin, Shao-Syuan; Chen, Jing-Min; Tsai, Han-Zen; Hsieh, Tao-Shih; Fu, Chi-Yu

    2017-03-30

    Within mitochondria, the ability to produce energy relies upon the architectural hallmarks of double membranes and cristae invaginations. Herein, we describe novel features of mitochondrial cristae structure, which correspond to the energetic state of the organelle. In concordance with high-energy demand, mitochondria of Drosophila indirect flight muscle exhibited extensive intra-mitochondrial membrane switches between densely packed lamellar cristae that resulted in a spiral-like cristae network and allowed for bidirectional matrix confluency. This highly interconnected architecture is expected to allow rapid equilibration of membrane potential and biomolecules across integrated regions. In addition, mutant flies with mtDNA replication defect and an accelerated aging phenotype accumulated mitochondria that contained subsections of swirling membrane alongside normal cristae. The swirling membrane had impaired energy production capacity as measured by protein composition and function. Furthermore, mitochondrial fusion and fission dynamics were affected in the prematurely aged flies. Interestingly, the normal cristae that remained in the mitochondria with swirling membranes maintained acceptable function that camouflaged them from quality control elimination. Overall, structural features of mitochondrial cristae were described in three-dimension from serial section electron tomographic analysis which reflect energetic state and mtDNA-mediated aging.

  13. Analysis of the cell surface layer ultrastructure of the oral pathogen Tannerella forsythia.

    PubMed

    Sekot, Gerhard; Posch, Gerald; Oh, Yoo Jin; Zayni, Sonja; Mayer, Harald F; Pum, Dietmar; Messner, Paul; Hinterdorfer, Peter; Schäffer, Christina

    2012-06-01

    The Gram-negative oral pathogen Tannerella forsythia is decorated with a 2D crystalline surface (S-) layer, with two different S-layer glycoprotein species being present. Prompted by the predicted virulence potential of the S-layer, this study focused on the analysis of the arrangement of the individual S-layer glycoproteins by a combination of microscopic, genetic, and biochemical analyses. The two S-layer genes are transcribed into mRNA and expressed into protein in equal amounts. The S-layer was investigated on intact bacterial cells by transmission electron microscopy, by immune fluorescence microscopy, and by atomic force microscopy. The analyses of wild-type cells revealed a distinct square S-layer lattice with an overall lattice constant of 10.1 ± 0.7 nm. In contrast, a blurred lattice with a lattice constant of 9.0 nm was found on S-layer single-mutant cells. This together with in vitro self-assembly studies using purified (glyco)protein species indicated their increased structural flexibility after self-assembly and/or impaired self-assembly capability. In conjunction with TEM analyses of thin-sectioned cells, this study demonstrates the unusual case that two S-layer glycoproteins are co-assembled into a single S-layer. Additionally, flagella and pilus-like structures were observed on T. forsythia cells, which might impact the pathogenicity of this bacterium.

  14. Pathological and ultrastructural analysis of surgical lung biopsies in patients with swine‐origin influenza type A/H1N1 and acute respiratory failure

    PubMed Central

    Capelozzi, Vera Luiza; Parra, Edwin Roger; Ximenes, Manoel; Bammann, Ricardo Helbert; Barbas, Carmen Silvia Valente; Duarte, Marid Irmd Seixas

    2010-01-01

    BACKGROUND: Cases of H1N1 and other pulmonary infections evolve to acute respiratory failure and death when co‐infections or lung injury predominate over the immune response, thus requiring early diagnosis to improve treatment. OBJECTIVE: To perform a detailed histopathological analysis of the open lung biopsy specimens from five patients with ARDS with confirmed H1N1. METHODS: Lung specimens underwent microbiologic analysis, and examination by optical and electron microscopy. Immunophenotyping was used to characterize macrophages, natural killer, T and B cells, and expression of cytokines and iNOS. RESULTS: The pathological features observed were necrotizing bronchiolitis, diffuse alveolar damage, alveolar hemorrhage and abnormal immune response. Ultrastructural analysis showed viral‐like particles in all cases. CONCLUSIONS: Viral‐like particles can be successfully demonstrated in lung tissue by ultrastructural examination, without confirmation of the virus by RT‐PCR on nasopharyngeal aspirates. Bronchioles and epithelium, rather than endothelium, are probably the primary target of infection, and diffuse alveolar damage the consequence of the effect of airways obliteration and dysfunction on innate immunity, suggesting that treatment should be focused on epithelial repair. PMID:21340209

  15. Quantitative infrared analysis of hydrogen fluoride

    SciTech Connect

    Manuta, D.M.

    1997-04-01

    This work was performed at the Portsmouth Gaseous Diffusion Plant where hydrogen fluoride is produced upon the hydrolysis of UF{sub 6}. This poses a problem for in this setting and a method for determining the mole percent concentration was desired. HF has been considered to be a non-ideal gas for many years. D. F. Smith utilized complex equations in his HF studies in the 1950s. We have evaluated HF behavior as a function of pressure from three different perspectives. (1) Absorbance at 3877 cm{sup -1} as a function of pressure for 100% HF. (2) Absorbance at 3877 cm{sup -1} as a function of increasing partial pressure HF. Total pressure = 300 mm HgA maintained with nitrogen. (3) Absorbance at 3877 cm{sup -1} for constant partial pressure HF. Total pressure is increased to greater than 800 mm HgA with nitrogen. These experiments have shown that at partial pressures up to 35mm HgA, HIF follows the ideal gas law. The absorbance at 3877 cm{sup -1} can be quantitatively analyzed via infrared methods.

  16. Quantitative Analysis of HIV-1 Preintegration Complexes

    PubMed Central

    Engelman, Alan; Oztop, Ilker; Vandegraaff, Nick; Raghavendra, Nidhanapati K.

    2009-01-01

    Retroviral replication proceeds through the formation of a provirus, an integrated DNA copy of the viral RNA genome. The linear cDNA product of reverse transcription is the integration substrate and two different integrase activities, 3′ processing and DNA strand transfer, are required for provirus formation. Integrase nicks the cDNA ends adjacent to phylogenetically-conserved CA dinucleotides during 3′ processing. After nuclear entry and locating a suitable chromatin acceptor site, integrase joins the recessed 3′-OHs to the 5′-phosphates of a double-stranded staggered cut in the DNA target. Integrase functions in the context of a large nucleoprotein complex, called the preintegration complex (PIC), and PICs are analyzed to determine levels of integrase 3′ processing and DNA strand transfer activities that occur during acute virus infection. Denatured cDNA end regions are monitored by indirect end-labeling to measure the extent of 3′ processing. Native PICs can efficiently integrate their viral cDNA into exogenously added target DNA in vitro, and Southern blotting or nested PCR assays are used to quantify the resultant DNA strand transfer activity. This study details HIV-1 infection, PIC extraction, partial purification, and quantitative analyses of integrase 3′ processing and DNA strand transfer activities. PMID:19233280

  17. Quantitative multi-modal NDT data analysis

    SciTech Connect

    Heideklang, René; Shokouhi, Parisa

    2014-02-18

    A single NDT technique is often not adequate to provide assessments about the integrity of test objects with the required coverage or accuracy. In such situations, it is often resorted to multi-modal testing, where complementary and overlapping information from different NDT techniques are combined for a more comprehensive evaluation. Multi-modal material and defect characterization is an interesting task which involves several diverse fields of research, including signal and image processing, statistics and data mining. The fusion of different modalities may improve quantitative nondestructive evaluation by effectively exploiting the augmented set of multi-sensor information about the material. It is the redundant information in particular, whose quantification is expected to lead to increased reliability and robustness of the inspection results. There are different systematic approaches to data fusion, each with its specific advantages and drawbacks. In our contribution, these will be discussed in the context of nondestructive materials testing. A practical study adopting a high-level scheme for the fusion of Eddy Current, GMR and Thermography measurements on a reference metallic specimen with built-in grooves will be presented. Results show that fusion is able to outperform the best single sensor regarding detection specificity, while retaining the same level of sensitivity.

  18. The quantitative failure of human reliability analysis

    SciTech Connect

    Bennett, C.T.

    1995-07-01

    This philosophical treatise argues the merits of Human Reliability Analysis (HRA) in the context of the nuclear power industry. Actually, the author attacks historic and current HRA as having failed in informing policy makers who make decisions based on risk that humans contribute to systems performance. He argues for an HRA based on Bayesian (fact-based) inferential statistics, which advocates a systems analysis process that employs cogent heuristics when using opinion, and tempers itself with a rational debate over the weight given subjective and empirical probabilities.

  19. Quantitative analysis of myocardial tissue with digital autofluorescence microscopy.

    PubMed

    Jensen, Thomas; Holten-Rossing, Henrik; Svendsen, Ida M H; Jacobsen, Christina; Vainer, Ben

    2016-01-01

    The opportunity offered by whole slide scanners of automated histological analysis implies an ever increasing importance of digital pathology. To go beyond the importance of conventional pathology, however, digital pathology may need a basic histological starting point similar to that of hematoxylin and eosin staining in conventional pathology. This study presents an automated fluorescence-based microscopy approach providing highly detailed morphological data from unstained microsections. This data may provide a basic histological starting point from which further digital analysis including staining may benefit. This study explores the inherent tissue fluorescence, also known as autofluorescence, as a mean to quantitate cardiac tissue components in histological microsections. Data acquisition using a commercially available whole slide scanner and an image-based quantitation algorithm are presented. It is shown that the autofluorescence intensity of unstained microsections at two different wavelengths is a suitable starting point for automated digital analysis of myocytes, fibrous tissue, lipofuscin, and the extracellular compartment. The output of the method is absolute quantitation along with accurate outlines of above-mentioned components. The digital quantitations are verified by comparison to point grid quantitations performed on the microsections after Van Gieson staining. The presented method is amply described as a prestain multicomponent quantitation and outlining tool for histological sections of cardiac tissue. The main perspective is the opportunity for combination with digital analysis of stained microsections, for which the method may provide an accurate digital framework.

  20. Quantitive and Sociological Analysis of Blog Networks

    NASA Astrophysics Data System (ADS)

    Bachnik, W.; Szymczyk, S.; Leszczynski, S.; Podsiadlo, R.; Rymszewicz, E.; Kurylo, L.; Makowiec, D.; Bykowska, B.

    2005-10-01

    This paper examines the emerging phenomenon of blogging, using three different Polish blogging services as the base of the research. Authors show that blog networks are sharing their characteristics with complex networks (gamma coefficients, small worlds, cliques, etc.). Elements of sociometric analysis were used to prove existence of some social structures in the blog networks.

  1. Quantitative analysis of Li by PIGE technique

    NASA Astrophysics Data System (ADS)

    Fonseca, M.; Mateus, R.; Santos, C.; Cruz, J.; Silva, H.; Luis, H.; Martins, L.; Jesus, A. P.

    2017-09-01

    In this work, the cross section of the reactions 7Li(p,pγ)7Li (γ - 478 keV) at the proton energy range 2.0-4.2 MeV was measured. The measurements were carried out at the 3 MV Tandem Accelerator at the CTN/IST Laboratory in Lisbon. To validate the obtained results, calculated gamma-ray yields were compared, at several proton energy values, with experimental yields for thick samples made of inorganic compounds containing lithium. In order to quantify the light elements present in the samples, we used a standard free method for PIGE in thick samples, based on a code - Emitted Radiation Yield Analysis (ERYA), which integrates the nuclear reaction excitation function along the depth of the sample. We also demonstrated the capacity of the technique for analysis of Li ores, as Spodumene, Lithium Muscovite and Holmquistite, and Li-alloys for plasma facing materials showing that this is a reliable and accurate method for PIGE analysis of Li in thick samples.

  2. Histological, ultrastructural and quantitative investigations on the response of healthy human pulps to experimental capping with mineral trioxide aggregate: a randomized controlled trial.

    PubMed

    Nair, P N R; Duncan, H F; Pitt Ford, T R; Luder, H U

    2008-02-01

    To investigate the pulpal response to direct pulp capping in healthy human teeth with mineral trioxide aggregate (MTA) as against calcium hydroxide cement (Dycal) as control. Twenty healthy human third molars had iatrogenic pulpotomy and direct pulp capping with MTA. Another 13 teeth were capped with Dycal as controls. The teeth were restored, with IRM, clinically reviewed and extracted after a number of pre-determined intervals (1 week, 1 month and 3 months). The specimens were fixed, decalcified, subdivided axially into two halves in the oro-buccal (lingual-buccal) plane, embedded in plastic, serial sectioned and evaluated qualitatively and quantitatively by correlative light and transmission electron microscopy with appropriate statistical evaluation of the quantitative data. Iatrogenic pulpal wounds treated with MTA were mostly free from inflammation after 1 week and became covered with a compact, hard tissue barrier of steadily increasing length and thickness within 3 months following capping. Control teeth treated with Dycal revealed distinctly less consistent formation of a hard tissue barrier that had numerous tunnel defects. The presence of pulpal inflammation up to the longest observation period (3 months) after capping, was a common feature in Dycal specimens. The MTA was clinically easier to use as a direct pulp-capping agent and resulted in less pulpal inflammation and more predictable hard tissue barrier formation than Dycal. Therefore, MTA or equivalent products should be the material of choice for direct pulp capping procedures instead of hard setting calcium hydroxide cements.

  3. Quantitative Analysis of Immunohistochemistry in Melanoma Tumors.

    PubMed

    Lilyquist, Jenna; White, Kirsten Anne Meyer; Lee, Rebecca J; Philips, Genevieve K; Hughes, Christopher R; Torres, Salina M

    2017-04-01

    Identification of positive staining is often qualitative and subjective. This is particularly troublesome in pigmented melanoma lesions, because melanin is difficult to distinguish from the brown stain resulting from immunohistochemistry (IHC) using horse radish peroxidase developed with 3,3'-Diaminobenzidine (HRP-DAB). We sought to identify and quantify positive staining, particularly in melanoma lesions. We visualized G-protein coupled estrogen receptor (GPER) expression developed with HRP-DAB and counterstained with Azure B (stains melanin) in melanoma tissue sections (n = 3). Matched sections (n = 3), along with 22 unmatched sections, were stained only with Azure B as a control. Breast tissue (n = 1) was used as a positive HRP-DAB control. Images of the stained tissues were generated using a Nuance Spectral Imaging Camera. Analysis of the images was performed using the Nuance Spectral Imaging software and SlideBook. Data was analyzed using a Kruskal-Wallis one way analysis of variance (ANOVA). We showed that a pigmented melanoma tissue doubly stained with anti-GPER HRP-DAB and Azure B can be unmixed using spectra derived from a matched, Azure B-only section, and an anti-GPER HRP-DAB control. We unmixed each of the melanoma lesions using each of the Azure B spectra, evaluated the mean intensity of positive staining, and examined the distribution of the mean intensities (P = .73; Kruskal-Wallis). These results suggest that this method does not require a matched Azure B-only stained control tissue for every melanoma lesion, allowing precious tissues to be conserved for other studies. Importantly, this quantification method reduces the subjectivity of protein expression analysis, and provides a valuable tool for accurate evaluation, particularly for pigmented tissues.

  4. Chromatic Image Analysis For Quantitative Thermal Mapping

    NASA Technical Reports Server (NTRS)

    Buck, Gregory M.

    1995-01-01

    Chromatic image analysis system (CIAS) developed for use in noncontact measurements of temperatures on aerothermodynamic models in hypersonic wind tunnels. Based on concept of temperature coupled to shift in color spectrum for optical measurement. Video camera images fluorescence emitted by phosphor-coated model at two wavelengths. Temperature map of model then computed from relative brightnesses in video images of model at those wavelengths. Eliminates need for intrusive, time-consuming, contact temperature measurements by gauges, making it possible to map temperatures on complex surfaces in timely manner and at reduced cost.

  5. Influence of corrosion layers on quantitative analysis

    NASA Astrophysics Data System (ADS)

    Denker, A.; Bohne, W.; Opitz-Coutureau, J.; Rauschenberg, J.; Röhrich, J.; Strub, E.

    2005-09-01

    Art historians and restorers in charge of ancient metal objects are often reluctant to remove the corrosion layer evolved over time, as this would change the appearance of the artefact dramatically. Therefore, when an elemental analysis of the objects is required, this has to be done by penetrating the corrosion layer. In this work the influence of corrosion was studied on Chinese and Roman coins, where removal of oxidized material was possible. Measurements on spots with and without corrosion are presented and the results discussed.

  6. Quantitative Analysis in Nuclear Medicine Imaging

    NASA Astrophysics Data System (ADS)

    Zaidi, Habib

    This book provides a review of image analysis techniques as they are applied in the field of diagnostic and therapeutic nuclear medicine. Driven in part by the remarkable increase in computing power and its ready and inexpensive availability, this is a relatively new yet rapidly expanding field. Likewise, although the use of radionuclides for diagnosis and therapy has origins dating back almost to the discovery of natural radioactivity itself, radionuclide therapy and, in particular, targeted radionuclide therapy has only recently emerged as a promising approach for therapy of cancer and, to a lesser extent, other diseases.

  7. Segmentation and Quantitative Analysis of Epithelial Tissues.

    PubMed

    Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

    2016-01-01

    Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

  8. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    ERIC Educational Resources Information Center

    Katharaki, Maria; Katharakis, George

    2010-01-01

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

  9. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    ERIC Educational Resources Information Center

    Katharaki, Maria; Katharakis, George

    2010-01-01

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

  10. Quantitative Analysis of Seismicity in Iran

    NASA Astrophysics Data System (ADS)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2016-12-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  11. Quantitative Analysis of Seismicity in Iran

    NASA Astrophysics Data System (ADS)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2017-03-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  12. Quantitative analysis of heart rate variability

    NASA Astrophysics Data System (ADS)

    Kurths, J.; Voss, A.; Saparin, P.; Witt, A.; Kleiner, H. J.; Wessel, N.

    1995-03-01

    In the modern industrialized countries every year several hundred thousands of people die due to sudden cardiac death. The individual risk for this sudden cardiac death cannot be defined precisely by common available, noninvasive diagnostic tools like Holter monitoring, highly amplified ECG and traditional linear analysis of heart rate variability (HRV). Therefore, we apply some rather unconventional methods of nonlinear dynamics to analyze the HRV. Especially, some complexity measures that are based on symbolic dynamics as well as a new measure, the renormalized entropy, detect some abnormalities in the HRV of several patients who have been classified in the low risk group by traditional methods. A combination of these complexity measures with the parameters in the frequency domain seems to be a promising way to get a more precise definition of the individual risk. These findings have to be validated by a representative number of patients.

  13. 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.

  14. Proteomic and ultrastructural analysis of the effect of a new nitazoxanide-N-methyl-1H-benzimidazole hybrid against Giardia intestinalis.

    PubMed

    Matadamas-Martínez, Félix; Castillo, Rafael; Hernández-Campos, Alicia; Méndez-Cuesta, Carlos; de Souza, Wanderley; Gadelha, Ana Paula; Nogueda-Torres, Benjamín; Hernández, José Manuel; Yépez-Mulia, Lilián

    2016-04-01

    In an effort to develop alternative drugs for the treatment of giardiasis our research group has synthesized and evaluated a novel nitazoxanide and N-methyl-1H-benzimidazole hybrid molecule, named CMC-20. It showed an IC50 of 0.010 μM on Giardia intestinalis, lower than the IC50 values of 0.015, 0.037 and 1.224 μM for nitazoxanide, albendazole and metronidazole, respectively. In addition, we report studies carried out on its mechanism of action and effect at the ultrastructural level on G. intestinalis. The proteomic analysis of trophozoites treated with CMC-20 revealed significant changes in the expression level of proteins of the cytoskeleton, alpha and beta tubulin, alpha-1, beta giardin and axoneme-associated protein, among other molecules. Ultrastructural studies demonstrated that CMC-20 induces morphological changes on the parasite that loses its characteristic pear shape. Uncommon large bulbous structure at the flagella end, and parasites showing flange membrane bending and a concave depression in the ventral region, resembling an encystation process, were also observed. In addition, some apoptotic and autophagic-like features, such as membrane blebbing, intense vacuolation, chromatin condensation and multilamellar bodies were detected. Phosphatidylserine externalization was determined as an apoptotic marker by flow cytometry and immunofluorescence microscopy; however, a typical ladder-like DNA fragmentation profile was not detected. Although it was found that CMC-20 triggers the encystation process, damage to the cyst wall indicates loss of viability.

  15. Ultrastructural characterization and multilocus sequence analysis (MLSA) of 'Candidatus Rickettsiella isopodorum', a new lineage of intracellular bacteria infecting woodlice (Crustacea: Isopoda).

    PubMed

    Kleespies, Regina G; Federici, Brian A; Leclerque, Andreas

    2014-07-01

    The taxonomic genus Rickettsiella (Gammaproteobacteria; Legionellales) comprises intracellular bacteria associated with a wide range of arthropods including insects, arachnids and crustaceans. The present study provides ultrastructural together with genetic evidence for a Rickettsiella bacterium in the common rough woodlouse, Porcellio scaber (Isopoda, Porcellionidae), occurring in Germany, and shows that this bacterium is very closely related to one of the same genus occurring in California that infects the pill bug, Armadillidium vulgare (Isopoda, Armadillidiidae). Both bacterial isolates displayed the ultrastructural features described previously for crustacean-associated bacteria of the genus Rickettsiella, including the absence of well-defined associated protein crystals; occurrence of the latter is a typical characteristic of infection by this type of bacteria in insects, but has not been reported in crustaceans. A molecular systematic approach combining multilocus sequence analysis (MLSA) with likelihood-based significance testing demonstrated that despite their distant geographic origins, both bacteria form a tight sub-clade within the genus Rickettsiella. In the 16S rRNA gene trees, this sub-clade includes other bacterial sequences from woodlice. Moreover, the bacterial specimens from P. scaber and A. vulgare are found genetically or morphologically different from each of the four currently recognized Rickettsiella species. Therefore, the designation 'Candidatus Rickettsiella isopodorum' is introduced for this new lineage of isopod-associated Rickettsiella bacteria.

  16. Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

    PubMed

    Gunar, O V; Sakhno, N G

    2015-12-30

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

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

    PubMed

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

    2017-07-17

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

  18. Control of separation and quantitative analysis by GC-FTIR

    NASA Astrophysics Data System (ADS)

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

    1992-03-01

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

  19. Quantitative flow cytometric analysis of membrane antigen expression.

    PubMed

    D'hautcourt, Jean-Luc

    2002-11-01

    Immunological analysis for cell antigens has been performed by flow cytometry in a qualitative fashion for over thirty years. During that time it has become increasingly apparent that quantitative measurements such as number of antigens per cell provide unique and useful information. This unit on quantitative flow cytometry (QFCM) describes the most commonly used protocols, both direct and indirect, and the major methods of analysis for the number of antibody binding sites on a cell or particle. Practical applications include detection of antigen under- or overexpression in hematological malignancies, distinguishing between B cell lymphoproliferative disorders, and precise diagnosis of certain rare diseases.

  20. Comparative Analysis of the Morphology, Ultrastructure, and Glycosylation Pattern of the Jejunum and Ileum of the Wild Rodent Lagostomus maximus.

    PubMed

    Tano De La Hoz, María Florencia; Flamini, Mirta Alicia; Díaz, Alcira Ofelia

    2016-05-01

    Morphological and histochemical analyses were performed to characterize the histology, ultrastructure, and glycosylation pattern of the jejunum and ileum of the wild rodent Lagostomus maximus. Enterocytes, goblet cells, Paneth cells, and enteroendocrine cells were identified in both intestinal epithelia. Two morphological types of enterocytes were identified only in the ileum based on their cytoplasm electron density. Although the histological and ultrastructural examination showed that the epithelia of both anatomical regions were morphologically similar, a certain specialization in their secretory products was evident. The glycosylation pattern of the jejunum and ileum was characterized in situ by histochemical and lectin histochemical methods. Histochemical results revealed the presence of carboxylated and sulfated gycoconjugates in both regions, although sulfomucins were clearly prevalent in the ileum. Sialic acid was highly O-acetylated and particularly abundant in the jejunum. The KOH/PA*/Bh/PAS technique evidenced a more intense histochemical reaction in the jejunal than in the ileum goblet cells, demonstrating a reduction of neutral mucin secretion in the distal small intestine. Further specific differences were revealed by lectin histochemistry. These data evidenced that the nature of mucus varies at different anatomical regions, probably adapted to physiological requirements.

  1. A quantitative analysis of the F18 flight control system

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  2. A quantitative analysis of the F18 flight control system

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  3. 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.

  4. 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.

  5. Quantitative elemental analysis on aluminum accumulation by HVTEM-EDX in liver tissues of mice orally administered with aluminum chloride.

    PubMed

    Kametani, Kiyokazu; Nagata, Tetsuji

    2006-06-01

    Quantitative elemental analysis on Al was carried out by high-accelerating voltage transmission electron microscopy (HVTEM) equipped with energy-dispersive X-ray microanalysis (EDX) using an accelerating voltage at 300 kV with high permeability in 1-mum-thick samples obtained from mice administered with aluminum chloride solution for 3, 9, and 17 weeks. By light microscopic observation, no morphological changes were observed in the hepatocytes and macrophages in the liver tissues of mice that were administered with excess Al as compared with the normal control mice. In contrast, by electron microscopic observation, ultrastructural changes were observed in the lysosomes in the hepatocytes as well as the pinocytotic vesicles in the macrophages in the experimental animals. Therefore, the concentrations of Al detected in lysosomes in hepatocytes and pinocytotic vesicles in macrophages of livers of mice administered with Al were measured in relationship to those administration periods. Moreover, transitional changes of hepatocyte lysosome ratios by image analysis and the macrophage counts in the unit area increased in liver tissues of mice administered with Al as compared with normal control mice. From the results, it was demonstrated that hepatocyte lysosome ratio and macrophage count increased in liver tissues of treated mice during those short-term excessive Al administration periods. It was also clarified that the concentrations of Al in both hepatocytes and macrophages increased as observed by HVTEM-EDX. In conclusion, Al accumulated in hepatocytes and macrophages at 3 and 9 weeks administration, while the ultrastructural changes remained in the hepatocytes and macrophages. In contrast, Al concentration did not increase in the liver at 17 weeks administration.

  6. CUMULATIVE RISK ASSESSMENT: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS

    EPA Science Inventory

    INTRODUCTION: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS FOR CUMULATIVE RISK

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

  7. CUMULATIVE RISK ASSESSMENT: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS

    EPA Science Inventory

    INTRODUCTION: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS FOR CUMULATIVE RISK

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

  8. Quantitating the subtleties of microglial morphology with fractal analysis

    PubMed Central

    Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F.

    2013-01-01

    It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between “ramified resting” and “activated amoeboid” has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology. PMID:23386810

  9. Quantitating the subtleties of microglial morphology with fractal analysis.

    PubMed

    Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F

    2013-01-01

    It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between "ramified resting" and "activated amoeboid" has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology.

  10. Phylogenetic analysis of HSP70 and cyt b gene sequences for Chinese Leishmania isolates and ultrastructural characteristics of Chinese Leishmania sp.

    PubMed

    Yuan, Dongmei; Qin, Hanxiao; Zhang, Jianguo; Liao, Lin; Chen, Qiwei; Chen, Dali; Chen, Jianping

    2017-02-01

    Leishmaniasis is a worldwide epidemic disease caused by the genus Leishmania, which is still endemic in the west and northwest areas of China. Some viewpoints of the traditional taxonomy of Chinese Leishmania have been challenged by recent phylogenetic researches based on different molecular markers. However, the taxonomic positions and phylogenetic relationships of Chinese Leishmania isolates remain controversial, which need for more data and further analysis. In this study, the heat shock protein 70 (HSP70) gene and cytochrome b (cyt b) gene were used for phylogenetic analysis of Chinese Leishmania isolates from patients, dogs, gerbils, and sand flies in different geographic origins. Besides, for the interesting Leishmania sp. in China, the ultrastructure of three Chinese Leishmania sp. strains (MHOM/CN/90/SC10H2, SD, GL) were observed by transmission electron microscopy. Bayesian trees from HSP70 and cyt b congruently indicated that the 14 Chinese Leishmania isolates belong to three Leishmania species including L. donovani complex, L. gerbilli, and L. (Sauroleishmania) sp. Their identity further confirmed that the undescribed Leishmania species causing visceral Leishmaniasis (VL) in China is closely related to L. tarentolae. The phylogenetic results from HSP70 also suggested the classification of subspecies within L. donovani complex: KXG-918, KXG-927, KXG-Liu, KXG-Xu, 9044, SC6, and KXG-65 belong to L. donovani; Cy, WenChuan, and 801 were proposed to be L. infantum. Through transmission electron microscopy, unexpectedly, the Golgi apparatus were not observed in SC10H2, SD, and GL, which was similar to previous reports of reptilian Leishmania. The statistical analysis of microtubule counts separated SC10H2, SD, and GL as one group from any other reference strain (L. donovani MHOM/IN/80/DD8; L. tropica MHOM/SU/74/K27; L. gerbilli MRHO/CN/60/GERBILLI). The ultrastructural characteristics of Leishmania sp. partly lend support to the phylogenetic inference that

  11. Quantitative analysis of regional myocardial performance in coronary artery disease

    NASA Technical Reports Server (NTRS)

    Stewart, D. K.; Dodge, H. T.; Frimer, M.

    1975-01-01

    Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.

  12. Quantitative analysis of regional myocardial performance in coronary artery disease

    NASA Technical Reports Server (NTRS)

    Stewart, D. K.; Dodge, H. T.; Frimer, M.

    1975-01-01

    Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.

  13. Quantitative transverse flow assessment using OCT speckle decorrelation analysis

    NASA Astrophysics Data System (ADS)

    Liu, Xuan; Huang, Yong; Ramella-Roman, Jessica C.; Kang, Jin U.

    2013-03-01

    In this study, we demonstrate the use of inter-Ascan speckle decorrelation analysis of optical coherence tomography (OCT) to assess fluid flow. This method allows quantitative measurement of fluid flow in a plane normal to the scanning beam. To validate this method, OCT images were obtained from a micro fluid channel with bovine milk flowing at different speeds. We also imaged a blood vessel from in vivo animal models and performed speckle analysis to asses blood flow.

  14. Improved method and apparatus for chromatographic quantitative analysis

    DOEpatents

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

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

  15. Quantitative analysis of single-molecule superresolution images

    PubMed Central

    Coltharp, Carla; Yang, Xinxing; Xiao, Jie

    2014-01-01

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

  16. Quantitative analysis of culture using millions of digitized books.

    PubMed

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

    2011-01-14

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

  17. Quantitative analysis of culture using millions of digitized books

    PubMed Central

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

    2011-01-01

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

  18. Quantitative numerical analysis of transient IR-experiments on buildings

    NASA Astrophysics Data System (ADS)

    Maierhofer, Ch.; Wiggenhauser, H.; Brink, A.; Röllig, M.

    2004-12-01

    Impulse-thermography has been established as a fast and reliable tool in many areas of non-destructive testing. In recent years several investigations have been done to apply active thermography to civil engineering. For quantitative investigations in this area of application, finite difference calculations have been performed for systematic studies on the influence of environmental conditions, heating power and time, defect depth and size and thermal properties of the bulk material (concrete). The comparison of simulated and experimental data enables the quantitative analysis of defects.

  19. Markov chain Monte Carlo linkage analysis of complex quantitative phenotypes.

    PubMed

    Hinrichs, A; Reich, T

    2001-01-01

    We report a Markov chain Monte Carlo analysis of the five simulated quantitative traits in Genetic Analysis Workshop 12 using the Loki software. Our objectives were to determine the efficacy of the Markov chain Monte Carlo method and to test a new scoring technique. Our initial blind analysis, on replicate 42 (the "best replicate") successfully detected four out of the five disease loci and found no false positives. A power analysis shows that the software could usually detect 4 of the 10 trait/gene combinations at an empirical point-wise p-value of 1.5 x 10(-4).

  20. Effect of Electrocautery on Endothelial Integrity of the Internal Thoracic Artery: Ultrastructural Analysis with Transmission Electron Microscopy

    PubMed Central

    Onan, Burak; Yeniterzi, Mehmet; Onan, Ismihan Selen; Ersoy, Burak; Gonca, Suheyla; Gelenli, Elif; Solakoglu, Seyhun

    2014-01-01

    The internal thoracic artery (ITA) is typically harvested from the chest wall by means of conventional electrocautery. We investigated the effects of electrocautery on endothelial-cell and vessel-wall morphology at the ultrastructural level during ITA harvesting. Internal thoracic artery specimens from 20 patients who underwent elective coronary artery bypass grafting were investigated in 2 groups. The ITA grafts were sharply dissected with use of a scalpel and clips in the control group (n=10) and were harvested by means of electrocautery in the study group (n=10). Each sample was evaluated for intimal, elastic-tissue, muscular-layer, and adventitial changes. Free flow was measured intraoperatively. Light microscopic examinations were performed after hematoxylin-eosin and Masson's trichrome staining. Transmission electron microscopy was used to evaluate ultrastructural changes in the endothelial cells and vessel walls of each ITA. In the sharp-dissection group, the endothelial surfaces were lined with normal amounts of original endothelium, endothelial cells were distinctly attached to the basal lamina, cytoplasmic organelles were evident, and intercellular junctional complexes were intact. Conversely, in the electrocautery group, the morphologic integrity of endothelial cells was distorted, with some cell separations and splits, contracted cells, numerous large cytoplasmic vacuoles, and no visible cytoplasmic organelles. The subendothelial layer exhibited disintegration. Free ITA flow was higher in the sharp-dissection group (P=0.04). The integrity of endothelial cells can be better preserved when the ITA is mobilized by means of sharp dissection, rather than solely by electrocautery; we recommend a combined approach. PMID:25425979

  1. Effect of electrocautery on endothelial integrity of the internal thoracic artery: ultrastructural analysis with transmission electron microscopy.

    PubMed

    Onan, Burak; Yeniterzi, Mehmet; Onan, Ismihan Selen; Ersoy, Burak; Gonca, Suheyla; Gelenli, Elif; Solakoglu, Seyhun; Bakir, Ihsan

    2014-10-01

    The internal thoracic artery (ITA) is typically harvested from the chest wall by means of conventional electrocautery. We investigated the effects of electrocautery on endothelial-cell and vessel-wall morphology at the ultrastructural level during ITA harvesting. Internal thoracic artery specimens from 20 patients who underwent elective coronary artery bypass grafting were investigated in 2 groups. The ITA grafts were sharply dissected with use of a scalpel and clips in the control group (n=10) and were harvested by means of electrocautery in the study group (n=10). Each sample was evaluated for intimal, elastic-tissue, muscular-layer, and adventitial changes. Free flow was measured intraoperatively. Light microscopic examinations were performed after hematoxylin-eosin and Masson's trichrome staining. Transmission electron microscopy was used to evaluate ultrastructural changes in the endothelial cells and vessel walls of each ITA. In the sharp-dissection group, the endothelial surfaces were lined with normal amounts of original endothelium, endothelial cells were distinctly attached to the basal lamina, cytoplasmic organelles were evident, and intercellular junctional complexes were intact. Conversely, in the electrocautery group, the morphologic integrity of endothelial cells was distorted, with some cell separations and splits, contracted cells, numerous large cytoplasmic vacuoles, and no visible cytoplasmic organelles. The subendothelial layer exhibited disintegration. Free ITA flow was higher in the sharp-dissection group (P=0.04). The integrity of endothelial cells can be better preserved when the ITA is mobilized by means of sharp dissection, rather than solely by electrocautery; we recommend a combined approach.

  2. Spotsizer: High-throughput quantitative analysis of microbial growth.

    PubMed

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

    2016-10-01

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

  3. Quantitative Rietveld analysis of CAC clinker phases using synchrotron radiation

    SciTech Connect

    Guirado, F. . E-mail: francesc.guirado@urv.cat; Gali, S.

    2006-11-15

    The quantitative Rietveld analyses of twenty samples of CAC from four different manufacturers over the world, one synthetic mixture and a NIST standard were performed using synchrotron radiation. As compared with conventional XRD, synchrotron powder diffraction permitted to find new minor phases, improve the characterization of solid solutions of iron rich CAC phases and reduce preferential orientation and microabsorption effects. Diffraction data were complemented with XRF and TG/DT analyses. Synchrotron results were used as a reference test to improve the performance of conventional powder diffraction, by an accurate selection of refinable profile and structural parameters, and permitted to extract several recommendations for conventional quantitative Rietveld procedures. It is shown that with these recommendations in mind, conventional XRD based Rietveld analyses are comparable to those obtained from synchrotron data. In summary, quantitative XRD Rietveld analysis is confirmed as an excellent tool for the CAC cement industry.

  4. Spotsizer: High-throughput quantitative analysis of microbial growth

    PubMed Central

    Jeffares, Daniel C.; Arzhaeva, Yulia; Bähler, Jürg

    2017-01-01

    Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license. PMID:27712582

  5. A strategy to apply quantitative epistasis analysis on developmental traits.

    PubMed

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

    2017-05-15

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

  6. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

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

    2015-01-01

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

  7. Quantitative proteomics and bioinformatic analysis provide new insight into protein function during avian eggshell biomineralization.

    PubMed

    Marie, Pauline; Labas, Valérie; Brionne, Aurélien; Harichaux, Grégoire; Hennequet-Antier, Christelle; Nys, Yves; Gautron, Joël

    2015-01-15

    Gallus gallus eggshell is a bioceramic composed of 95% calcium carbonate in calcitic form and 3.5% extracellular organic matrix. The calcification process occurs in the uterine fluid where biomineralization follows a temporal sequence corresponding to the initiation, growth and termination stages of crystal growth. Eggshell texture and its ultrastructure are regulated by organic matrix proteins, which control mineralization process and influence the eggshell biomechanical properties. We performed proteomic qualitative analyses and identified 308 uterine fluid proteins. Quantitative analysis showed differential abundances at the three stages of shell biomineralization for 64 of them. Cluster analysis revealed a first group of proteins related to mineralization and mainly present at the onset of calcification including OVOT, OVAL, OC-17, and two novel calcium binding proteins (EDIL3, MFGE8). A second group of proteins mainly present at the initiation and termination of shell formation was potentially involved in the regulation of the activity of the uterine fluid proteins (e.g. molecular chaperones, folding proteins, proteases and protease inhibitors). OCX21, a protein highly concentrated in the fluid and the shell, belongs to this group. A third group equally represented at all stages of shell mineralization corresponded to antibacterial proteins that could protect the forming egg against microbial invasion. The calcitic avian eggshell protects the developing embryo and, moreover, ensures that the nutritious table egg remains free of pathogens. The eggshell is formed by nucleation upon a fibrous scaffold (the eggshell membranes) followed by an interaction between the growing mineral crystals and the shell organic matrix. This interaction leads to a highly ordered shell microstructure and texture which contribute to its exceptional mechanical properties. Shell mineralization occurs in three distinct phases of calcification (initiation, growth and termination), which

  8. Data from quantitative label free proteomics analysis of rat spleen.

    PubMed

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

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

  9. Quantitative risk analysis of oil storage facilities in seismic areas.

    PubMed

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

    2005-08-31

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

  10. An improved quantitative analysis method for plant cortical microtubules.

    PubMed

    Lu, Yi; Huang, Chenyang; Wang, Jia; Shang, Peng

    2014-01-01

    The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD) algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1) image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM) algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies.

  11. Quantitative analysis of synchrotron radiation intravenous angiographic images

    NASA Astrophysics Data System (ADS)

    Sarnelli, Anna; Nemoz, Christian; Elleaume, Hélène; Estève, François; Bertrand, Bernard; Bravin, Alberto

    2005-02-01

    A medical research protocol on clinical intravenous coronary angiography has been completed at the European Synchrotron Radiation Facility (ESRF) biomedical beamline. The aim was to investigate the accuracy of intravenous coronary angiography based on the K-edge digital subtraction technique for the detection of in-stent restenosis. For each patient, diagnosis has been performed on the synchrotron radiation images and monitored with the conventional selective coronary angiography method taken as the golden standard. In this paper, the methods of image processing and the results of the quantitative analysis are described. Image processing includes beam harmonic contamination correction, spatial deconvolution and the extraction of a 'contrast' and a 'tissue' image from each couple of radiograms simultaneously acquired at energies bracketing the K-edge of iodine. Quantitative analysis includes the estimation of the vessel diameter, the calculation of the absolute iodine concentration profiles along the coronary arteries and the stenosis degree measurement.

  12. Implementing a Quantitative Analysis Design Tool for Future Generation Interfaces

    DTIC Science & Technology

    2012-03-01

    future MAC-enabled systems. A human-computer interaction ( HCI ) Index, originally applied to multi-function displays was applied to the prototype Vigilant...Spirit interface. A modified version of the HCI Index was successfully applied to perform a quantitative analysis of the baseline VSCS interface and...two modified interface designs. The modified HCI Index incorporates the Hick-Hyman decision time, Fitts’ Law time, and the physical actions

  13. Quantitative NMR Analysis of Partially Substituted Biodiesel Glycerols

    SciTech Connect

    Nagy, M.; Alleman, T. L.; Dyer, T.; Ragauskas, A. J.

    2009-01-01

    Phosphitylation of hydroxyl groups in biodiesel samples with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane followed by 31P-NMR analysis provides a rapid quantitative analytical technique for the determination of substitution patterns on partially esterified glycerols. The unique 31P-NMR chemical shift data was established with a series mono and di-substituted fatty acid esters of glycerol and then utilized to characterize an industrial sample of partially processed biodiesel.

  14. Comprehensive Quantitative Analysis of SQ Injection Using Multiple Chromatographic Technologies.

    PubMed

    Chau, Siu-Leung; Huang, Zhi-Bing; Song, Yan-Gang; Yue, Rui-Qi; Ho, Alan; Lin, Chao-Zhan; Huang, Wen-Hua; Han, Quan-Bin

    2016-08-19

    Quality control of Chinese medicine injections remains a challenge due to our poor knowledge of their complex chemical profile. This study aims to investigate the chemical composition of one of the best-selling injections, Shenqi Fuzheng (SQ) injection (SQI), via a full component quantitative analysis. A total of 15 representative small molecular components of SQI were simultaneously determined using ultra-high performance liquid chromatography (UHPLC) coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS); saccharide composition of SQI was also quantitatively determined by high performance liquid chromatography (HPLC) with evaporative light scattering detector (ELSD) on an amino column before and after acid hydrolysis. The existence of polysaccharides was also examined on a gel permeation chromatography column. The method was well validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to analyze 13 SQI samples. The results demonstrate that up to 94.69% (w/w) of this injection product are quantitatively determined, in which small molecules and monosaccharide/sucrose account for 0.18%-0.21%, and 53.49%-58.2%, respectively. The quantitative information contributes to accumulating scientific evidence to better understand the therapy efficacy and safety of complex Chinese medicine injections.

  15. Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation.

    PubMed

    Qu, Zhe; Greenlief, C Michael; Gu, Zezong

    2016-01-04

    S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central nervous system, aberrant S-nitrosylation, due to excessive NO production, is known to cause protein misfolding, mitochondrial dysfunction, transcriptional dysregulation, and neuronal death. This leads to an altered physiological state and consequently contributes to pathogenesis of neurodegenerative disorders. To date, much effort has been made to understand the mechanisms underlying protein S-nitrosylation, and several approaches have been developed to unveil S-nitrosylated proteins from different organisms. Interest in determining the dynamic changes of protein S-nitrosylation under different physiological and pathophysiological conditions has underscored the need for the development of quantitative proteomic approaches. Currently, both gel-based and gel-free mass spectrometry-based quantitative methods are widely used, and they each have advantages and disadvantages but may also be used together to produce complementary data. This review evaluates current available quantitative proteomic techniques for the analysis of protein S-nitrosylation and highlights recent advances, with emphasis on applications in neurodegenerative diseases. An important goal is to provide a comprehensive guide of feasible quantitative proteomic methodologies for examining protein S-nitrosylation in research to yield insights into disease mechanisms, diagnostic biomarkers, and drug discovery.

  16. Quantitative analysis of the heterogeneous population of endocytic vesicles.

    PubMed

    Kozlov, Konstantin; Kosheverova, Vera; Kamentseva, Rimma; Kharchenko, Marianna; Sokolkova, Alena; Kornilova, Elena; Samsonova, Maria

    2017-03-07

    The quantitative characterization of endocytic vesicles in images acquired with microscope is critically important for deciphering of endocytosis mechanisms. Image segmentation is the most important step of quantitative image analysis. In spite of availability of many segmentation methods, the accurate segmentation is challenging when the images are heterogeneous with respect to object shapes and signal intensities what is typical for images of endocytic vesicles. We present a Morphological reconstruction and Contrast mapping segmentation method (MrComas) for the segmentation of the endocytic vesicle population that copes with the heterogeneity in their shape and intensity. The method uses morphological opening and closing by reconstruction in the vicinity of local minima and maxima respectively thus creating the strong contrast between their basins of attraction. As a consequence, the intensity is flattened within the objects and their edges are enhanced. The method accurately recovered quantitative characteristics of synthetic images that preserve characteristic features of the endocytic vesicle population. In benchmarks and quantitative comparisons with two other popular segmentation methods, namely manual thresholding and Squash plugin, MrComas shows the best segmentation results on real biological images of EGFR (Epidermal Growth Factor Receptor) endocytosis. As a proof of feasibility, the method was applied to quantify the dynamical behavior of Early Endosomal Autoantigen 1 (EEA1)-positive endosome subpopulations during EGF-stimulated endocytosis.

  17. Sperm dynamics in spiders (Araneae): ultrastructural analysis of the sperm activation process in the garden spider Argiope bruennichi (Scopoli, 1772).

    PubMed

    Vöcking, Oliver; Uhl, Gabriele; Michalik, Peter

    2013-01-01

    Storage of sperm inside the female genital tract is an integral phase of reproduction in many animal species. The sperm storage site constitutes the arena for sperm activation, sperm competition and female sperm choice. Consequently, to understand animal mating systems information on the processes that occur from sperm transfer to fertilization is required. Here, we focus on sperm activation in spiders. Male spiders produce sperm whose cell components are coiled within the sperm cell and that are surrounded by a proteinaceous sheath. These inactive and encapsulated sperm are transferred to the female spermathecae where they are stored for later fertilization. We analyzed the ultrastructural changes of sperm cells during residency time in the female genital system of the orb-web spider Argiope bruennichi. We found three clearly distinguishable sperm conditions: encapsulated sperm (secretion sheath present), decapsulated (secretion sheath absent) and uncoiled sperm (cell components uncoiled, presumably activated). After insemination, sperm remain in the encapsulated condition for several days and become decapsulated after variable periods of time. A variable portion of the decapsulated sperm transforms rapidly to the uncoiled condition resulting in a simultaneous occurrence of decapsulated and uncoiled sperm. After oviposition, only decapsulated and uncoiled sperm are left in the spermathecae, strongly suggesting that the activation process is not reversible. Furthermore, we found four different types of secretion in the spermathecae which might play a role in the decapsulation and activation process.

  18. Sperm Dynamics in Spiders (Araneae): Ultrastructural Analysis of the Sperm Activation Process in the Garden Spider Argiope bruennichi (Scopoli, 1772)

    PubMed Central

    Vöcking, Oliver; Uhl, Gabriele; Michalik, Peter

    2013-01-01

    Storage of sperm inside the female genital tract is an integral phase of reproduction in many animal species. The sperm storage site constitutes the arena for sperm activation, sperm competition and female sperm choice. Consequently, to understand animal mating systems information on the processes that occur from sperm transfer to fertilization is required. Here, we focus on sperm activation in spiders. Male spiders produce sperm whose cell components are coiled within the sperm cell and that are surrounded by a proteinaceous sheath. These inactive and encapsulated sperm are transferred to the female spermathecae where they are stored for later fertilization. We analyzed the ultrastructural changes of sperm cells during residency time in the female genital system of the orb-web spider Argiope bruennichi. We found three clearly distinguishable sperm conditions: encapsulated sperm (secretion sheath present), decapsulated (secretion sheath absent) and uncoiled sperm (cell components uncoiled, presumably activated). After insemination, sperm remain in the encapsulated condition for several days and become decapsulated after variable periods of time. A variable portion of the decapsulated sperm transforms rapidly to the uncoiled condition resulting in a simultaneous occurrence of decapsulated and uncoiled sperm. After oviposition, only decapsulated and uncoiled sperm are left in the spermathecae, strongly suggesting that the activation process is not reversible. Furthermore, we found four different types of secretion in the spermathecae which might play a role in the decapsulation and activation process. PMID:24039790

  19. Histologic and ultrastructural analysis of regenerated bone in maxillary sinus augmentation using a porcine bone-derived biomaterial.

    PubMed

    Orsini, Giovanna; Scarano, Antonio; Piattelli, Maurizio; Piccirilli, Marcello; Caputi, Sergio; Piattelli, Adriano

    2006-12-01

    The purpose of the present study was the histologic and ultrastructural evaluation of a biomaterial composed of cortical pig bone in the form of granules. After maxillary sinus augmentation using this biomaterial, 10 specimens were retrieved after 5 months in 10 patients using this biomaterial. The specimens were processed to be observed under light microscopy (LM) and transmission electron microscopy (TEM). Histomorphometric measurements were presented by means +/- standard deviations. LM showed that most of the particles were surrounded by newly formed bone. In some areas, the osteoid matrix was present; however, mainly compact bone was present at the interface. There was no evidence of an acute inflammatory infiltrate. The newly formed bone was 36% +/- 2.8% and marrow spaces were 38% +/- 1.6%, whereas residual grafted material was 31% +/- 1.6%. Under TEM, all phases of bone formation (osteoid matrix, woven, and lamellar bone) were observed in proximity with the biomaterial particles. The bone-biomaterial interface showed a close contact between the porcine bone particles and the surrounding bone that had mainly features of mature bone with numerous osteocytes. A lamina limitans was sometimes present at this interface. According to our knowledge, this is the first study presenting data on TEM of a porcine bone-derived biomaterial used in sinus augmentation procedures in humans. Our findings show that this is a biocompatible biomaterial that can be used for maxillary sinus augmentation procedures without interfering with the normal reparative bone processes.

  20. Ultrastructural and chemotaxonomic analysis of a xylanolytic strain of Cryptococcus adeliensis isolated from sheep droppings in Spain.

    PubMed

    Velázquez, Encarna; del Villar, María; Grondona, Isabel; Monte, Enrique; González-Villa, Tomás

    2006-09-01

    Cryptococcus adeliensis was initially described as a psycrophilic species containing a single strain CBS 8351(T) isolated from decayed algae in Terre Adelie (Antartida). Later, a second strain of this species was isolated from an immunosuppressed patient affected by leukaemia in Germany and recently several strains from this species have been found in human patients and pigeon droppings of the same country. In this study, we isolated from sheep droppings in Spain a xylanolytic strain named LEVX01 that was phenotypically related to the strain CBS 8351(T) and showed a 100% similarity in the D1/D2 domain and 5.8S-ITS region sequences with respect to the remaining described strains of C. adeliensis. These findings suggest that this species has a wide geographical distribution and that the animal faeces are a common habitat for C. adeliensis. The chemotaxonomic analyses showed the absence of detectable amounts of xylose in the cell walls of the strains LEVX01 and CBS8351(T) in contrast to other Cryptococcus species. Interestingly, the ultrastructural study showed the presence of fimbriae in these two strains that could be involved in the attachment to the host cells and, as occurs in Candida albicans, they could also be a pathogenicity factor for the man.

  1. Ultrastructural analysis of olfactory ensheathing cells derived from olfactory bulb and nerve of neonatal and juvenile rats.

    PubMed

    Gómez, Rosa M; Ghotme, Kemel; Botero, Lucía; Bernal, Jaime E; Pérez, Rosalía; Barreto, George E; Bustos, Rosa Helena

    2016-02-01

    Olfactory nerve derived and olfactory bulb derived olfactory ensheathing cells (OECs) have the ability to promote axonal regeneration and remyelination, both of which are essential in a successful cell transplant. Thus, morphological identification of OECs is a key aspect to develop an applicable cell therapy for injuries to the nervous system. However, there is no clear definition regarding which developmental stage or anatomical origin of OECs is more adequate for neural repair. In the present study, an ultrastructural comparison was made between OECs recovered from primary cultures of olfactory nerve and bulb in two developmental stages. The most notorious difference between cells obtained from olfactory nerve and bulb was the presence of indented nuclei in bulb derived OECs, suggesting a greater ability for possible chemotaxis. In neonatal OECs abundant mitochondria, lipid vacuoles, and smooth endoplasmic reticulum were detected, suggesting an active lipid metabolism, probably involved in synthesis of myelin. Our results suggest that neonatal OECs obtained from olfactory bulb have microscopic properties that could make them more suitable for neural repair. Copyright © 2015 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

  2. Ultrastructure of nerve endings and synaptic junctions in rabbit intrapulmonary neuroepithelial bodies: a single and serial section analysis.

    PubMed Central

    Lauweryns, J M; Van Lommel, A

    1987-01-01

    This study on the innervation of rabbit intrapulmonary neuroepithelial bodies (NEB) was undertaken to obtain more information about the detailed ultrastructure of morphologically afferent and efferent intracorpuscular NEB nerve endings, the extent to which they are in cytoplasmic continuity with one another, and the structure of the synaptic junctions they form with the NEB corpuscular cells. As in earlier studies, NEB exhibit intracorpuscular nerve endings containing predominantly either mitochondria (morphologically afferent) or synaptic vesicles (morphologically efferent). Both types of nerve endings form synaptic junctions with the NEB corpuscular cells, arranged so that a NEB corpuscular cell is the presynaptic element and the nerve ending the postsynaptic element. This arrangement implies that NEB can transmit nerve impulses to the central nervous system, thus arguing in favour of their hypothetical neuroreceptor function. Moreover, on serial sections, the morphologically afferent and efferent intracorpuscular nerve endings are often found in cytoplasmic continuity. Hence, transduction of stimuli in the NEB implies concomitant efferent modulation of the NEB corpuscular cells. In conclusion, intrapulmonary NEB apparently function as neuroreceptors that are locally modulated by axon reflexes. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 6 (cont.) Fig. 6 (cont.) Fig. 6 PMID:3654362

  3. Transgenerational, ultrastructural analysis on the antioxidative effects of tocopherol on early gametogenesis in Caenorhabditis elegans grown in 100% oxygen.

    PubMed

    Goldstein, P; Modric, T

    1994-02-01

    The random, free-radical-mediated oxidations of biological molecules result in membrane degradation leading to cellular deterioration (B. Halliwell, Free Radical Res. Commun. 9, 1-32, 1990). External oxygen, prooxidants, and internally produced oxygen free radicals (oxyradicals), interact and alter the nature of biomembranes. Antioxidants, e.g., tocopherol (Vitamin E), inhibit such oxidative damage of free radicals. In the present study, the nematode Caenorhabditis elegans was grown under hyperoxia (100% oxygen) with or without the addition of Vitamin E to the growth media. The nematodes were viable under such conditions for at least eight generations, although fecundity gradually decreased through successive generations, presumably due to genetic load. Vitamin E was also shown to have a protective effect against paraquat, which is a strong, intracellular, oxidizing agent. Ultrastructural observations of early meiosis showed that the formation of synaptonemal complexes was compromised and that the telomeres failed to attach to the nuclear envelope. Those nematodes grown in 100% oxygen with 200 micrograms/ml Vitamin E had normal meiotic structures and normal fecundity. Thus, the presence of enhanced levels of intracellular Vitamin E resulted in protection against oxidative stress during gametogenesis.

  4. An ultrastructural analysis of endothelial change paralleling platelet aggregation in a light/dye model of microvascular insult.

    PubMed Central

    Povlishock, J. T.; Rosenblum, W. I.; Sholley, M. M.; Wei, E. P.

    1983-01-01

    Those microvascular endothelial events that parallel the evolution of platelet aggregation were evaluated in a well-controlled animal model. Cat pial microvessels were observed through a cranial window while local platelet aggregation was produced by intravenous injection of sodium fluorescein and simultaneous exposure of the pial vessels to light from a filtered mercury lamp that excited the fluorescein. The vessels were fixed in situ when the in vivo observations of a preselected vessel indicated early, intermediate, or advanced aggregation in that vessel. The preselected vessel was then harvested for ultrastructural study together with adjacent vessels from the illuminated field. These vessels and appropriate controls were compared in semiserial thin sections. The onset of platelet aggregation in both venules and arterioles was accompanied by focal endothelial lucency, vacuole formation, luminal membrane rupture, and swelling of the nuclear envelope. These changes were not found in control material. With intermediate aggregation these changes were more common, while with advanced aggregation these abnormalities occurred together with focal endothelial denudation. Thus, in this model denudation occurred only with advanced aggregation and was not a prerequisite for aggregation. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 PMID:6824062

  5. Prostaglandin E1-induced deconsolidation of thrombin-activated platelet aggregates I: ultrastructure-computer image analysis.

    PubMed

    Salganicoff, L; Russo, M A; Sevy, R W

    1999-06-15

    We have compared, at an ultrastructural-computer image morphometric level, the relaxation induced by Mg-ethylene-bis-oxyethylenenitrilo-tetracetic acid and prostaglandin E1 on a model of a thrombin-activated platelet aggregate. Mg-ethylene-bisoxyethylenenitrilo-tetracetic acid produced a small increase of 5.0% of the intercellular space over the control levels, and a decrease of 10.0+/-1.3% of the cross-sectional area of the platelets, with no apparent cytoskeletal alterations. In contrast, the prostaglandin El-treated preparation shows a 360% increase in the intercellular space and a decrease of the average platelet cross-sectional area of 30.0+/-2.0% with marked cytoskeletal alterations. We use the term "deconsolidation" to describe this effect. The enlargement of the intercellular space allows the observation of two types of contacts: (1) a type S (segmental) complex, of approximately 200-nm length that maintains a narrow interplatelet gap of 20-30 nm, filled with a dense intercellular material, and (2) a type R (reticular) complex, formed by scant focal regions of the plasma membrane from opposing platelets that are connected through a mesh of fibrillar or granular material contained within a variable-size space. We hypothesize that deconsolidation is caused by fluid loss from the platelets into the intercellular space. As a result, platelet volume decreases and intercellular space increases.

  6. Quantitative Phosphoproteomic Analysis of T-Cell Receptor Signaling.

    PubMed

    Ahsan, Nagib; Salomon, Arthur R

    2017-01-01

    TCR signaling critically depends on protein phosphorylation across many proteins. Localization of each phosphorylation event relative to the T-cell receptor (TCR) and canonical T-cell signaling proteins will provide clues about the structure of TCR signaling networks. Quantitative phosphoproteomic analysis by mass spectrometry provides a wide-scale view of cellular phosphorylation networks. However, analysis of phosphorylation by mass spectrometry is still challenging due to the relative low abundance of phosphorylated proteins relative to all proteins and the extraordinary diversity of phosphorylation sites across the proteome. Highly selective enrichment of phosphorylated peptides is essential to provide the most comprehensive view of the phosphoproteome. Optimization of phosphopeptide enrichment methods coupled with highly sensitive mass spectrometry workflows significantly improves the sequencing depth of the phosphoproteome to over 10,000 unique phosphorylation sites from complex cell lysates. Here we describe a step-by-step method for phosphoproteomic analysis that has achieved widespread success for identification of serine, threonine, and tyrosine phosphorylation. Reproducible quantification of relative phosphopeptide abundance is provided by intensity-based label-free quantitation. An ideal set of mass spectrometry analysis parameters is also provided that optimize the yield of identified sites. We also provide guidelines for the bioinformatic analysis of this type of data to assess the quality of the data and to comply with proteomic data reporting requirements.

  7. A Quantitative Method for Microtubule Analysis in Fluorescence Images.

    PubMed

    Lan, Xiaodong; Li, Lingfei; Hu, Jiongyu; Zhang, Qiong; Dang, Yongming; Huang, Yuesheng

    2015-12-01

    Microtubule analysis is of significant value for a better understanding of normal and pathological cellular processes. Although immunofluorescence microscopic techniques have proven useful in the study of microtubules, comparative results commonly rely on a descriptive and subjective visual analysis. We developed an objective and quantitative method based on image processing and analysis of fluorescently labeled microtubular patterns in cultured cells. We used a multi-parameter approach by analyzing four quantifiable characteristics to compose our quantitative feature set. Then we interpreted specific changes in the parameters and revealed the contribution of each feature set using principal component analysis. In addition, we verified that different treatment groups could be clearly discriminated using principal components of the multi-parameter model. High predictive accuracy of four commonly used multi-classification methods confirmed our method. These results demonstrated the effectiveness and efficiency of our method in the analysis of microtubules in fluorescence images. Application of the analytical methods presented here provides information concerning the organization and modification of microtubules, and could aid in the further understanding of structural and functional aspects of microtubules under normal and pathological conditions.

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

    ERIC Educational Resources Information Center

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

    2017-01-01

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

  9. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.

    PubMed

    White, Douglas E; Sylvester, Jonathan B; Levario, Thomas J; Lu, Hang; Streelman, J Todd; McDevitt, Todd C; Kemp, Melissa L

    2015-07-01

    Interrogating fundamental cell biology principles that govern tissue morphogenesis is critical to better understanding of developmental biology and engineering novel multicellular systems. Recently, functional micro-tissues derived from pluripotent embryonic stem cell (ESC) aggregates have provided novel platforms for experimental investigation; however elucidating the factors directing emergent spatial phenotypic patterns remains a significant challenge. Computational modelling techniques offer a unique complementary approach to probe mechanisms regulating morphogenic processes and provide a wealth of spatio-temporal data, but quantitative analysis of simulations and comparison to experimental data is extremely difficult. Quantitative descriptions of spatial phenomena across multiple systems and scales would enable unprecedented comparisons of computational simulations with experimental systems, thereby leveraging the inherent power of computational methods to interrogate the mechanisms governing emergent properties of multicellular biology. To address these challenges, we developed a portable pattern recognition pipeline consisting of: the conversion of cellular images into networks, extraction of novel features via network analysis, and generation of morphogenic trajectories. This novel methodology enabled the quantitative description of morphogenic pattern trajectories that could be compared across diverse systems: computational modelling of multicellular structures, differentiation of stem cell aggregates, and gastrulation of cichlid fish. Moreover, this method identified novel spatio-temporal features associated with different stages of embryo gastrulation, and elucidated a complex paracrine mechanism capable of explaining spatiotemporal pattern kinetic differences in ESC aggregates of different sizes.

  10. Cell poking: quantitative analysis of indentation of thick viscoelastic layers.

    PubMed

    Duszyk, M; Schwab, B; Zahalak, G I; Qian, H; Elson, E L

    1989-04-01

    A recently introduced device, the cell poker, measures the force required to indent the exposed surface of a cell adherent to a rigid substratum. The cell poker has provided phenomenological information about the viscoelastic properties of several different types of cells, about mechanical changes triggered by external stimuli, and about the role of the cytoskeleton in these mechanical functions. Except in special cases, however, it has not been possible to extract quantitative estimates of viscosity and elasticity moduli from cell poker measurements. This paper presents cell poker measurements of well characterized viscoelastic polymeric materials, polydimethylsiloxanes of different degrees of polymerization, in a simple shape, a flat, thick layer, which for our purposes can be treated as a half space. Analysis of the measurements in terms of a linear viscoelasticity theory yields viscosity values for three polymer samples in agreement with those determined by measurements on a macroscopic scale. Theoretical analysis further indicates that the measured limiting static elasticity of the layers may result from the tension generated at the interface between the polymer and water. This work demonstrates the possibility of obtaining quantitative viscoelastic material properties from cell poker measurements and represents the first step in extending these quantitative studies to more complicated structures including cells.

  11. Cell poking: quantitative analysis of indentation of thick viscoelastic layers.

    PubMed Central

    Duszyk, M; Schwab, B; Zahalak, G I; Qian, H; Elson, E L

    1989-01-01

    A recently introduced device, the cell poker, measures the force required to indent the exposed surface of a cell adherent to a rigid substratum. The cell poker has provided phenomenological information about the viscoelastic properties of several different types of cells, about mechanical changes triggered by external stimuli, and about the role of the cytoskeleton in these mechanical functions. Except in special cases, however, it has not been possible to extract quantitative estimates of viscosity and elasticity moduli from cell poker measurements. This paper presents cell poker measurements of well characterized viscoelastic polymeric materials, polydimethylsiloxanes of different degrees of polymerization, in a simple shape, a flat, thick layer, which for our purposes can be treated as a half space. Analysis of the measurements in terms of a linear viscoelasticity theory yields viscosity values for three polymer samples in agreement with those determined by measurements on a macroscopic scale. Theoretical analysis further indicates that the measured limiting static elasticity of the layers may result from the tension generated at the interface between the polymer and water. This work demonstrates the possibility of obtaining quantitative viscoelastic material properties from cell poker measurements and represents the first step in extending these quantitative studies to more complicated structures including cells. PMID:2720066

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

    ERIC Educational Resources Information Center

    Anderson, James L.; And Others

    1980-01-01

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

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

    ERIC Educational Resources Information Center

    Anderson, James L.; And Others

    1980-01-01

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

  14. Quantitative analysis of endocytosis with cytoplasmic pHluorin chimeras.

    PubMed

    Prosser, Derek C; Whitworth, Karen; Wendland, Beverly

    2010-09-01

    The pH-sensitive green fluorescent protein (GFP) variant pHluorin is typically fused to the extracellular domain of transmembrane proteins to monitor endocytosis. Here, we have turned pHluorin inside-out, and show that cytoplasmic fusions of pHluorin are effective quantitative reporters for endocytosis and multivesicular body (MVB) sorting. In yeast in particular, fusion of GFP and its variants on the extracellular side of transmembrane proteins can result in perturbed trafficking. In contrast, cytoplasmic fusions are well tolerated, allowing for the quantitative assessment of trafficking of virtually any transmembrane protein. Quenching of degradation-resistant pHluorin in the acidic vacuole permits quantification of extravacuolar cargo proteins at steady-state levels and is compatible with kinetic analysis of endocytosis in live cells.

  15. Biomechanical cell analysis using quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wax, Adam; Park, Han Sang; Eldridge, William J.

    2016-03-01

    Quantitative phase imaging provides nanometer scale sensitivity and has been previously used to study spectral and temporal characteristics of individual cells in vitro, especially red blood cells. Here we extend this work to study the mechanical responses of individual cells due to the influence of external stimuli. Cell stiffness may be characterized by analyzing the inherent thermal fluctuations of cells but by applying external stimuli, additional information can be obtained. The time dependent response of cells due to external shear stress is examined with high speed quantitative phase imaging and found to exhibit characteristics that relate to their stiffness. However, analysis beyond the cellular scale also reveals internal organization of the cell and its modulation due to pathologic processes such as carcinogenesis. Further studies with microfluidic platforms point the way for using this approach in high throughput assays.

  16. [Simultaneous quantitative analysis of four lignanoids in Schisandra chinensis by quantitative analysis of multi-components by single marker].

    PubMed

    He, Feng-Cheng; Li, Shou-Xin; Zhao, Zhi-Quan; Dong, Jin-Ping; Liu, Wu-Zhan; Su, Rui-Qiang

    2012-07-01

    The aim of the study is to establish a new method of quality evaluation and validate its feasibilities by the simultaneous quantitative assay of four lignanoids in Schisandra chinensis. A new quality evaluation method, quantitative analysis of multi-components by single marker (QAMS), was established and validated with Schisandra chinensis. Four main lignanoids, schisandrin, schisantherin A, deoxyschizandrin and gamma-schizandrin, were selected as analytes and schisandrin as internal reference substance to evaluate the quality. Their contents in 13 different batches of samples, collected from different bathes, were determined by both external standard method and QAMS. The method was evaluated by comparison of the quantitative results between external standard method and QAMS. No significant differences were found in the quantitative results of four lignanoids in 13 batches of S. chinensis determined by external standard method and QAMS. QAMS is feasible for determination of four lignanoids simultaneously when some authentic standard substances were unavailable, and the developed method can be used for quality control of S. chinensis.

  17. Quantitative 3D analysis of huge nanoparticle assemblies

    NASA Astrophysics Data System (ADS)

    Zanaga, Daniele; Bleichrodt, Folkert; Altantzis, Thomas; Winckelmans, Naomi; Palenstijn, Willem Jan; Sijbers, Jan; de Nijs, Bart; van Huis, Marijn A.; Sánchez-Iglesias, Ana; Liz-Marzán, Luis M.; van Blaaderen, Alfons; Joost Batenburg, K.; Bals, Sara; van Tendeloo, Gustaaf

    2015-12-01

    Nanoparticle assemblies can be investigated in 3 dimensions using electron tomography. However, it is not straightforward to obtain quantitative information such as the number of particles or their relative position. This becomes particularly difficult when the number of particles increases. We propose a novel approach in which prior information on the shape of the individual particles is exploited. It improves the quality of the reconstruction of these complex assemblies significantly. Moreover, this quantitative Sparse Sphere Reconstruction approach yields directly the number of particles and their position as an output of the reconstruction technique, enabling a detailed 3D analysis of assemblies with as many as 10 000 particles. The approach can also be used to reconstruct objects based on a very limited number of projections, which opens up possibilities to investigate beam sensitive assemblies where previous reconstructions with the available electron tomography techniques failed.Nanoparticle assemblies can be investigated in 3 dimensions using electron tomography. However, it is not straightforward to obtain quantitative information such as the number of particles or their relative position. This becomes particularly difficult when the number of particles increases. We propose a novel approach in which prior information on the shape of the individual particles is exploited. It improves the quality of the reconstruction of these complex assemblies significantly. Moreover, this quantitative Sparse Sphere Reconstruction approach yields directly the number of particles and their position as an output of the reconstruction technique, enabling a detailed 3D analysis of assemblies with as many as 10 000 particles. The approach can also be used to reconstruct objects based on a very limited number of projections, which opens up possibilities to investigate beam sensitive assemblies where previous reconstructions with the available electron tomography techniques

  18. Quantitative MRI for analysis of peritumoral edema in malignant gliomas

    PubMed Central

    Warntjes, J. B. Marcel; Smedby, Örjan; Lundberg, Peter

    2017-01-01

    Background and purpose Damage to the blood-brain barrier with subsequent contrast enhancement is a hallmark of glioblastoma. Non-enhancing tumor invasion into the peritumoral edema is, however, not usually visible on conventional magnetic resonance imaging. New quantitative techniques using relaxometry offer additional information about tissue properties. The aim of this study was to evaluate longitudinal relaxation R1, transverse relaxation R2, and proton density in the peritumoral edema in a group of patients with malignant glioma before surgery to assess whether relaxometry can detect changes not visible on conventional images. Methods In a prospective study, 24 patients with suspected malignant glioma were examined before surgery. A standard MRI protocol was used with the addition of a quantitative MR method (MAGIC), which measured R1, R2, and proton density. The diagnosis of malignant glioma was confirmed after biopsy/surgery. In 19 patients synthetic MR images were then created from the MAGIC scan, and ROIs were placed in the peritumoral edema to obtain the quantitative values. Dynamic susceptibility contrast perfusion was used to obtain cerebral blood volume (rCBV) data of the peritumoral edema. Voxel-based statistical analysis was performed using a mixed linear model. Results R1, R2, and rCBV decrease with increasing distance from the contrast-enhancing part of the tumor. There is a significant increase in R1 gradient after contrast agent injection (P < .0001). There is a heterogeneous pattern of relaxation values in the peritumoral edema adjacent to the contrast-enhancing part of the tumor. Conclusion Quantitative analysis with relaxometry of peritumoral edema in malignant gliomas detects tissue changes not visualized on conventional MR images. The finding of decreasing R1 and R2 means shorter relaxation times closer to the tumor, which could reflect tumor invasion into the peritumoral edema. However, these findings need to be validated in the future. PMID

  19. Quantitative analysis of in vivo confocal microscopy images: a review.

    PubMed

    Patel, Dipika V; McGhee, Charles N

    2013-01-01

    In vivo confocal microscopy (IVCM) is a non-invasive method of examining the living human cornea. The recent trend towards quantitative studies using IVCM has led to the development of a variety of methods for quantifying image parameters. When selecting IVCM images for quantitative analysis, it is important to be consistent regarding the location, depth, and quality of images. All images should be de-identified, randomized, and calibrated prior to analysis. Numerous image analysis software are available, each with their own advantages and disadvantages. Criteria for analyzing corneal epithelium, sub-basal nerves, keratocytes, endothelium, and immune/inflammatory cells have been developed, although there is inconsistency among research groups regarding parameter definition. The quantification of stromal nerve parameters, however, remains a challenge. Most studies report lower inter-observer repeatability compared with intra-observer repeatability, and observer experience is known to be an important factor. Standardization of IVCM image analysis through the use of a reading center would be crucial for any future large, multi-centre clinical trials using IVCM.

  20. An ultrastructural analysis of the effects of ethanol self-administration on the hypothalamic paraventricular nucleus in rhesus macaques

    PubMed Central

    Jimenez, Vanessa A.; Helms, Christa M.; Cornea, Anda; Meshul, Charles K.; Grant, Kathleen A.

    2015-01-01

    A bidirectional relationship between stress and ethanol exists whereby stressful events are comorbid with problematic ethanol use and prolonged ethanol exposure results in adaptations of the physiological stress response. Endocrine response to stress is initiated in the hypothalamic paraventricular nucleus (PVN) with the synthesis and release of corticotropin-releasing hormone (CRH) and arginine-vasopressin (AVP). Alterations in CRH and AVP following long-term ethanol exposure in rodents is well demonstrated, however little is known about the response to ethanol in primates or the mechanisms of adaptation. We hypothesized that long-term ethanol self-administration in nonhuman primates would lead to ultrastructural changes in the PVN underlying adaptation to chronic ethanol. Double-label immunogold electron microscopy (EM) was used to measure presynaptic gamma-aminobutyric acid (GABA) and glutamate density within synaptic terminals contacting CRH- and AVP-immunoreactive dendrites. Additionally, pituitary-adrenal hormones (ACTH, cortisol, DHEA-s and aldosterone) under two conditions (low and mild stress) were compared before and after self-administration. All hormones were elevated in response to the mild stressor independent of ethanol consumption. The presynaptic glutamate density in recurrent (i.e., intra-hypothalamic) CRH terminals was highly related to ethanol intake, and may be a permissive factor in increased drinking due to stress. Conversely, glutamate density within recurrent AVP terminals showed a trend-level increase following ethanol, but was not related to average daily consumption. Glutamate density in non-recurrent AVP terminals was related to aldosterone under the low stress condition while GABAergic density in this terminal population was related to water consumption. The results reveal distinct populations of presynaptic terminals whose glutamatergic or GABAergic density were uniquely related to water and ethanol consumption and circulating

  1. Structural and mechanical architecture of the intestinal villi and crypts in the rat intestine: integrative reevaluation from ultrastructural analysis.

    PubMed

    Hosoyamada, Yasue; Sakai, Tatsuo

    2005-08-01

    The ultrastructure of the rat intestinal interstitium was analyzed from the viewpoint of mechanical dynamics to stabilize the intestinal villi, crypts and mucosal folds. In the rat, the small intestine lacks circular folds, but the large intestine possesses spiral folds. The intestinal villi, the largest in the duodenum, decreased in size in the jejunum and ileum successively, and were absent in the large intestine. The intestinal interstitium consisted of lamina propria mucosae (LPM) and tela submucosa (TSM) separated by muscularis mucosae (MM), the LPM was subdivided into an upper part within the villi and a lower part among the crypts in the small intestine. The light microscopic density of interstitium in the intestinal wall was lowest in the upper LPM, moderately dense in the lower LPM and highest in the TSM, and that among the intestinal region was highest in the duodenum and decreased successively in the jejunum and ileum. In the large intestine, the TSM bulged to form spiral folds with very low density. The intestinal epithelium in the villi possessed wide intercellular spaces and that in the crypts had closed intercellular spaces. At electron microscopic level, the upper and lower LPM contained subepithelial supportive meshwork that consisted of collagen fibrils and myofibroblast processes. The lower LPM and TSM contained conspicuous bundles of collagen fibrils and, in addition, TSM contained minor populations of scattered collagen fibrils near the smooth muscle layer (SML). The diameter of collagen fibrils was the largest in the bundles of TSM, and decreased from the duodenum through the jejunum and ileum to the large intestine. On the basis of these observations, we hypothesize that the intestinal villi are mechanically stabilized by the balance between the expansive interstitial pressure and inward pull by the subepithelial supportive meshwork. This hypothesis explains the hitherto neglected fact that the intestinal epithelium possesses wide

  2. Morphometric and ultrastructural analysis of the effect of bromocriptine and cyclosporine on the vasospastic femoral artery of rats

    PubMed Central

    Tokmak, Mehmet; Başocak, Kahan; Canaz, Hüseyin; Canaz, Gökhan; İplikçioğlu, Celal

    2015-01-01

    Vasospasm is the main causes of mortality and morbidity in patiens with subarachnoid hemorrhage (SAH). The arterial narrowing mechanism that develops after SAH is not yet fully understood but many studies showed that hypotension, neurogenic reflexes, clots in the subarachnoidal space, spasmogenic agents, humoral and celluler immunity play a role in the etiology. In this study we investigate the effects of Bromocriptine and Cyclosporine A in vasospasm secondary to SAH on rat femoral artery from ultrastructural and morphometric perspectives. 120 male Sprague-Dawley rats divided into 12 groups: Vasospasm (V), control (K), surgical control (CK) groups, vasospasm+Bromocriptine and/or Cyclosporine-A groups (VCyA, VBr, VBr+CyA), Bromocriptine and/or Cyclosporine-A control groups (CK, BK, Br+CyAK), Bromocriptine and/or Cyclosporine-A surgical control groups (BCK, CyCK, Br+CyACK). In order to create SAH model, 0, 1 cm3 blood injected into silastic sheath wrapped rat femoral artery. Bromocriptine (2 mg/kg/d) and Cyclosporine A (10 mg/kg/d) combinations applied to control, surgical control and vasospastic models. Light microscopy, transmission electron microscopy and scanning electron microscopy used during this study. Statistical evaluation of the morphometric measurement data concerning vascular wall thickness and luminal cross-sectional areas of all groups were performed using Mann-Whitney U, Wilcoxon-signed rank, and Student-t tests. Cyclosporine A, whose effects in the prevention of vasospasm have been demonstrated in previous studies. In this study we discovered that Bromocriptine demonstrated strong effects similar to Cyclosporine-A. Bromocriptine and Cyclosporine A markedly prevent the development of chronic morphologic vasospasm following SAH. The combined use of both drugs does not change this preventive effect. PMID:26770311

  3. Quantitative Remote Laser-Induced Breakdown Spectroscopy by Multivariate Analysis

    NASA Astrophysics Data System (ADS)

    Clegg, S. M.; Sklute, E. C.; Dyar, M. D.; Barefield, J. E.; Wiens, R. C.

    2007-12-01

    The ChemCam instrument selected for the Mars Science Laboratory (MSL) rover includes a remote Laser- Induced Breakdown Spectrometer (LIBS) that will quantitatively probe samples up to 9m from the rover mast. LIBS is fundamentally an elemental analysis technique. LIBS involves focusing a Nd:YAG laser operating at 1064 nm onto the surface of the sample. The laser ablates material from the surface, generating an expanding plasma containing electronically excited ions, atoms, and small molecules. As these electronically excited species relax back to the ground state, they emit light at wavelengths characteristic of the species present in the sample. Some of this emission is directed into one of three dispersive spectrometers. In this paper, we studied a suite of 18 igneous and highly-metamorphosed samples from a wide variety of parageneses for which chemical analyses by XRF were already available. Rocks were chosen to represent a range of chemical composition from basalt to rhyolite, thus providing significant variations in all of the major element contents (Si, Fe, Al, Ca, Na, K, O, Ti, Mg, and Mn). These samples were probed at a 9m standoff distance under experimental conditions that are similar to ChemCam. Extracting quantitative elemental concentrations from LIBS spectra is complicated by the chemical matrix effects. Conventional methods for obtaining quantitative chemical data from LIBS analyses are compared with new multivariate analysis (MVA) techniques that appear to compensate for these chemical matrix effects. The traditional analyses use specific elemental peak heights or areas, which compared with calibration curves for each element at one or more emission lines for a series of standard samples. Because of matrix effects, the calibration standards generally must have similar chemistries to the unknown samples, and thus this conventional approach imposes severe limitations on application of the technique to remote analyses. In this suite of samples, the use

  4. A quantitative analysis of IRAS maps of molecular clouds

    NASA Technical Reports Server (NTRS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  5. Binary imaging analysis for comprehensive quantitative histomorphometry of peripheral nerve.

    PubMed

    Hunter, Daniel A; Moradzadeh, Arash; Whitlock, Elizabeth L; Brenner, Michael J; Myckatyn, Terence M; Wei, Cindy H; Tung, Thomas H H; Mackinnon, Susan E

    2007-10-15

    Quantitative histomorphometry is the current gold standard for objective measurement of nerve architecture and its components. Many methods still in use rely heavily upon manual techniques that are prohibitively time consuming, predisposing to operator fatigue, sampling error, and overall limited reproducibility. More recently, investigators have attempted to combine the speed of automated morphometry with the accuracy of manual and semi-automated methods. Systematic refinements in binary imaging analysis techniques combined with an algorithmic approach allow for more exhaustive characterization of nerve parameters in the surgically relevant injury paradigms of regeneration following crush, transection, and nerve gap injuries. The binary imaging method introduced here uses multiple bitplanes to achieve reproducible, high throughput quantitative assessment of peripheral nerve. Number of myelinated axons, myelinated fiber diameter, myelin thickness, fiber distributions, myelinated fiber density, and neural debris can be quantitatively evaluated with stratification of raw data by nerve component. Results of this semi-automated method are validated by comparing values against those obtained with manual techniques. The use of this approach results in more rapid, accurate, and complete assessment of myelinated axons than manual techniques.

  6. Variability in quantitative cardiac magnetic resonance perfusion analysis

    PubMed Central

    Bratis, K.

    2013-01-01

    By taking advantage of its high spatial resolution, noninvasive and nontoxic nature first-pass perfusion cardiovascular magnetic resonance (CMR) has rendered an indispensable tool for the noninvasive detection of reversible myocardial ischemia. A potential advantage of perfusion CMR is its ability to quantitatively assess perfusion reserve within a myocardial segment, as expressed semi- quantitatively by myocardial perfusion reserve index (MPRI) and fully- quantitatively by absolute myocardial blood flow (MBF). In contrast to the high accuracy and reliability of CMR in evaluating cardiac function and volumes, perfusion CMR is adversely affected by multiple potential reasons during data acquisition as well as post-processing. Various image acquisition techniques, various contrast agents and doses as well as variable blood flow at rest as well as variable reactions to stress all influence the acquired data. Mechanisms underlying the variability in perfusion CMR post processing, as well as their clinical significance, are yet to be fully elucidated. The development of a universal, reproducible, accurate and easily applicable tool in CMR perfusion analysis remains a challenge and will substantially enforce the role of perfusion CMR in improving clinical care. PMID:23825774

  7. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  8. A quantitative analysis of IRAS maps of molecular clouds

    NASA Technical Reports Server (NTRS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  9. Quantitative option analysis for implementation and management of landfills.

    PubMed

    Kerestecioğlu, Merih

    2016-09-01

    The selection of the most feasible strategy for implementation of landfills is a challenging step. Potential implementation options of landfills cover a wide range, from conventional construction contracts to the concessions. Montenegro, seeking to improve the efficiency of the public services while maintaining affordability, was considering privatisation as a way to reduce public spending on service provision. In this study, to determine the most feasible model for construction and operation of a regional landfill, a quantitative risk analysis was implemented with four steps: (i) development of a global risk matrix; (ii) assignment of qualitative probabilities of occurrences and magnitude of impacts; (iii) determination of the risks to be mitigated, monitored, controlled or ignored; (iv) reduction of the main risk elements; and (v) incorporation of quantitative estimates of probability of occurrence and expected impact for each risk element in the reduced risk matrix. The evaluated scenarios were: (i) construction and operation of the regional landfill by the public sector; (ii) construction and operation of the landfill by private sector and transfer of the ownership to the public sector after a pre-defined period; and (iii) operation of the landfill by the private sector, without ownership. The quantitative risk assessment concluded that introduction of a public private partnership is not the most feasible option, unlike the common belief in several public institutions in developing countries. A management contract for the first years of operation was advised to be implemented, after which, a long term operating contract may follow. © The Author(s) 2016.

  10. Quantitative phosphoproteomic analysis using iTRAQ method.

    PubMed

    Asano, Tomoya; Nishiuchi, Takumi

    2014-01-01

    The MAPK (mitogen-activated kinase) cascade plays important roles in plant perception of and reaction to developmental and environmental cues. Phosphoproteomics are useful to identify target proteins regulated by MAPK-dependent signaling pathway. Here, we introduce the quantitative phosphoproteomic analysis using a chemical labeling method. The isobaric tag for relative and absolute quantitation (iTRAQ) method is a MS-based technique to quantify protein expression among up to eight different samples in one experiment. In this technique, peptides were labeled by some stable isotope-coded covalent tags. We perform quantitative phosphoproteomics comparing Arabidopsis wild type and a stress-responsive mapkk mutant after phytotoxin treatment. To comprehensively identify the downstream phosphoproteins of MAPKK, total proteins were extracted from phytotoxin-treated wild-type and mapkk mutant plants. The phosphoproteins were purified by Pro-Q(®) Diamond Phosphoprotein Enrichment Kit and were digested with trypsin. Resulting peptides were labeled with iTRAQ reagents and were quantified and identified by MALDI TOF/TOF analyzer. We identified many phosphoproteins that were decreased in the mapkk mutant compared with wild type.

  11. Lipid biomarker analysis for the quantitative analysis of airborne microorganisms

    SciTech Connect

    Macnaughton, S.J.; Jenkins, T.L.; Cormier, M.R.

    1997-08-01

    There is an ever increasing concern regarding the presence of airborne microbial contaminants within indoor air environments. Exposure to such biocontaminants can give rise to large numbers of different health effects including infectious diseases, allergenic responses and respiratory problems, Biocontaminants typically round in indoor air environments include bacteria, fungi, algae, protozoa and dust mites. Mycotoxins, endotoxins, pollens and residues of organisms are also known to cause adverse health effects. A quantitative detection/identification technique independent of culturability that assays both culturable and non culturable biomass including endotoxin is critical in defining risks from indoor air biocontamination. Traditionally, methods employed for the monitoring of microorganism numbers in indoor air environments involve classical culture based techniques and/or direct microscopic counting. It has been repeatedly documented that viable microorganism counts only account for between 0.1-10% of the total community detectable by direct counting. The classic viable microbiologic approach doe`s not provide accurate estimates of microbial fragments or other indoor air components that can act as antigens and induce or potentiate allergic responses. Although bioaerosol samplers are designed to damage the microbes as little as possible, microbial stress has been shown to result from air sampling, aerosolization and microbial collection. Higher collection efficiency results in greater cell damage while less cell damage often results in lower collection efficiency. Filtration can collect particulates at almost 100% efficiency, but captured microorganisms may become dehydrated and damaged resulting in non-culturability, however, the lipid biomarker assays described herein do not rely on cell culture. Lipids are components that are universally distributed throughout cells providing a means to assess independent of culturability.

  12. Some selected quantitative methods of thermal image analysis in Matlab.

    PubMed

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 3D visualization and quantitative analysis of human erythrocyte phagocytosis.

    PubMed

    Stachurska, Anna; Król, Teodora; Trybus, Wojciech; Szary, Karol; Fabijańska-Mitek, Jadwiga

    2016-11-01

    Since the erythrophagocytosis of opsonized erythrocytes is investigated mainly by calculating the phagocytic index using subjective light microscopy evaluation, we present methods for the quantitative and qualitative analysis of human cell erythrophagocytosis. Erythrocytes from two storage periods were used. Using Imaris software, we were able to create a three-dimensional model of erythrophagocytosis. The use of microscopy instead of cytometry revealed a significantly higher number of monocytes and erythrocytes that appeared active in phagocytosis. Spatial reconstruction allowed for detailed analysis of the process by precisely locating erythrocytes in phagocytes. Additionally, a technique of sequential image registration using Nis Elements software allowed for observation of the course of phagocytosis over a range of time intervals. This in vitro research may be helpful for understanding the cellular interactions between monocytes and erythrocytes. The cytometric method-being relatively rapid, sensitive, and specific-can serve as an alternative technique to microscopy in the quantitative analysis of erythrophagocytosis. This allows us to avoid counting the erythrocytes nonspecifically attached to monocytes and gives objective results. © 2016 International Federation for Cell Biology.

  14. QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

    PubMed Central

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

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

  15. Quantitative analysis of motion control in long term microgravity.

    PubMed

    Baroni, G; Ferrigno, G; Anolli, A; Andreoni, G; Pedotti, A

    1998-01-01

    In the frame of the 179-days EUROMIR '95 space mission, two in-flight experiments have foreseen quantitative three-dimensional human movement analysis in microgravity. For this aim, a space qualified opto-electronic motion analyser based on passive markers has been installed onboard the Russian Space Station MIR and 8 in flight sessions have been performed. Techhology and method for the collection of kinematics data are described, evaluating the accuracy in three-dimensional marker localisation. Results confirm the suitability of opto-electronic technology for quantitative human motion analysis on orbital modules and raise a set of "lessons learned", leading to the improvement of motion analyser performance with a contemporary swiftness of the on-board operations. Among the experimental program of T4, results of three voluntary posture perturbation protocols are described. The analysis suggests that a short term reinterpretation of proprioceptive information and re-calibration of sensorimotor mechanisms seem to end within the first weeks of flight, while a continuous long term adaptation process allows the refinement of motor performance, in the frame of never abandoned terrestrial strategies.

  16. 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.

  17. Computer compensation for NMR quantitative analysis of trace components

    SciTech Connect

    Nakayama, T.; Fujiwara, Y.

    1981-07-22

    A computer program has been written that determines trace components and separates overlapping components in multicomponent NMR spectra. This program uses the Lorentzian curve as a theoretical curve of NMR spectra. The coefficients of the Lorentzian are determined by the method of least squares. Systematic errors such as baseline/phase distortion are compensated and random errors are smoothed by taking moving averages, so that there processes contribute substantially to decreasing the accumulation time of spectral data. The accuracy of quantitative analysis of trace components has been improved by two significant figures. This program was applied to determining the abundance of 13C and the saponification degree of PVA.

  18. Quantitative analysis of sideband coupling in photoinduced force microscopy

    NASA Astrophysics Data System (ADS)

    Jahng, Junghoon; Kim, Bongsu; Lee, Eun Seong; Potma, Eric Olaf

    2016-11-01

    We present a theoretical and experimental analysis of the cantilever motions detected in photoinduced force microscopy (PiFM) using the sideband coupling detection scheme. In sideband coupling, the cantilever dynamics are probed at a combination frequency of a fundamental mechanical eigenmode and the modulation frequency of the laser beam. Using this detection mode, we develop a method for reconstructing the modulated photoinduced force gradient from experimental parameters in a quantitative manner. We show evidence, both theoretically and experimentally, that the sideband coupling detection mode provides PiFM images with superior contrast compared to images obtained when detecting the cantilever motions directly at the laser modulation frequency.

  19. Flow quantitation by radio frequency analysis of contrast echocardiography.

    PubMed

    Rovai, D; Lombardi, M; Mazzarisi, A; Landini, L; Taddei, L; Distante, A; Benassi, A; L'Abbate, A

    1993-03-01

    Contrast echocardiography has the potential for measuring cardiac output and regional blood flow. However, accurate quantitation is limited both by the use of non-standard contrast agents and by the electronic signal distortion inherent to the echocardiographic instruments. Thus, the aim of this study is to quantify flow by combining a stable contrast agent and a modified echo equipment, able to sample the radio frequency (RF) signal from a region of interest (ROI) in the echo image. The contrast agent SHU-454 (0.8 ml) was bolus injected into an in vitro calf vein, at 23 flow rates (ranging from 376 to 3620 ml/min) but constant volume and pressure. The ROI was placed in the centre of the vein, the RF signal was processed in real time and transferred to a personal computer to generate time-intensity curves. In the absence of recirculation, contrast washout slope and mean transit time (MTT) of curves (1.11-8.52 seconds) yielded excellent correlations with flow: r = 0.93 and 0.95, respectively. To compare the accuracy of RF analysis with that of conventional image processing as to flow quantitation, conventional images were collected in the same flow model by two different scanners: a) the mechanical sector scanner used for RF analysis, and b) a conventional electronic sector scanner. These images were digitized off-line, mean videodensity inside an identical ROI was measured and time-intensity curves were built. MTT by RF was shorter than by videodensitometric analysis of the images generated by the same scanner (p < 0.001). In contrast, MTT by RF was longer than by the conventional scanner (p < 0.001). Significant differences in MTT were also found with changes in the gain setting controls of the conventional scanner. To study the stability of the contrast effect, 6 contrast injections (20 ml) were performed at a constant flow rate during recirculation: the spontaneous decay in RF signal intensity (t1/2 = 64 +/- 8 seconds) was too long to affect MTT significantly

  20. Simulating the focal volume effect: a quantitative analysis

    NASA Astrophysics Data System (ADS)

    Scarborough, Timothy D.; Uiterwaal, Cornelis J. G. J.

    2013-12-01

    We present quantitative simulations of the focal volume effect. Intensity distributions in detection volumes with two- and three-dimensional spatial resolution are calculated. Results include an analysis of translations of these volumes in the focus along the direction of laser propagation as well as discussion of varying sizes of the spatially resolved volumes. We find that detection volumes less than half the 1/e full-width beam waist and less than half the Rayleigh length along the propagation direction offer an optimal compromise of maintaining intensity resolution without sacrificing peak intensity.

  1. Neutron diffractometer INES for quantitative phase analysis of archaeological objects

    NASA Astrophysics Data System (ADS)

    Imberti, S.; Kockelmann, W.; Celli, M.; Grazzi, F.; Zoppi, M.; Botti, A.; Sodo, A.; Imperiale, M. Leo; de Vries-Melein, M.; Visser, D.; Postma, H.

    2008-03-01

    With the Italian Neutron Experimental Station (INES) a new general purpose neutron powder diffractometer is available at ISIS, characterized by a high resolution at low d-spacings, and particularly suited for the quantitative phase analysis of a wide range of archaeological materials. Time-of-flight neutron diffraction is notable for being a non-destructive technique, allowing a reliable determination of the phase compositions of multiphase artefacts, with or without superficial corrosion layers. A selection of archaeometric studies carried out during the first year of the INES user programme is presented here to demonstrate the capabilities of the instrument.

  2. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

    PubMed

    Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

  3. A quantitative analysis of lectin binding to adult rat hepatocyte cell surfaces.

    PubMed

    Jauregui, H O; McMillan, P N; Hevey, K; Naik, S

    1988-05-01

    A quantitative evaluation of lectin binding to adult rat hepatocyte cell surfaces was done using cells isolated by two different collagenase perfusion methodologies and cultured as monolayers with two different tissue culture media formulations (protocol I vs. protocol II). The presence of alpha-D-mannosyl and alpha-D-glucosyl groups was detected by the binding of Concanavalin A (Con A), Lens culinaris agglutinin (LCA), and Pisum sativum agglutinin (PSA) to freshly isolated cells. Furthermore, beta-D-galactose [Ricinus communis agglutinin (RCA)] and sialic acid residues [wheat germ (WGA)] were also found. Protocols I and II served as models for evaluation of: a) the stripping effect of collagenase separation procedures, b) the restoration in culture of collagenase-stripped sugar residues, c) the effect of the culture environment on cell viability [as measured by lactic acid dehydrogenase (LDH) leakage] and the protein content of hepatocytes, and d) the presence of cell surface sugar residues as a function of culture duration. The ultrastructural morphology of freshly isolated and cultured hepatocytes was also evaluated. These studies indicated that a decline in lectin binding invariably occurred earlier than a massive leakage of LDH and a decrease in the protein content of the cells in culture. Ultrastructurally, autophagocytosis was an early phenomenon in cells isolated and cultured by protocol I, which was also inferior to protocol II regarding the preservation of hepatocyte glycocalyces. Sugar residues lost due to the collagenase-stripping effect were restored, as shown by lectin binding, within the first 24 h of culture. This stripping effect was confirmed by quantitative evaluations of lectin binding to hepatocytes in culture after an incubation with collagenase. This study shows that the binding of peroxidase-labeled lectins is a useful tool for quantitative evaluation of the sugar composition of hepatocyte cultures.

  4. Quantitative chemical analysis of ocular melanosomes in the TEM.

    PubMed

    Eibl, O; Schultheiss, S; Blitgen-Heinecke, P; Schraermeyer, U

    2006-01-01

    Melanosomes in retinal tissues of a human, monkey and rat were analyzed by EDX in the TEM. Samples were prepared by ultramicrotomy at different thicknesses. The material was mounted on Al grids and samples were analyzed in a Zeiss 912 TEM equipped with an Omega filter and EDX detector with ultrathin window. Melanosomes consist of C and O as main components, mole fractions are about 90 and 3-10 at.%, respectively, and small mole fraction ratios, between 2 and 0.1 at.%, of Na, Mg, K, Si, P, S, Cl, Ca. All elements were measured quantitatively by standardless EDX with high precision. Mole fractions of transition metals Fe, Cu and Zn were also measured. For Fe a mole fraction ratio of less than 0.1at.% was found and gives the melanin its paramagnetic properties. Its mole fraction is however close to or below the minimum detectable mass fraction of the used equipment. Only in the human eye and only in the retinal pigment epitelium (rpe) the mole fractions of Zn (0.1 at.% or 5000 microg/g) and Cu were clearly beyond the minimum detectable mass fraction. In the rat and monkey eye the mole fraction of Zn was at or below the minimum detectable mass fraction and could not be measured quantitatively. The obtained results yielded the chemical composition of the melanosomes in the choroidal tissue and the retinal pigment epitelium (rpe) of the three different species. The results of the chemical analysis are discussed by mole fraction correlation diagrams. Similarities and differences between the different species are outlined. Correlation behavior was found to hold over species, e.g. the Ca-O correlation. It indicates that Ca is bound to oxygen rich sites in the melanin. These are the first quantitative analyses of melanosomes by EDX reported so far. The quantitative chemical analysis should open a deeper understanding of the metabolic processes in the eye that are of central importance for the understanding of a large number of eye-related diseases. The chemical analysis also

  5. Quantitative sonographic image analysis for hepatic nodules: a pilot study.

    PubMed

    Matsumoto, Naoki; Ogawa, Masahiro; Takayasu, Kentaro; Hirayama, Midori; Miura, Takao; Shiozawa, Katsuhiko; Abe, Masahisa; Nakagawara, Hiroshi; Moriyama, Mitsuhiko; Udagawa, Seiichi

    2015-10-01

    The aim of this study was to investigate the feasibility of quantitative image analysis to differentiate hepatic nodules on gray-scale sonographic images. We retrospectively evaluated 35 nodules from 31 patients with hepatocellular carcinoma (HCC), 60 nodules from 58 patients with liver hemangioma, and 22 nodules from 22 patients with liver metastasis. Gray-scale sonographic images were evaluated with subjective judgment and image analysis using ImageJ software. Reviewers classified the shape of nodules as irregular or round, and the surface of nodules as rough or smooth. Circularity values were lower in the irregular group than in the round group (median 0.823, 0.892; range 0.641-0.915, 0.784-0.932, respectively; P = 3.21 × 10(-10)). Solidity values were lower in the rough group than in the smooth group (median 0.957, 0.968; range 0.894-0.986, 0.933-0.988, respectively; P = 1.53 × 10(-4)). The HCC group had higher circularity and solidity values than the hemangioma group. The HCC and liver metastasis groups had lower median, mean, modal, and minimum gray values than the hemangioma group. Multivariate analysis showed circularity [standardized odds ratio (OR), 2.077; 95 % confidential interval (CI) = 1.295-3.331; P = 0.002] and minimum gray value (OR 0.482; 95 % CI = 0.956-0.990; P = 0.001) as factors predictive of malignancy. The combination of subjective judgment and image analysis provided 58.3 % sensitivity and 89.5 % specificity with AUC = 0.739, representing an improvement over subjective judgment alone (68.4 % sensitivity, 75.0 % specificity, AUC = 0.701) (P = 0.008). Quantitative image analysis for ultrasonic images of hepatic nodules may correlate with subjective judgment in predicting malignancy.

  6. Quantitative Proteomic and Phosphoproteomic Analysis of Trypanosoma cruzi Amastigogenesis*

    PubMed Central

    Queiroz, Rayner M. L.; Charneau, Sébastien; Mandacaru, Samuel C.; Schwämmle, Veit; Lima, Beatriz D.; Roepstorff, Peter; Ricart, Carlos A. O.

    2014-01-01

    Chagas disease is a tropical neglected disease endemic in Latin America caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote, and amastigote. The differentiation from infective trypomastigotes into replicative amastigotes, called amastigogenesis, takes place in vivo inside mammalian host cells after a period of incubation in an acidic phagolysosome. This differentiation process can be mimicked in vitro by incubating tissue-culture-derived trypomastigotes in acidic DMEM. Here we used this well-established differentiation protocol to perform a comprehensive quantitative proteomic and phosphoproteomic analysis of T. cruzi amastigogenesis. Samples from fully differentiated forms and two biologically relevant intermediate time points were Lys-C/trypsin digested, iTRAQ-labeled, and multiplexed. Subsequently, phosphopeptides were enriched using a TiO2 matrix. Non-phosphorylated peptides were fractionated via hydrophilic interaction liquid chromatography prior to LC-MS/MS analysis. LC-MS/MS and bioinformatics procedures were used for protein and phosphopeptide quantitation, identification, and phosphorylation site assignment. We were able to identify regulated proteins and pathways involved in coordinating amastigogenesis. We also observed that a significant proportion of the regulated proteins were membrane proteins. Modulated phosphorylation events coordinated by protein kinases and phosphatases that are part of the signaling cascade induced by incubation in acidic medium were also evinced. To our knowledge, this work is the most comprehensive quantitative proteomics study of T. cruzi amastigogenesis, and these data will serve as a trustworthy basis for future studies, and possibly for new potential drug targets. PMID:25225356

  7. Ultrastructural demonstration of chemical modification of melanogenesis in hairless mouse skin

    SciTech Connect

    Nishimura, M.; Gellin, G.A.; Hoshino, S.; Epstein, J.H.; Epstein, W.L.; Fukuyama, K.

    1982-02-01

    We investigated chemical and physical modifications of the genetically determined ultrastructure of melanosomes. The flank skin of hairless mice was treated with ultraviolet energy (UV) shorter than 320 nm or with a combination of a photosensitizer and UV (PUVA treatment). All melanosomes in the induced melanocytes and those in resident melanocytes in the ear skin showed eumelanogenesis, although the degree of melanin deposition differed considerably according to the induction process. Eumelanogenesis was most advanced in the resident melanocytes while PUVA-induced melanocytes showed more immature premelanosomes. We then topically applied 4-tertiary butyl catechol on the skin. The depigmenting agent caused an appearance of pheomelanosomes. The alteration in melanogenesis was seen most distinctly in premelanosomes of the PUVA-induced cells. Altered ultrastructure was also observed in matured melanosomes; this change was most apparent in the resident melanocytes. These findings indicate that cells with eumelanogenesis may undergo pheomelanogenesis. The present study demonstrated effects of chemicals on genetically determined function of melanocytes by quantitative analysis of melanosome ultrastructure.

  8. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-01-01

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations. PMID:26306198

  9. Multivariate calibration applied to the quantitative analysis of infrared spectra

    SciTech Connect

    Haaland, D.M.

    1991-01-01

    Multivariate calibration methods are very useful for improving the precision, accuracy, and reliability of quantitative spectral analyses. Spectroscopists can more effectively use these sophisticated statistical tools if they have a qualitative understanding of the techniques involved. A qualitative picture of the factor analysis multivariate calibration methods of partial least squares (PLS) and principal component regression (PCR) is presented using infrared calibrations based upon spectra of phosphosilicate glass thin films on silicon wafers. Comparisons of the relative prediction abilities of four different multivariate calibration methods are given based on Monte Carlo simulations of spectral calibration and prediction data. The success of multivariate spectral calibrations is demonstrated for several quantitative infrared studies. The infrared absorption and emission spectra of thin-film dielectrics used in the manufacture of microelectronic devices demonstrate rapid, nondestructive at-line and in-situ analyses using PLS calibrations. Finally, the application of multivariate spectral calibrations to reagentless analysis of blood is presented. We have found that the determination of glucose in whole blood taken from diabetics can be precisely monitored from the PLS calibration of either mind- or near-infrared spectra of the blood. Progress toward the non-invasive determination of glucose levels in diabetics is an ultimate goal of this research. 13 refs., 4 figs.

  10. Quantitative analysis of live cells using digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Lewis, Tan Rongwei; Qu, Weijuan; Chee, Oi Choo; Singh, Vijay Raj; Asundi, Anand

    2010-03-01

    During the life time of a cell, it goes through changes to the plasma membrane as well as its internal structures especially distinctive during processes like cell division and death. Different types of microscope are used to fulfill the observation of the cell's variation. In our experiment, Vero cells have been investigated by using phase contrast microscopy and digital holographic microscopy (DHM). A comparison of the images obtained for cell division is presented here. The conventional phase contrast microscope provided a good imaging method in the real time analysis of cell division. The off-axis digital hologram recorded by the DHM system can be reconstructed to obtain both the intensity image and phase contrast image of the test object. These can be used for live cell imaging to provide multiple results from a single equipment setup. The DHM system, besides being a qualitative tool, is able to provide quantitative results and 3D images of the cell division process. The ability of DHM to provide quantitative analysis makes it an ideal tool for life science applications.

  11. Quantitative analysis of live cells using digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Lewis, Tan Rongwei; Qu, Weijuan; Chee, Oi Choo; Singh, Vijay Raj; Asundi, Anand

    2009-12-01

    During the life time of a cell, it goes through changes to the plasma membrane as well as its internal structures especially distinctive during processes like cell division and death. Different types of microscope are used to fulfill the observation of the cell's variation. In our experiment, Vero cells have been investigated by using phase contrast microscopy and digital holographic microscopy (DHM). A comparison of the images obtained for cell division is presented here. The conventional phase contrast microscope provided a good imaging method in the real time analysis of cell division. The off-axis digital hologram recorded by the DHM system can be reconstructed to obtain both the intensity image and phase contrast image of the test object. These can be used for live cell imaging to provide multiple results from a single equipment setup. The DHM system, besides being a qualitative tool, is able to provide quantitative results and 3D images of the cell division process. The ability of DHM to provide quantitative analysis makes it an ideal tool for life science applications.

  12. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGES

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

    2015-08-14

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically,more » the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.« less

  13. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    SciTech Connect

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  14. Quantitative analysis in outcome assessment of instrumented lumbosacral arthrodesis.

    PubMed

    Champain, Sabina; Mazel, Christian; Mitulescu, Anca; Skalli, Wafa

    2007-08-01

    The outcome assessment in instrumented lumbosacral fusion mostly focuses on clinical criteria, complications and scores, with a high variability of imaging means, methods of fusion grading and parameters describing degenerative changes, making comparisons between studies difficult. The aim of this retrospective evaluation was to evaluate the interest of quantified radiographic analysis of lumbar spine in global outcome assessment and to highlight the key biomechanical factors involved. Clinical data and Beaujon-Lassale scores were collected for 49 patients who underwent lumbosacral arthrodesis after prior lumbar discectomy (mean follow-up: 5 years). Sagittal standing and lumbar flexion-extension X-ray films allowed quantifying vertebral, lumbar, pelvic and kinematic parameters of the lumbar spine, which were compared to reference values. Statistics were performed to assess evolution for all variables. At long-term follow-up, 90% of patients presented satisfactory clinical outcomes, associated to normal sagittal alignment; vertebral parameters objectified adjacent level degeneration in four cases (8%). Clinical outcome was correlated (r = 0.8) with fusion that was confirmed in 80% of cases, doubtful in 16% and pseudarthrosis seemed to occur in 4% (2) of cases. In addition to clinical data (outcomes comparable to the literature), quantitative analysis accurately described lumbar spine geometry and kinematics, highlighting parameters related to adjacent level's degeneration and a significant correlation between clinical outcome and fusion. Furthermore, criteria proposed to quantitatively evaluate fusion from lumbar dynamic radiographs seem to be appropriate and in agreement with surgeon's qualitative grading in 87% of cases.

  15. Quantitative analysis of Caenorhabditis elegans chemotaxis using a microfluidic device.

    PubMed

    Hu, Liang; Ye, Jinjuan; Tan, Haowei; Ge, Anle; Tang, Lichun; Feng, Xiaojun; Du, Wei; Liu, Bi-Feng

    2015-08-05

    Caenorhabditis elegans, one of the widely studied model organisms, sense external chemical cues and perform relative chemotaxis behaviors through its simple chemosensory neuronal system. To study the mechanism underlying chemosensory behavior, a rapid and reliable method for quantitatively analyzing the worms' behaviors is essential. In this work, we demonstrated a microfluidic approach for investigating chemotaxis responses of worms to chemical gradients. The flow-based microfluidic chip was consisted of circular tree-like microchannels, which was able to generate eight flow streams containing stepwise chemical concentrations without the difference in flow velocity. Worms' upstream swimming into microchannels with various concentrations was monitored for quantitative analysis of the chemotaxis behavior. By using this microfluidic chip, the attractive and repellent responses of C. elegans to NaCl were successfully quantified within several minutes. The results demonstrated the wild type-like repellent responses and severely impaired attractive responses in grk-2 mutant animals with defects in calcium influx. In addition, the chemotaxis analysis of the third stage larvae revealed that its gustatory response was different from that in the adult stage. Thus, our microfluidic method provided a useful platform for studying the chemosensory behaviors of C. elegans and screening of chemosensation-related chemical drugs.

  16. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    NASA Technical Reports Server (NTRS)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  17. 3D quantitative analysis of brain SPECT images

    NASA Astrophysics Data System (ADS)

    Loncaric, Sven; Ceskovic, Ivan; Petrovic, Ratimir; Loncaric, Srecko

    2001-07-01

    The main purpose of this work is to develop a computer-based technique for quantitative analysis of 3-D brain images obtained by single photon emission computed tomography (SPECT). In particular, the volume and location of ischemic lesion and penumbra is important for early diagnosis and treatment of infracted regions of the brain. SPECT imaging is typically used as diagnostic tool to assess the size and location of the ischemic lesion. The segmentation method presented in this paper utilizes a 3-D deformable model in order to determine size and location of the regions of interest. The evolution of the model is computed using a level-set implementation of the algorithm. In addition to 3-D deformable model the method utilizes edge detection and region growing for realization of a pre-processing. Initial experimental results have shown that the method is useful for SPECT image analysis.

  18. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics

    PubMed Central

    Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999–2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics. PMID:26352604

  19. [Quantitative analysis of transformer oil dissolved gases using FTIR].

    PubMed

    Zhao, An-xin; Tang, Xiao-jun; Wang, Er-zhen; Zhang, Zhong-hua; Liu, Jun-hua

    2013-09-01

    For the defects of requiring carrier gas and regular calibration, and low safety using chromatography to on line monitor transformer dissolved gases, it was attempted to establish a dissolved gas analysis system based on Fourier transform infrared spectroscopy. Taking into account the small amount of characteristic gases, many components, detection limit and safety requirements and the difficulty of degasser to put an end to the presence of interference gas, the quantitative analysis model was established based on sparse partial least squares, piecewise section correction and feature variable extraction algorithm using improvement TR regularization. With the characteristic gas of CH4, C2H6, C2H6, and CO2, the results show that using FTIR meets DGA requirements with the spectrum wave number resolution of 1 cm(-1) and optical path of 10 cm.

  20. Quantitative Phase Analysis by the Rietveld Method for Forensic Science.

    PubMed

    Deng, Fei; Lin, Xiaodong; He, Yonghong; Li, Shu; Zi, Run; Lai, Shijun

    2015-07-01

    Quantitative phase analysis (QPA) is helpful to determine the type attribute of the object because it could present the content of the constituents. QPA by Rietveld method requires neither measurement of calibration data nor the use of an internal standard; however, the approximate crystal structure of each phase in a mixture is necessary. In this study, 8 synthetic mixtures composed of potassium nitrate and sulfur were analyzed by Rietveld QPA method. The Rietveld refinement was accomplished with a material analysis using diffraction program and evaluated by three agreement indices. Results showed that Rietveld QPA yielded precise results, with errors generally less than 2.0% absolute. In addition, a criminal case which was broken successfully with the help of Rietveld QPA method was also introduced. This method will allow forensic investigators to acquire detailed information of the material evidence, which could point out the direction for case detection and court proceedings.

  1. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

    PubMed

    Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics.

  2. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    NASA Technical Reports Server (NTRS)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  3. Tendon’s ultrastructure

    PubMed Central

    Tresoldi, Ilaria; Oliva, Francesco; Benvenuto, Monica; Fantini, Massimo; Masuelli, Laura; Bei, Roberto; Modesti, Andrea

    2013-01-01

    Summary The structure of a tendon is an important example of complexity of ECM three-dimensional organization. The extracellular matrix (ECM) is a macromolecular network with both structural and regulatory functions. ECM components belong to four major types of macromolecules: the collagens, elastin, proteoglycans, and noncollagenous glycoproteins. Tendons are made by a fibrous, compact connective tissue that connect muscle to bone designed to transmit forces and withstand tension during muscle contraction. Here we show the ultrastructural features of tendon’s components. PMID:23885339

  4. Quantitative morphometric analysis for the tectonic characterisation of northern Tunisia.

    NASA Astrophysics Data System (ADS)

    Camafort, Miquel; Pérez-Peña, José Vicente; Booth-Rea, Guillermo; Ranero, César R.; Gràcia, Eulàlia; Azañón, José Miguel; Melki, Fetheddine; Ouadday, Mohamed

    2016-04-01

    Northern Tunisia is characterized by low deformation rates and low to moderate seismicity. Although instrumental seismicity reaches maximum magnitudes of Mw 5.5, some historical earthquakes have occurred with catastrophic consequences in this region. Aiming to improve our knowledge of active tectonics in Tunisia, we carried out both a quantitative morphometric analysis and field study in the north-western region. We applied different morphometric tools, like river profiles, knickpoint analysis, hypsometric curves and integrals and drainage pattern anomalies in order to differentiate between zones with high or low recent tectonic activity. This analysis helps identifying uplift and subsidence zones, which we relate to fault activity. Several active faults in a sparse distribution were identified. A selected sector was studied with a field campaign to test the results obtained with the quantitative analysis. During the fieldwork we identified geological evidence of recent activity and a considerable seismogenic potential along El Alia-Teboursouk (ETF) and Dkhila (DF) faults. The ETF fault could be responsible of one of the most devastating historical earthquakes in northern Tunisia that destroyed Utique in 412 A.D. Geological evidence include fluvial terraces folded by faults, striated and cracked pebbles, clastic dikes, sand volcanoes, coseismic cracks, etc. Although not reflected in the instrumental seismicity, our results support an important seismic hazard, evidenced by the several active tectonic structures identified and the two seismogenic faults described. After obtaining the current active tectonic framework of Tunisia we discuss our results within the western Mediterranean trying to contribute to the understanding of the western Mediterranean tectonic context. With our results, we suggest that the main reason explaining the sparse and scarce seismicity of the area in contrast with the adjacent parts of the Nubia-Eurasia boundary is due to its extended

  5. Continuous electrical current and zinc sulphate administered by transdermal iontophoresis improves skin healing in diabetic rats induced by alloxan: morphological and ultrastructural analysis.

    PubMed

    Langoni Cassettari, Lucas; Colli Rocha Dias, Pedro; Natália Lucchesi, Amanda; Ferraz de Arruda, Maurício; Veruska Paiva Ortolan, Erika; Marques, Mariângela Esther A; Spadella, César Tadeu

    2014-01-01

    Evaluated the effects of continuous electrical current (CEC) or zinc administrated by transdermal iontophoresis (Zn+TDI). 120 male Wistar rats were submitted to an incision surgery at the anterior region of abdomen and distributed into 6 experimental groups with 40 animals: 3 diabetic groups and 3 normal groups, untreated and treated with CEC alone or with Zn + TDI. Each group was further divided into 4 subgroups with 10 rats each to be evaluated on the 4th, 7th, 14th, and 21st day after surgery. In each period, clinical and laboratory parameters from the animals were analyzed. The analysis by optical and scanning electron microscopy showed a delay in the phases of wound healing in diabetic rats without treatment in all periods of the experiment; breaking strength (BS) was significantly reduced in skin scars of untreated diabetic rats when compared to other groups. In contrast, BS in skin scars of nondiabetic groups and diabetic rats treated with Zn + TDI showed significant increase in those, besides not presenting delayed healing. Electrical stimulation of surgical wounds used alone or in association with zinc by TDI is able to consistently improve the morphological and ultrastructural changes observed in the healing of diabetic animals.

  6. The myocardial microangiopathy in human and experimental diabetes mellitus. (A microscopic, ultrastructural, morphometric and computer-assisted symbolic-logic analysis).

    PubMed

    Taşcă, C; Stefăneanu, L; Vasilescu, C

    1986-01-01

    The following microscopical aspects were found in the small intramural arteries in the myocardium of 30 diabetic patients: endothelial proliferations with focal protuberances leading to partial narrowing of the lumen, increased thickness of the arterial wall due to fibrosis and accumulations of neutral mucopolysaccharides: alteration of elastic fibres. Morphometrically, the arterial wall thickness and the arterial diameter were increased whereas the arterial density decreased in the diabetic heart. In 25 rats with streptozotocin-induced diabetes the small intramyocardial arteries were investigated at 11 to 40 weeks of diabetic state. Using morphometrical analysis a constant increase of arterial wall thickness paralleling the diabetes duration was found. Microscopically, the lesions consist in endothelial proliferation with bridging across the vascular lumen and slight perivascular and diffuse fibrosis. Ultrastructurally, the capillary basal lamina was thickened in the diabetic myocardium. In order to investigate the morphometrical data we used symbolic-logic as a decision method, by applying an original computer program based on the Quine-McCluskey algorithm. All our results together with the final symbolic-logic expression suggest that damage of the small intramyocardial arteries plays an important role in the pathogenesis of diabetic cardiomyopathy.

  7. Novel characteristics of normal supraspinatus insertion in rats: an ultrastructural analysis using three-dimensional reconstruction using focused ion beam/scanning electron microscope tomography

    PubMed Central

    Kanazawa, Tomonoshin; Gotoh, Masafumi; Ohta, Keisuke; Shiba, Naoto; Nakamura, Kei-ichiro

    2014-01-01

    Summary Background: the histological architecture of the insertion after a rotator cuff repair is completely different from that of normal tendon-bone insertions. Analysis of normal insertions by electron microscopy may enhance the understanding of the pathophysiology of tendon-to-bone healing after rotator cuff repair. The present study examined the normal supraspinatus insertion in rats using a new three-dimensional (3D) electron microscopic method, focused ion beam/scanning electron microscope (FIB/SEM) tomography. Methods: normal supraspinatus insertion of adult Sprague-Dawley rats was analyzed. FIB/SEM tomography was performed on the entire insertion. The obtained serial images were reconstructed, and the 3D cellular morphology and organization of collagen bundles was observed. Results: the cellular shapes between the tendon-cartilage interface were successfully reconstructed. The cells in the cartilage region were spherical without any cellular processes, while the cells in the intermediate region had some cellular processes oriented longitudinally along the collagen bundles. In addition, these 2 regions were smoothly transferred under ultrastructural resolution. Conclusions: structures at the normal insertion gradually changed from the fibrous cartilage to the tendon midsubstance, which may contribute to the biomechanical strength of the site. These novel cell characteristics may provide necessary knowledge for better regeneration of tendon-to-bone insertions after rotator cuff repair. PMID:25332933

  8. Quick 96FASP for high throughput quantitative proteome analysis.

    PubMed

    Yu, Yanbao; Bekele, Shiferaw; Pieper, Rembert

    2017-08-23

    Filter aided sample preparation (FASP) is becoming a central method for proteomic sample cleanup and peptide generation prior to LC-MS analysis. We previously adapted this method to a 96-well filter plate, and applied to prepare protein digests from cell lysate and body fluid samples in a high throughput quantitative manner. While the 96FASP approach is scalable and can handle multiple samples simultaneously, two key advantages compared to single FASP, it is also time-consuming. The centrifugation-based liquid transfer on the filter plate takes 3-5 times longer than single filter. To address this limitation, we now present a quick 96FASP (named q96FASP) approach that, relying on the use of filter membranes with a large MWCO size (~30kDa), significantly reduces centrifugal times. We show that q96FASP allows the generation of protein digests derived from whole cell lysates and body fluids in a quality similar to that of the single FASP method. Processing a sample in multiple wells in parallel, we observed excellent experimental repeatability by label-free quantitation approach. We conclude that the q96FASP approach promises to be a promising cost- and time-effective method for shotgun proteomics and will be particularly useful in large scale biomarker discovery studies. High throughput sample processing is of particular interests for quantitative proteomics. The previously developed 96FASP is high throughput and appealing, however it is time-consuming in the context of centrifugation-based liquid transfer (~1.5h per spin). This study presents a truly high throughput sample preparation method based on large cut-off 96-well filter plate, which shortens the spin time to ~20min. To our knowledge, this is the first multi-well method that is entirely comparable with conventional FASP. This study thoroughly examined two types of filter plates and performed side-by-side comparisons with single FASP. Two types of samples, whole cell lysate of a UTI (urinary tract infection

  9. Quantitative analysis of cyclic beta-turn models.

    PubMed Central

    Perczel, A.; Fasman, G. D.

    1992-01-01

    The beta-turn is a frequently found structural unit in the conformation of globular proteins. Although the circular dichroism (CD) spectra of the alpha-helix and beta-pleated sheet are well defined, there remains some ambiguity concerning the pure component CD spectra of the different types of beta-turns. Recently, it has been reported (Hollósi, M., Kövér, K.E., Holly, S., Radics, L., & Fasman, G.D., 1987, Biopolymers 26, 1527-1572; Perczel, A., Hollósi, M., Foxman, B.M., & Fasman, G.D., 1991a, J. Am. Chem. Soc. 113, 9772-9784) that some pseudohexapeptides (e.g., the cyclo[(delta)Ava-Gly-Pro-Aaa-Gly] where Aaa = Ser, Ser(OtBu), or Gly) in many solvents adopt a conformational mixture of type I and the type II beta-turns, although the X-ray-determined conformation was an ideal type I beta-turn. In addition to these pseudohexapeptides, conformational analysis was also carried out on three pseudotetrapeptides and three pseudooctapeptides. The target of the conformation analysis reported herein was to determine whether the ring stress of the above beta-turn models has an influence on their conformational properties. Quantitative nuclear Overhauser effect (NOE) measurements yielded interproton distances. The conformational average distances so obtained were interpreted utilizing molecular dynamics (MD) simulations to yield the conformational percentages. These conformational ratios were correlated with the conformational weights obtained by quantitative CD analysis of the same compounds. The pure component CD curves of type I and type II beta-turns were also obtained, using a recently developed algorithm (Perczel, A., Tusnády, G., Hollósi, M., & Fasman, G.D., 1991b, Protein Eng. 4(6), 669-679). For the first time the results of a CD deconvolution, based on the CD spectra of 14 beta-turn models, were assigned by quantitative NOE results. The NOE experiments confirmed the ratios of the component curves found for the two major beta-turns by CD analysis. These results

  10. Quantitative analysis of cyclic beta-turn models.

    PubMed

    Perczel, A; Fasman, G D

    1992-03-01

    The beta-turn is a frequently found structural unit in the conformation of globular proteins. Although the circular dichroism (CD) spectra of the alpha-helix and beta-pleated sheet are well defined, there remains some ambiguity concerning the pure component CD spectra of the different types of beta-turns. Recently, it has been reported (Hollósi, M., Kövér, K.E., Holly, S., Radics, L., & Fasman, G.D., 1987, Biopolymers 26, 1527-1572; Perczel, A., Hollósi, M., Foxman, B.M., & Fasman, G.D., 1991a, J. Am. Chem. Soc. 113, 9772-9784) that some pseudohexapeptides (e.g., the cyclo[(delta)Ava-Gly-Pro-Aaa-Gly] where Aaa = Ser, Ser(OtBu), or Gly) in many solvents adopt a conformational mixture of type I and the type II beta-turns, although the X-ray-determined conformation was an ideal type I beta-turn. In addition to these pseudohexapeptides, conformational analysis was also carried out on three pseudotetrapeptides and three pseudooctapeptides. The target of the conformation analysis reported herein was to determine whether the ring stress of the above beta-turn models has an influence on their conformational properties. Quantitative nuclear Overhauser effect (NOE) measurements yielded interproton distances. The conformational average distances so obtained were interpreted utilizing molecular dynamics (MD) simulations to yield the conformational percentages. These conformational ratios were correlated with the conformational weights obtained by quantitative CD analysis of the same compounds. The pure component CD curves of type I and type II beta-turns were also obtained, using a recently developed algorithm (Perczel, A., Tusnády, G., Hollósi, M., & Fasman, G.D., 1991b, Protein Eng. 4(6), 669-679). For the first time the results of a CD deconvolution, based on the CD spectra of 14 beta-turn models, were assigned by quantitative NOE results. The NOE experiments confirmed the ratios of the component curves found for the two major beta-turns by CD analysis. These results

  11. 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.

  12. Quantitative image analysis in sonograms of the thyroid gland

    NASA Astrophysics Data System (ADS)

    Catherine, Skouroliakou; Maria, Lyra; Aristides, Antoniou; Lambros, Vlahos

    2006-12-01

    High-resolution, real-time ultrasound is a routine examination for assessing the disorders of the thyroid gland. However, the current diagnosis practice is based mainly on qualitative evaluation of the resulting sonograms, therefore depending on the physician's experience. Computerized texture analysis is widely employed in sonographic images of various organs (liver, breast), and it has been proven to increase the sensitivity of diagnosis by providing a better tissue characterization. The present study attempts to characterize thyroid tissue by automatic texture analysis. The texture features that are calculated are based on co-occurrence matrices as they have been proposed by Haralick. The sample consists of 40 patients. For each patient two sonographic images (one for each lobe) are recorded in DICOM format. The lobe is manually delineated in each sonogram, and the co-occurrence matrices for 52 separation vectors are calculated. The texture features extracted from each one of these matrices are: contrast, correlation, energy and homogeneity. Primary component analysis is used to select the optimal set of features. The statistical analysis resulted in the extraction of 21 optimal descriptors. The optimal descriptors are all co-occurrence parameters as the first-order statistics did not prove to be representative of the images characteristics. The bigger number of components depends mainly on correlation for very close or very far distances. The results indicate that quantitative analysis of thyroid sonograms can provide an objective characterization of thyroid tissue.

  13. Phenotypic analysis of Arabidopsis mutants: quantitative analysis of root growth.

    PubMed

    Doerner, Peter

    2008-03-01

    INTRODUCTIONThe growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses "snapshots" of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.

  14. EBprot: Statistical analysis of labeling-based quantitative proteomics data.

    PubMed

    Koh, Hiromi W L; Swa, Hannah L F; Fermin, Damian; Ler, Siok Ghee; Gunaratne, Jayantha; Choi, Hyungwon

    2015-08-01

    Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/).

  15. In vivo osteogenesis assay: a rapid method for quantitative analysis.

    PubMed

    Dennis, J E; Konstantakos, E K; Arm, D; Caplan, A I

    1998-08-01

    A quantitative in vivo osteogenesis assay is a useful tool for the analysis of cells and bioactive factors that affect the amount or rate of bone formation. There are currently two assays in general use for the in vivo assessment of osteogenesis by isolated cells: diffusion chambers and porous calcium phosphate ceramics. Due to the relative ease of specimen preparation and reproducibility of results, the porous ceramic assay was chosen for the development of a rapid method for quantitating in vivo bone formation. The ceramic cube implantation technique consists of combining osteogenic cells with 27-mm3 porous calcium phosphate ceramics, implanting the cell-ceramic composites subcutaneously into an immuno-tolerant host, and, after 2-6 weeks, harvesting and preparing the ceramic implants for histologic analysis. A drawback to the analysis of bone formation within these porous ceramics is that the entire cube must be examined to find small foci of bone present in some samples; a single cross-sectional area is not representative. For this reason, image analysis of serial sections from ceramics is often prohibitively time-consuming. Two alternative scoring methodologies were tested and compared to bone volume measurements obtained by image analysis. The two subjective scoring methods were: (1) Bone Scale: the amount of bone within pores of the ceramic implant is estimated on a scale of 0-4 based on the degree of bone fill (0=no bone, 1=up to 25%, 2=25 to 75%, 4=75 to 100% fill); and (2) Percentage Bone: the amount of bone is estimated by determining the percentage of ceramic pores which contain bone. Every tenth section of serially sectioned cubes was scored by each of these methods under double-blind conditions, and the Bone Scale and Percentage Bone results were directly compared to image analysis measurements from identical samples. Correlation coefficients indicate that the Percentage Bone method was more accurate than the Bone Scale scoring method. The Bone Scale

  16. Functional linear models for association analysis of quantitative traits.

    PubMed

    Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study.

  17. From screening to quantitative sensitivity analysis. A unified approach

    NASA Astrophysics Data System (ADS)

    Campolongo, Francesca; Saltelli, Andrea; Cariboni, Jessica

    2011-04-01

    The present work is a sequel to a recent one published on this journal where the superiority of 'radial design' to compute the 'total sensitivity index' was ascertained. Both concepts belong to sensitivity analysis of model output. A radial design is the one whereby starting from a random point in the hyperspace of the input factors one step in turn is taken for each factor. The procedure is iterated a number of times with a different starting random point as to collect a sample of elementary shifts for each factor. The total sensitivity index is a powerful sensitivity measure which can be estimated based on such a sample. Given the similarity between the total sensitivity index and a screening test known as method of the elementary effects (or method of Morris), we test the radial design on this method. Both methods are best practices: the total sensitivity index in the class of the quantitative measures and the elementary effects in that of the screening methods. We find that the radial design is indeed superior even for the computation of the elementary effects method. This opens the door to a sensitivity analysis strategy whereby the analyst can start with a small number of points (screening-wise) and then - depending on the results - possibly increase the numeral of points up to compute a fully quantitative measure. Also of interest to practitioners is that a radial design is nothing else than an iterated 'One factor At a Time' (OAT) approach. OAT is a radial design of size one. While OAT is not a good practice, modelers in all domains keep using it for sensitivity analysis for reasons discussed elsewhere (Saltelli and Annoni, 2010) [23]. With the present approach modelers are offered a straightforward and economic upgrade of their OAT which maintain OAT's appeal of having just one factor moved at each step.

  18. Functional Linear Models for Association Analysis of Quantitative Traits

    PubMed Central

    Fan, Ruzong; Wang, Yifan; Mills, James L.; Wilson, Alexander F.; Bailey-Wilson, Joan E.; Xiong, Momiao

    2014-01-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. PMID:24130119

  19. Quantitative Analysis of Single-Molecule RNA-Protein Interaction

    PubMed Central

    Fuhrmann, Alexander; Schoening, Jan C.; Anselmetti, Dario; Staiger, Dorothee; Ros, Robert

    2009-01-01

    Abstract RNA-binding proteins impact gene expression at the posttranscriptional level by interacting with cognate cis elements within the transcripts. Here, we apply dynamic single-molecule force spectroscopy to study the interaction of the Arabidopsis glycine-rich RNA-binding protein AtGRP8 with its RNA target. A dwell-time-dependent analysis of the single-molecule data in combination with competition assays and site-directed mutagenesis of both the RNA target and the RNA-binding domain of the protein allowed us to distinguish and quantify two different binding modes. For dwell times <0.21 s an unspecific complex with a lifetime of 0.56 s is observed, whereas dwell times >0.33 s result in a specific interaction with a lifetime of 208 s. The corresponding reaction lengths are 0.28 nm for the unspecific and 0.55 nm for the specific AtGRP8-RNA interactions, indicating formation of a tighter complex with increasing dwell time. These two binding modes cannot be dissected in ensemble experiments. Quantitative titration in RNA bandshift experiments yields an ensemble-averaged equilibrium constant of dissociation of KD = 2 × 10−7 M. Assuming comparable on-rates for the specific and nonspecific binding modes allows us to estimate their free energies as ΔG0 = −42 kJ/mol and ΔG0 = −28 kJ/mol for the specific and nonspecific binding modes, respectively. Thus, we show that single-molecule force spectroscopy with a refined statistical analysis is a potent tool for the analysis of protein-RNA interactions without the drawback of ensemble averaging. This makes it possible to discriminate between different binding modes or sites and to analyze them quantitatively. We propose that this method could be applied to complex interactions of biomolecules in general, and be of particular interest for the investigation of multivalent binding reactions. PMID:19527663

  20. QuASAR: quantitative allele-specific analysis of reads.

    PubMed

    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. QuASAR: quantitative allele-specific analysis of reads

    PubMed Central

    Harvey, Chris T.; Moyerbrailean, Gregory A.; Davis, Gordon O.; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-01-01

    Motivation: Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. Results: We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. Availability and implementation: http://github.com/piquelab/QuASAR. Contact: fluca@wayne.edu or rpique@wayne.edu Supplementary information: Supplementary Material is available at Bioinformatics online. PMID:25480375

  2. The Quantitative Analysis of Chennai Automotive Industry Cluster

    NASA Astrophysics Data System (ADS)

    Bhaskaran, Ethirajan

    2016-07-01

    Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity

  3. Quantitative Analysis of Peripheral Tissue Perfusion Using Spatiotemporal Molecular Dynamics

    PubMed Central

    Lee, Jungsul; Koh, Gou Young; Kwon, Kihwan; Choi, Chulhee

    2009-01-01

    Background Accurate measurement of peripheral tissue perfusion is challenging but necessary to diagnose peripheral vascular insufficiency. Because near infrared (NIR) radiation can penetrate relatively deep into tissue, significant attention has been given to intravital NIR fluorescence imaging. Methodology/Principal Findings We developed a new optical imaging-based strategy for quantitative measurement of peripheral tissue perfusion by time-series analysis of local pharmacokinetics of the NIR fluorophore, indocyanine green (ICG). Time-series NIR fluorescence images were obtained after injecting ICG intravenously in a murine hindlimb ischemia model. Mathematical modeling and computational simulations were used for translating time-series ICG images into quantitative pixel perfusion rates and a perfusion map. We could successfully predict the prognosis of ischemic hindlimbs based on the perfusion profiles obtained immediately after surgery, which were dependent on the preexisting collaterals. This method also reflected increases in perfusion and improvements in prognosis of ischemic hindlimbs induced by treatment with vascular endothelial growth factor and COMP-angiopoietin-1. Conclusions/Significance We propose that this novel NIR-imaging-based strategy is a powerful tool for biomedical studies related to the evaluation of therapeutic interventions directed at stimulating angiogenesis. PMID:19169354

  4. Quantitative analysis of incipient mineral loss in hard tissues

    NASA Astrophysics Data System (ADS)

    Matvienko, Anna; Mandelis, Andreas; Hellen, Adam; Jeon, Raymond; Abrams, Stephen; Amaechi, Bennett

    2009-02-01

    A coupled diffuse-photon-density-wave and thermal-wave theoretical model was developed to describe the biothermophotonic phenomena in multi-layered hard tissue structures. Photothermal Radiometry was applied as a safe, non-destructive, and highly sensitive tool for the detection of early tooth enamel demineralization to test the theory. Extracted human tooth was treated sequentially with an artificial demineralization gel to simulate controlled mineral loss in the enamel. The experimental setup included a semiconductor laser (659 nm, 120 mW) as the source of the photothermal signal. Modulated laser light generated infrared blackbody radiation from teeth upon absorption and nonradiative energy conversion. The infrared flux emitted by the treated region of the tooth surface and sub-surface was monitored with an infrared detector, both before and after treatment. Frequency scans with a laser beam size of 3 mm were performed in order to guarantee one-dimensionality of the photothermal field. TMR images showed clear differences between sound and demineralized enamel, however this technique is destructive. Dental radiographs did not indicate any changes. The photothermal signal showed clear change even after 1 min of gel treatment. As a result of the fittings, thermal and optical properties of sound and demineralized enamel were obtained, which allowed for quantitative differentiation of healthy and non-healthy regions. In conclusion, the developed model was shown to be a promising tool for non-invasive quantitative analysis of early demineralization of hard tissues.

  5. Quantitative analysis of tumor burden in mouse lung via MRI.

    PubMed

    Tidwell, Vanessa K; Garbow, Joel R; Krupnick, Alexander S; Engelbach, John A; Nehorai, Arye

    2012-02-01

    Lung cancer is the leading cause of cancer death in the United States. Despite recent advances in screening protocols, the majority of patients still present with advanced or disseminated disease. Preclinical rodent models provide a unique opportunity to test novel therapeutic drugs for targeting lung cancer. Respiratory-gated MRI is a key tool for quantitatively measuring lung-tumor burden and monitoring the time-course progression of individual tumors in mouse models of primary and metastatic lung cancer. However, quantitative analysis of lung-tumor burden in mice by MRI presents significant challenges. Herein, a method for measuring tumor burden based upon average lung-image intensity is described and validated. The method requires accurate lung segmentation; its efficiency and throughput would be greatly aided by the ability to automatically segment the lungs. A technique for automated lung segmentation in the presence of varying tumor burden levels is presented. The method includes development of a new, two-dimensional parametric model of the mouse lungs and a multi-faceted cost function to optimally fit the model parameters to each image. Results demonstrate a strong correlation (0.93), comparable with that of fully manual expert segmentation, between the automated method's tumor-burden metric and the tumor burden measured by lung weight.

  6. Advance in orientation microscopy: quantitative analysis of nanocrystalline structures.

    PubMed

    Seyring, Martin; Song, Xiaoyan; Rettenmayr, Markus

    2011-04-26

    The special properties of nanocrystalline materials are generally accepted to be a consequence of the high density of planar defects (grain and twin boundaries) and their characteristics. However, until now, nanograin structures have not been characterized with similar detail and statistical relevance as coarse-grained materials, due to the lack of an appropriate method. In the present paper, a novel method based on quantitative nanobeam diffraction in transmission electron microscopy (TEM) is presented to determine the misorientation of adjacent nanograins and subgrains. Spatial resolution of <5 nm can be achieved. This method is applicable to characterize orientation relationships in wire, film, and bulk materials with nanocrystalline structures. As a model material, nanocrystalline Cu is used. Several important features of the nanograin structure are discovered utilizing quantitative analysis: the fraction of twin boundaries is substantially higher than that observed in bright-field images in the TEM; small angle grain boundaries are prominent; there is an obvious dependence of the grain boundary characteristics on grain size distribution and mean grain size.

  7. Quantitative analysis of multiple sclerosis: a feasibility study

    NASA Astrophysics Data System (ADS)

    Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

    2006-03-01

    Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

  8. Quantitative colorimetric-imaging analysis of nickel in iron meteorites.

    PubMed

    Zamora, L Lahuerta; López, P Alemán; Fos, G M Antón; Algarra, R Martín; Romero, A M Mellado; Calatayud, J Martínez

    2011-02-15

    A quantitative analytical imaging approach for determining the nickel content of metallic meteorites is proposed. The approach uses a digital image of a series of standard solutions of the nickel-dimethylglyoxime coloured chelate and a meteorite sample solution subjected to the same treatment as the nickel standards for quantitation. The image is processed with suitable software to assign a colour-dependent numerical value (analytical signal) to each standard. Such a value is directly proportional to the analyte concentration, which facilitates construction of a calibration graph where the value for the unknown sample can be interpolated to calculate the nickel content of the meteorite. The results thus obtained were validated by comparison with the official, ISO-endorsed spectrophotometric method for nickel. The proposed method is fairly simple and inexpensive; in fact, it uses a commercially available digital camera as measuring instrument and the images it provides are processed with highly user-friendly public domain software (specifically, ImageJ, developed by the National Institutes of Health and freely available for download on the Internet). In a scenario dominated by increasingly sophisticated and expensive equipment, the proposed method provides a cost-effective alternative based on simple, robust hardware that is affordable and can be readily accessed worldwide. This can be especially advantageous for countries were available resources for analytical equipment investments are scant. The proposed method is essentially an adaptation of classical chemical analysis to current, straightforward, robust, cost-effective instrumentation. Copyright © 2010 Elsevier B.V. All rights reserved.

  9. Quantitative three-dimensional holographic interferometry for flow field analysis

    NASA Astrophysics Data System (ADS)

    Holden, C. M. E.; Parker, S. C. J.; Bryanston-Cross, P. J.

    Holographic interferometry offers the potential for quantitative, wholefield analysis of three-dimensional compressible flows. The technique is non-intrusive, does not require the introduction of seeding particles, and records the entire flow information within the pulse duration of a Q-switched ruby laser (~30ns). At present, however, holographic interferometry is mainly used qualitatively due to the practical restrictions of data recording, acquisition and processing. To address the potential of holographic flow analysis a prototype multi-channel interferometer has been designed and preliminary wind tunnel results have been obtained. The proposed configuration uses specular illumination which, unlike comparable diffuse systems, does not suffer from fringe localisation and speckle noise. Beam collimation and steering through the flow field is achieved in a single operation by the use of holographic optical elements (HOEs). The resulting design is compact, light efficient, has aberration compensation, and the recorded data are conducive to both tomographic analysis and direct comparison to computational fluid dynamics (CFD) predictions. Holograms have been recorded of simple two-dimensional and axisymmetric compressible flows, to compare the accuracy of holographic density measurements with data from conventional pressure sensors and CFD codes. Data extraction from the holograms, and the elimination of rigid body motion, was achieved using digital Fourier transform fringe analysis. The introduction of phase errors by image processing has been investigated by analysing simulated fringe patterns generated from a combination of experimental amplitude information and computer generated phase data.

  10. Multipoint quantitative-trait linkage analysis in general pedigrees.

    PubMed Central

    Almasy, L; Blangero, J

    1998-01-01

    Multipoint linkage analysis of quantitative-trait loci (QTLs) has previously been restricted to sibships and small pedigrees. In this article, we show how variance-component linkage methods can be used in pedigrees of arbitrary size and complexity, and we develop a general framework for multipoint identity-by-descent (IBD) probability calculations. We extend the sib-pair multipoint mapping approach of Fulker et al. to general relative pairs. This multipoint IBD method uses the proportion of alleles shared identical by descent at genotyped loci to estimate IBD sharing at arbitrary points along a chromosome for each relative pair. We have derived correlations in IBD sharing as a function of chromosomal distance for relative pairs in general pedigrees and provide a simple framework whereby these correlations can be easily obtained for any relative pair related by a single line of descent or by multiple independent lines of descent. Once calculated, the multipoint relative-pair IBDs can be utilized in variance-component linkage analysis, which considers the likelihood of the entire pedigree jointly. Examples are given that use simulated data, demonstrating both the accuracy of QTL localization and the increase in power provided by multipoint analysis with 5-, 10-, and 20-cM marker maps. The general pedigree variance component and IBD estimation methods have been implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package. PMID:9545414

  11. Quantitative multi-image analysis for biomedical Raman spectroscopic imaging.

    PubMed

    Hedegaard, Martin A B; Bergholt, Mads S; Stevens, Molly M

    2016-05-01

    Imaging by Raman spectroscopy enables unparalleled label-free insights into cell and tissue composition at the molecular level. With established approaches limited to single image analysis, there are currently no general guidelines or consensus on how to quantify biochemical components across multiple Raman images. Here, we describe a broadly applicable methodology for the combination of multiple Raman images into a single image for analysis. This is achieved by removing image specific background interference, unfolding the series of Raman images into a single dataset, and normalisation of each Raman spectrum to render comparable Raman images. Multivariate image analysis is finally applied to derive the contributing 'pure' biochemical spectra for relative quantification. We present our methodology using four independently measured Raman images of control cells and four images of cells treated with strontium ions from substituted bioactive glass. We show that the relative biochemical distribution per area of the cells can be quantified. In addition, using k-means clustering, we are able to discriminate between the two cell types over multiple Raman images. This study shows a streamlined quantitative multi-image analysis tool for improving cell/tissue characterisation and opens new avenues in biomedical Raman spectroscopic imaging. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Quantitative analysis of the reconstruction performance of interpolants

    NASA Technical Reports Server (NTRS)

    Lansing, Donald L.; Park, Stephen K.

    1987-01-01

    The analysis presented provides a quantitative measure of the reconstruction or interpolation performance of linear, shift-invariant interpolants. The performance criterion is the mean square error of the difference between the sampled and reconstructed functions. The analysis is applicable to reconstruction algorithms used in image processing and to many types of splines used in numerical analysis and computer graphics. When formulated in the frequency domain, the mean square error clearly separates the contribution of the interpolation method from the contribution of the sampled data. The equations provide a rational basis for selecting an optimal interpolant; that is, one which minimizes the mean square error. The analysis has been applied to a selection of frequently used data splines and reconstruction algorithms: parametric cubic and quintic Hermite splines, exponential and nu splines (including the special case of the cubic spline), parametric cubic convolution, Keys' fourth-order cubic, and a cubic with a discontinuous first derivative. The emphasis in this paper is on the image-dependent case in which no a priori knowledge of the frequency spectrum of the sampled function is assumed.

  13. Quantitative multielement analysis using high energy particle bombardment

    NASA Technical Reports Server (NTRS)

    Clark, P. J.; Neal, G. F.; Allen, R. O.

    1974-01-01

    Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma X-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays, while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y onto a thin formvar film or by extracting the sample (with or without an internal standard) onto ion exchange resin which is pressed into a pellet.

  14. Quantitative analysis of creatinine in urine by metalized nanostructured parylene

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Malvadkar, Niranjan; Koytek, S.; Bylander, J.; Reeves, W. Brian; Demirel, Melik C.

    2010-03-01

    A highly accurate, real-time multisensor agent monitor for biomarker detection is required for early detection of kidney diseases. Urine creatinine level can provide useful information on the status of the kidney. We prepare nanostructured surface-enhanced Raman spectroscopy (SERS) substrates without template or lithography, which provides controllable, well-organized nanostructures on the surface, for the quantitative analysis of creatinine concentration in urine. We present our work on sensitivity of the SERS substrate to urine samples collected from diabetic patients and healthy persons. We report the preparation of a new type of SERS substrate, which provides fast (<10 s), highly sensitive (creatinine concentration <0.5 μg/mL) and reproducible (<5% variation) detection of urine. Our method to analyze the creatinine level in urine is in good agreement with the enzymatic method.

  15. Quantitative multielement analysis using high energy particle bombardment

    NASA Technical Reports Server (NTRS)

    Clark, P. J.; Neal, G. F.; Allen, R. O.

    1975-01-01

    Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y a thin Formvar film or by extracting the sample onto ion exchange resin which is pressed into a pellet.

  16. Large-Scale Quantitative Analysis of Painting Arts

    NASA Astrophysics Data System (ADS)

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-12-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances.

  17. Large-Scale Quantitative Analysis of Painting Arts

    PubMed Central

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-01-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images – the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances. PMID:25501877

  18. qfasar: quantitative fatty acid signature analysis with R

    USGS Publications Warehouse

    Bromaghin, Jeffrey

    2017-01-01

    Knowledge of predator diets provides essential insights into their ecology, yet diet estimation is challenging and remains an active area of research.Quantitative fatty acid signature analysis (QFASA) is a popular method of estimating diet composition that continues to be investigated and extended. However, software to implement QFASA has only recently become publicly available.I summarize a new R package, qfasar, for diet estimation using QFASA methods. The package also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research. Several procedures in the package have not previously been published.qfasar makes traditional and recently published QFASA diet estimation methods accessible to ecologists for the first time. Use of the package is illustrated with signature data from Chukchi Sea polar bears and potential prey species.

  19. Automatic analysis of quantitative NMR data of pharmaceutical compound libraries.

    PubMed

    Liu, Xuejun; Kolpak, Michael X; Wu, Jiejun; Leo, Gregory C

    2012-08-07

    In drug discovery, chemical library compounds are usually dissolved in DMSO at a certain concentration and then distributed to biologists for target screening. Quantitative (1)H NMR (qNMR) is the preferred method for the determination of the actual concentrations of compounds because the relative single proton peak areas of two chemical species represent the relative molar concentrations of the two compounds, that is, the compound of interest and a calibrant. Thus, an analyte concentration can be determined using a calibration compound at a known concentration. One particularly time-consuming step in the qNMR analysis of compound libraries is the manual integration of peaks. In this report is presented an automated method for performing this task without prior knowledge of compound structures and by using an external calibration spectrum. The script for automated integration is fast and adaptable to large-scale data sets, eliminating the need for manual integration in ~80% of the cases.

  20. Quantitative Image Analysis of HIV-1 Infection in Lymphoid Tissue

    NASA Astrophysics Data System (ADS)

    Haase, Ashley T.; Henry, Keith; Zupancic, Mary; Sedgewick, Gerald; Faust, Russell A.; Melroe, Holly; Cavert, Winston; Gebhard, Kristin; Staskus, Katherine; Zhang, Zhi-Qiang; Dailey, Peter J.; Balfour, Henry H., Jr.; Erice, Alejo; Perelson, Alan S.

    1996-11-01

    Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productively infected cells Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment.

  1. Cerebellar dyssynergia in humans--a quantitative analysis.

    PubMed

    Miller, R G; Freund, H J

    1980-12-01

    Patients with cerebellar lesions and limb ataxia performed two types of continuous tracking tasks involving flexion and extension of the index finger. In both tasks, patients were provided cutaneous and proprioceptive cues, but visual feedback was given in the first task (visual tracking) and not in the second (arbitrarily termed proprioceptive tracking). Raw records and Fourier-analyzed power spectra were compared with results in normal controls. Harmonic distortion was determined for each task. In all patients, as well as normal subjects, tracking performance was markedly improved and harmonic distortion substantially reduced during proprioceptive tracking. This surprising finding may result from a much shorter feedback loop for proprioceptive stimuli compared to visual stimuli. The tracking records, power spectra analysis, and determination of harmonic distortion provide both qualitative and quantitative data in patients with dyssynergia.

  2. Quantitative image analysis for investigating cell-matrix interactions

    NASA Astrophysics Data System (ADS)

    Burkel, Brian; Notbohm, Jacob

    2017-07-01

    The extracellular matrix provides both chemical and physical cues that control cellular processes such as migration, division, differentiation, and cancer progression. Cells can mechanically alter the matrix by applying forces that result in matrix displacements, which in turn may localize to form dense bands along which cells may migrate. To quantify the displacements, we use confocal microscopy and fluorescent labeling to acquire high-contrast images of the fibrous material. Using a technique for quantitative image analysis called digital volume correlation, we then compute the matrix displacements. Our experimental technology offers a means to quantify matrix mechanics and cell-matrix interactions. We are now using these experimental tools to modulate mechanical properties of the matrix to study cell contraction and migration.

  3. Quantitative microstructure analysis of polymer-modified mortars.

    PubMed

    Jenni, A; Herwegh, M; Zurbriggen, R; Aberle, T; Holzer, L

    2003-11-01

    Digital light, fluorescence and electron microscopy in combination with wavelength-dispersive spectroscopy were used to visualize individual polymers, air voids, cement phases and filler minerals in a polymer-modified cementitious tile adhesive. In order to investigate the evolution and processes involved in formation of the mortar microstructure, quantifications of the phase distribution in the mortar were performed including phase-specific imaging and digital image analysis. The required sample preparation techniques and imaging related topics are discussed. As a form of case study, the different techniques were applied to obtain a quantitative characterization of a specific mortar mixture. The results indicate that the mortar fractionates during different stages ranging from the early fresh mortar until the final hardened mortar stage. This induces process-dependent enrichments of the phases at specific locations in the mortar. The approach presented provides important information for a comprehensive understanding of the functionality of polymer-modified mortars.

  4. Quantitative image analysis of WE43-T6 cracking behavior

    NASA Astrophysics Data System (ADS)

    Ahmad, A.; Yahya, Z.

    2013-06-01

    Environment-assisted cracking of WE43 cast magnesium (4.2 wt.% Yt, 2.3 wt.% Nd, 0.7% Zr, 0.8% HRE) in the T6 peak-aged condition was induced in ambient air in notched specimens. The mechanism of fracture was studied using electron backscatter diffraction, serial sectioning and in situ observations of crack propagation. The intermetallic (rare earthed-enriched divorced intermetallic retained at grain boundaries and predominantly at triple points) material was found to play a significant role in initiating cracks which leads to failure of this material. Quantitative measurements were required for this project. The populations of the intermetallic and clusters of intermetallic particles were analyzed using image analysis of metallographic images. This is part of the work to generate a theoretical model of the effect of notch geometry on the static fatigue strength of this material.

  5. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy.

    PubMed

    Singh, Vivek K; Singh, Vinita; Rai, Awadhesh K; Thakur, Surya N; Rai, Pradeep K; Singh, Jagdish P

    2008-11-01

    The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

  6. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy

    SciTech Connect

    Singh, Vivek K.; Singh, Vinita; Rai, Awadhesh K.; Thakur, Surya N.; Rai, Pradeep K.; Singh, Jagdish P

    2008-11-01

    The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

  7. Quantitative genetic analysis of injury liability in infants and toddlers

    SciTech Connect

    Phillips, K.; Matheny, A.P. Jr.

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  8. Energy efficiency quantitative analysis method of discrete manufacturing system

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Ji, Zhicheng

    2017-07-01

    The difficulty in the energy efficiency analysis of discrete manufacturing system is the lack of evaluation index system. In this paper, a novel evaluation index system with three layers and 10 indexes was presented to analyze the overall energy consumption level of the discrete manufacturing system. Then, with the consideration of the difficulties in directly obtaining machine energy efficiency, a prediction method based on recursive variable forgetting factor identification was put forward to calculate it. Furthermore, a comprehensive quantitative evaluation method of rough set and attribute hierarchical model was designed based on the index structure to evaluate the energy efficiency level. Finally, an experiment was used to illustrate the effectiveness of our evaluation index system and method.

  9. Quantitative analysis of forest island pattern in selected Ohio landscapes

    SciTech Connect

    Bowen, G.W.; Burgess, R.L.

    1981-07-01

    The purpose of this study was to quantitatively describe the various aspects of regional distribution patterns of forest islands and relate those patterns to other landscape features. Several maps showing the forest cover of various counties in Ohio were selected as representative examples of forest patterns to be quantified. Ten thousand hectare study areas (landscapes) were delineated on each map. A total of 15 landscapes representing a wide variety of forest island patterns was chosen. Data were converted into a series of continuous variables which contained information pertinent to the sizes, shape, numbers, and spacing of woodlots within a landscape. The continuous variables were used in a factor analysis to describe the variation among landscapes in terms of forest island pattern. The results showed that forest island patterns are related to topography and other environmental features correlated with topography.

  10. Quantitative analysis in outcome assessment of instrumented lumbosacral arthrodesis

    PubMed Central

    Mazel, Christian; Mitulescu, Anca

    2007-01-01

    The outcome assessment in instrumented lumbosacral fusion mostly focuses on clinical criteria, complications and scores, with a high variability of imaging means, methods of fusion grading and parameters describing degenerative changes, making comparisons between studies difficult. The aim of this retrospective evaluation was to evaluate the interest of quantified radiographic analysis of lumbar spine in global outcome assessment and to highlight the key biomechanical factors involved. Clinical data and Beaujon–Lassale scores were collected for 49 patients who underwent lumbosacral arthrodesis after prior lumbar discectomy (mean follow-up: 5 years). Sagittal standing and lumbar flexion-extension X-ray films allowed quantifying vertebral, lumbar, pelvic and kinematic parameters of the lumbar spine, which were compared to reference values. Statistics were performed to assess evolution for all variables. At long-term follow-up, 90% of patients presented satisfactory clinical outcomes, associated to normal sagittal alignment; vertebral parameters objectified adjacent level degeneration in four cases (8%). Clinical outcome was correlated (r = 0.8) with fusion that was confirmed in 80% of cases, doubtful in 16% and pseudarthrosis seemed to occur in 4% (2) of cases. In addition to clinical data (outcomes comparable to the literature), quantitative analysis accurately described lumbar spine geometry and kinematics, highlighting parameters related to adjacent level’s degeneration and a significant correlation between clinical outcome and fusion. Furthermore, criteria proposed to quantitatively evaluate fusion from lumbar dynamic radiographs seem to be appropriate and in agreement with surgeon’s qualitative grading in 87% of cases. PMID:17216227

  11. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  12. Quantitative Medical Image Analysis for Clinical Development of Therapeutics

    NASA Astrophysics Data System (ADS)

    Analoui, Mostafa

    There has been significant progress in development of therapeutics for prevention and management of several disease areas in recent years, leading to increased average life expectancy, as well as of quality of life, globally. However, due to complexity of addressing a number of medical needs and financial burden of development of new class of therapeutics, there is a need for better tools for decision making and validation of efficacy and safety of new compounds. Numerous biological markers (biomarkers) have been proposed either as adjunct to current clinical endpoints or as surrogates. Imaging biomarkers are among rapidly increasing biomarkers, being examined to expedite effective and rational drug development. Clinical imaging often involves a complex set of multi-modality data sets that require rapid and objective analysis, independent of reviewer's bias and training. In this chapter, an overview of imaging biomarkers for drug development is offered, along with challenges that necessitate quantitative and objective image analysis. Examples of automated and semi-automated analysis approaches are provided, along with technical review of such methods. These examples include the use of 3D MRI for osteoarthritis, ultrasound vascular imaging, and dynamic contrast enhanced MRI for oncology. Additionally, a brief overview of regulatory requirements is discussed. In conclusion, this chapter highlights key challenges and future directions in this area.

  13. In vitro quantitative chemical analysis of tattoo pigments.

    PubMed

    Timko, A L; Miller, C H; Johnson, F B; Ross, E

    2001-02-01

    The composition of cosmetic tattoos might prove relevant to their treatment by high-powered lasers. To test the accuracy and completeness of information supplied by the tattoo ink manufacturers and to perform an elemental assay of tattoo pigments using scanning electron microscopy with energy-dispersive x-ray analysis. Samples of 30 tattoo inks were examined using "standardless" energy-dispersive spectrometry. This technique uses quantitative electron x-ray microanalysis. The technique reliably identifies all elements with the exception of those elements with atomic numbers less than 11. A major national referral laboratory for microscopic examination and biochemical analysis of tissue. These results were compared with ink compositions compiled from manufacturer-supplied material safety data sheets. (1) The percentage of any given element in whole tattoo pigments. (2) The presence or absence of elements and/or compounds as recorded in material safety data sheets supplied by the tattoo ink manufacturers. Of the 30 tattoo inks studied, the most commonly identified elements were aluminum (87% of the pigments), oxygen (73% of the pigments), titanium (67% of the pigments), and carbon (67% of the pigments). The relative contribution of elements to the tattoo ink compositions was highly variable between different compounds. Overall, the manufacturer-supplied data sheets were consistent with the elemental analysis, but there were important exceptions. The composition of elements in tattoo inks varies greatly, even among like-colored pigments. Knowledge of the chemical composition of popular tattoo inks might aid the clinician in effective laser removal.

  14. A Quantitative Analysis of the Solar Composition Problem

    NASA Astrophysics Data System (ADS)

    Villante, F. L.; Serenelli, A. M.

    We perform a quantitative analysis of the solar composition problem by using a statistical approach that allows us to combine the information provided by helioseismic and solar neutrino data in an effective way. We show that the opacity profile of the Sun is well constrained by the solar observational properties. In the context of a two parameter analysis in which elements are grouped as volatiles (i.e. C, N, O and Ne) and refractories (i.e. Mg, Si, S, Fe), the optimal surface composition is found by increasing the abundance of volatiles by (45 ± 4) % and that of refractories by (19 ± 3) % with respect to the values provided by Asplund et al., 2009. As an additional result of our analysis, we show that the best fit to the observational data is obtained with values of input parameters of the standard solar models (radiative opacities, gravitational settling rate, the astrophysical factors S 34 and S 17) that differ at the ∼ 1σ level from those presently adopted.

  15. [Quantitative analysis of drug expenditures variability in dermatology units].

    PubMed

    Moreno-Ramírez, David; Ferrándiz, Lara; Ramírez-Soto, Gabriel; Muñoyerro, M Dolores

    2013-01-01

    Variability in adjusted drug expenditures among clinical departments raises the possibility of difficult access to certain therapies at the time that avoidable expenditures may also exist. Nevertheless, drug expenditures are not usually applied to clinical practice variability analysis. To identify and quantify variability in drug expenditures in comparable dermatology department of the Servicio Andaluz de Salud. Comparative economic analysis regarding the drug expenditures adjusted to population and health care production in 18 dermatology departments of the Servicio Andaluz de Salud. The 2012 cost and production data (homogeneous production units -HPU-)were provided by Inforcoan, the cost accounting information system of the Servicio Andaluz de Salud. The observed drug expenditure ratio ranged from 0.97?/inh to 8.90?/inh and from 208.45?/HPU to 1,471.95?/ HPU. The Pearson correlation between drug expenditure and population was 0.25 and 0.35 for the correlation between expenditure and homogeneous production (p=0.32 and p=0,15, respectively), both Pearson coefficients confirming the lack of correlation and arelevant degree of variability in drug expenditures. The quantitative analysis of variability performed through Pearson correlation has confirmed the existence of drug expenditure variability among comparable dermatology departments. Copyright © 2013 SEFH. Published by AULA MEDICA. All rights reserved.

  16. QTL analysis for some quantitative traits in bread wheat*

    PubMed Central

    Pushpendra, Kumar Gupta; Harindra, Singh Balyan; Pawan, Laxminarayan Kulwal; Neeraj, Kumar; Ajay, Kumar; Reyazul, Rouf Mir; Amita, Mohan; Jitendra, Kumar

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection. PMID:17973342

  17. Automatic quantitative analysis of cardiac MR perfusion images

    NASA Astrophysics Data System (ADS)

    Breeuwer, Marcel M.; Spreeuwers, Luuk J.; Quist, Marcel J.

    2001-07-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and accurate image analysis methods. This paper focuses on the evaluation of blood perfusion in the myocardium (the heart muscle) from MR images, using contrast-enhanced ECG-triggered MRI. We have developed an automatic quantitative analysis method, which works as follows. First, image registration is used to compensate for translation and rotation of the myocardium over time. Next, the boundaries of the myocardium are detected and for each position within the myocardium a time-intensity profile is constructed. The time interval during which the contrast agent passes for the first time through the left ventricle and the myocardium is detected and various parameters are measured from the time-intensity profiles in this interval. The measured parameters are visualized as color overlays on the original images. Analysis results are stored, so that they can later on be compared for different stress levels of the heart. The method is described in detail in this paper and preliminary validation results are presented.

  18. Quantitative polymerase chain reaction analysis by deconvolution of internal standard.

    PubMed

    Hirakawa, Yasuko; Medh, Rheem D; Metzenberg, Stan

    2010-04-29

    Quantitative Polymerase Chain Reaction (qPCR) is a collection of methods for estimating the number of copies of a specific DNA template in a sample, but one that is not universally accepted because it can lead to highly inaccurate (albeit precise) results. The fundamental problem is that qPCR methods use mathematical models that explicitly or implicitly apply an estimate of amplification efficiency, the error of which is compounded in the analysis to unacceptable levels. We present a new method of qPCR analysis that is efficiency-independent and yields accurate and precise results in controlled experiments. The method depends on a computer-assisted deconvolution that finds the point of concordant amplification behavior between the "unknown" template and an admixed amplicon standard. We apply the method to demonstrate dexamethasone-induced changes in gene expression in lymphoblastic leukemia cell lines. This method of qPCR analysis does not use any explicit or implicit measure of efficiency, and may therefore be immune to problems inherent in other qPCR approaches. It yields an estimate of absolute initial copy number of template, and controlled tests show it generates accurate results.

  19. An approach for quantitative image quality analysis for CT

    NASA Astrophysics Data System (ADS)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  20. Quantitative analysis and parametric display of regional myocardial mechanics

    NASA Astrophysics Data System (ADS)

    Eusemann, Christian D.; Bellemann, Matthias E.; Robb, Richard A.

    2000-04-01

    Quantitative assessment of regional heart motion has significant potential for more accurate diagnosis of heart disease and/or cardiac irregularities. Local heart motion may be studied from medical imaging sequences. Using functional parametric mapping, regional myocardial motion during a cardiac cycle can be color mapped onto a deformable heart model to obtain better understanding of the structure- to-function relationships in the myocardium, including regional patterns of akinesis or diskinesis associated with ischemia or infarction. In this study, 3D reconstructions were obtained from the Dynamic Spatial Reconstructor at 15 time points throughout one cardiac cycle of pre-infarct and post-infarct hearts. Deformable models were created from the 3D images for each time point of the cardiac cycles. Form these polygonal models, regional excursions and velocities of each vertex representing a unit of myocardium were calculated for successive time-intervals. The calculated results were visualized through model animations and/or specially formatted static images. The time point of regional maximum velocity and excursion of myocardium through the cardiac cycle was displayed using color mapping. The absolute value of regional maximum velocity and maximum excursion were displayed in a similar manner. Using animations, the local myocardial velocity changes were visualized as color changes on the cardiac surface during the cardiac cycle. Moreover, the magnitude and direction of motion for individual segments of myocardium could be displayed. Comparison of these dynamic parametric displays suggest that the ability to encode quantitative functional information on dynamic cardiac anatomy enhances the diagnostic value of 4D images of the heart. Myocardial mechanics quantified this way adds a new dimension to the analysis of cardiac functional disease, including regional patterns of akinesis and diskinesis associated with ischemia and infarction. Similarly, disturbances in

  1. Quantitative 3-dimensional computed tomography analysis of olecranon fractures.

    PubMed

    Lubberts, Bart; Janssen, Stein; Mellema, Jos; Ring, David

    2016-05-01

    Olecranon fractures have variable size of the proximal fragment, patterns of fragmentation, and subluxation of the ulnohumeral joint that might be better understood and categorized on the basis of quantitative 3-dimensional computed tomography analysis. Mayo type I fractures are undisplaced, Mayo type II are displaced and stable, and Mayo type III are displaced and unstable. The last is categorized into anterior and posterior dislocations. The purpose of this study was to further clarify fracture morphology between Mayo type I, II, and III fractures. Three-dimensional models were created for a consecutive series of 78 patients with olecranon fractures that were evaluated with computed tomography. We determined the total number of fracture fragments, the volume and articular surface area of each fracture fragment, and the degree of displacement of the most proximal olecranon fracture fragment. Displaced olecranon fractures were more comminuted than nondisplaced fractures (P = .02). Displaced fractures without ulnohumeral subluxation were smallest in terms of both volume (P < .001) and articular surface involvement (P < .001) of the most proximal olecranon fracture fragment. There was no difference in average displacement of the proximal fragment between displaced fractures with and without ulnohumeral subluxation (P = .74). Anterior olecranon fracture-dislocations created more displaced (P = .04) and smaller proximal fragments than posterior fracture-dislocations (P = .005), with comparable fragmentation on average (P = .60). The ability to quantify volume, articular surface area, displacement, and fragmentation using quantitative 3-dimensional computed tomography should be considered when increased knowledge of fracture morphology and fracture patterns might be useful. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  2. Towards quantitative analysis of retinal features in optical coherence tomography.

    PubMed

    Baroni, Maurizio; Fortunato, Pina; La Torre, Agostino

    2007-05-01

    The purpose of this paper was to propose a new computer method for quantitative evaluation of representative features of the retina using optical coherence tomography (OCT). A multi-step approach was devised and positively tested for segmentation of the three main retinal layers: the vitreo-retinal interface and the inner and outer retina. Following a preprocessing step, three regions of interest were delimited. Significant peaks corresponding to high and low intensity strips were located along the OCT A-scan lines and accurate boundaries between different layers were obtained by maximizing an edge likelihood function. For a quantitative description, thickness measurement, densitometry, texture and curvature analyses were performed. As a first application, the effect of intravitreal injection of triamcinolone acetonide (IVTA) for the treatment of vitreo-retinal interface syndrome was evaluated. Almost all the parameters, measured on a set of 16 pathologic OCT images, were statistically different before and after IVTA injection (p<0.05). Shape analysis of the internal limiting membrane confirmed the reduction of the pathological traction state. Other significant parameters, such as reflectivity and texture contrast, exhibited relevant changes both at the vitreo-retinal interface and in the inner retinal layers. Texture parameters in the inner and outer retinal layers significantly correlated with the visual acuity restoration. According to these findings an IVTA injection might be considered a possible alternative to surgery for selected patients. In conclusion, the proposed approach appeared to be a promising tool for the investigation of tissue changes produced by pathology and/or therapy.

  3. Quantitative analysis of drug-induced tremor in mice.

    PubMed

    Shinozaki, H

    1984-12-01

    A method of analyzing tremor in mice was developed using a power spectral analysis of the random current induced by the movement of a magnet attached to a mouse, on a wire coil. The power spectral density function defined the frequency composition of the tremor, and the mean square value of the data in any frequency range of concern was determined. It was possible to determine qualitative differences in the tremor caused by various tremorgenic agents, and to differentiate the drug-induced tremor from spontaneous motor activity. The power spectral densities of the tremorine- and oxotremorine-induced tremors were tentatively expressed as the sum of 3 main components (Cauchy distribution) with different peak frequencies, consisting of the spontaneous motor activity component and two tremor components. On the other hand, the power spectral densities of the harmaline-induced tremor were expressed as the sum of two components with two peak frequencies, and the plots of the power spectral densities versus frequency, consisting of the spontaneous motor activity component and a tremor component. The frequency of the peak spectral density was almost independent of the dose of tremorgenic agents, but changed slightly with the lapse of time after their injection. The severity of the tremor was determined quantitatively in terms of the sum of the mean square value. The sum of the mean square value for a period of 45 min after the injection of tremorine, changed in a dose-dependent manner. The severity of the tremor was different for each of the mouse strains. The method studied in the present paper is expected to be utilized for the quantitative examination of the fine motor movement of the experimental animal, particularly, for the screening test of new anti-tremor drugs.

  4. Quantitative analysis with the optoacoustic/ultrasound system OPUS

    NASA Astrophysics Data System (ADS)

    Haisch, Christoph; Zell, Karin; Sperl, Jonathan; Vogel, Mika W.; Niessner, Reinhard

    2009-02-01

    The OPUS (Optoacoustic plus Ultrasound) system is a combination of a medical ultrasound scanner with a highrepetition rate, wavelength-tunable laser system and a suitable triggering interface to synchronize the laser and the ultrasound system. The pulsed laser generates an optoacoustic (OA), or photoacoustic (PA), signal which is detected by the ultrasound system. Alternatively, imaging in conventional ultrasound mode can be performed. Both imaging modes can be superimposed. The laser light is coupled into the tissue laterally, parallel to the ultrasound transducer, which does not require for any major modification to the transducer or the ultrasound beam forming. This was a basic requirement on the instrument, as the intention of the project was to establish the optoacoustic imaging modality as add-on to a conventional standard ultrasound instrument. We believe that this approach may foster the introduction of OA imaging as routine tool in medical diagnosis. Another key aspect of the project was to exploit the capabilities of OA imaging for quantitative analysis. The intention of the presented work is to summarize all steps necessary to extract the significant information from the PA raw data, which are required for the quantification of local absorber distributions. We show results of spatially resolved absorption measurements in scattering samples and a comparison of four different image reconstruction algorithms, regarding their influence on lateral resolution as well as on the signal to noise ratio for different sample depths and absorption values. The reconstruction algorithms are based on Fourier transformation, on a generalized 2D Hough transformation, on circular back-projection and the classical delay-and-sum approach which is implemented in most ultrasound scanners. Furthermore, we discuss the influence of a newly developed laser source, combining diode and flash lamp pumping. Compared to all-flash-lamp pumped systems it features a significantly higher

  5. Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer

    PubMed Central

    Siegel, Erin M.; Riggs, Bridget M.; Delmas, Amber L.; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D.

    2015-01-01

    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97–1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated. PMID:25826459

  6. Quantitative Analysis Of Acoustic Emission From Rock Fracture Experiments

    NASA Astrophysics Data System (ADS)

    Goodfellow, Sebastian David

    This thesis aims to advance the methods of quantitative acoustic emission (AE) analysis by calibrating sensors, characterizing sources, and applying the results to solve engi- neering problems. In the first part of this thesis, we built a calibration apparatus and successfully calibrated two commercial AE sensors. The ErgoTech sensor was found to have broadband velocity sensitivity and the Panametrics V103 was sensitive to surface normal displacement. These calibration results were applied to two AE data sets from rock fracture experiments in order to characterize the sources of AE events. The first data set was from an in situ rock fracture experiment conducted at the Underground Research Laboratory (URL). The Mine-By experiment was a large scale excavation response test where both AE (10 kHz - 1 MHz) and microseismicity (MS) (1 Hz - 10 kHz) were monitored. Using the calibration information, magnitude, stress drop, dimension and energy were successfully estimated for 21 AE events recorded in the tensile region of the tunnel wall. Magnitudes were in the range -7.5 < Mw < -6.8, which is consistent with other laboratory AE results, and stress drops were within the range commonly observed for induced seismicity in the field (0.1 - 10 MPa). The second data set was AE collected during a true-triaxial deformation experiment, where the objectives were to characterize laboratory AE sources and identify issues related to moving the analysis from ideal in situ conditions to more complex laboratory conditions in terms of the ability to conduct quantitative AE analysis. We found AE magnitudes in the range -7.8 < Mw < -6.7 and as with the in situ data, stress release was within the expected range of 0.1 - 10 MPa. We identified four major challenges to quantitative analysis in the laboratory, which in- hibited our ability to study parameter scaling (M0 ∝ fc -3 scaling). These challenges were 0c (1) limited knowledge of attenuation which we proved was continuously evolving, (2

  7. Quantitative analysis of cryptic splicing associated with TDP-43 depletion.

    PubMed

    Humphrey, Jack; Emmett, Warren; Fratta, Pietro; Isaacs, Adrian M; Plagnol, Vincent

    2017-05-26

    Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.

  8. A quantitative risk analysis approach to port hydrocarbon logistics.

    PubMed

    Ronza, A; Carol, S; Espejo, V; Vílchez, J A; Arnaldos, J

    2006-01-16

    A method is presented that allows quantitative risk analysis to be performed on marine hydrocarbon terminals sited in ports. A significant gap was identified in the technical literature on QRA for the handling of hazardous materials in harbours published prior to this work. The analysis is extended to tanker navigation through port waters and loading and unloading facilities. The steps of the method are discussed, beginning with data collecting. As to accident scenario identification, an approach is proposed that takes into account minor and massive spills due to loading arm failures and tank rupture. Frequency estimation is thoroughly reviewed and a shortcut approach is proposed for frequency calculation. This allows for the two-fold possibility of a tanker colliding/grounding at/near the berth or while navigating to/from the berth. A number of probability data defining the possibility of a cargo spill after an external impact on a tanker are discussed. As to consequence and vulnerability estimates, a scheme is proposed for the use of ratios between the numbers of fatal victims, injured and evacuated people. Finally, an example application is given, based on a pilot study conducted in the Port of Barcelona, where the method was tested.

  9. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    DOE PAGES

    Xu, Zhe; Wu, Chaochao; Xie, Fang; ...

    2014-10-28

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective andmore » robust analytical platform for comprehensive analyses of tissue peptidomes, and which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Additionally, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. In conclusion, peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.« less

  10. Optimal display conditions for quantitative analysis of stereoscopic cerebral angiograms

    SciTech Connect

    Charland, P.; Peters, T. |

    1996-10-01

    For several years the authors have been using a stereoscopic display as a tool in the planning of stereotactic neurosurgical techniques. This PC-based workstation allows the surgeon to interact with and view vascular images in three dimensions, as well as to perform quantitative analysis of the three-dimensional (3-D) space. Some of the perceptual issues relevant to the presentation of medical images on this stereoscopic display were addressed in five experiments. The authors show that a number of parameters--namely the shape, color, and depth cue, associated with a cursor--as well as the image filtering and observer position, have a role in improving the observer`s perception of a 3-D image and his ability to localize points within the stereoscopically presented 3-D image. However, an analysis of the results indicates that while varying these parameters can lead to an effect on the performance of individual observers, the effects are not consistent across observers, and the mean accuracy remains relatively constant under the different experimental conditions.

  11. Comparative analysis of quantitative efficiency evaluation methods for transportation networks

    PubMed Central

    He, Yuxin; Hong, Jian

    2017-01-01

    An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess’s Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified. PMID:28399165

  12. Therapeutic electrical stimulation for spasticity: quantitative gait analysis.

    PubMed

    Pease, W S

    1998-01-01

    Improvement in motor function following electrical stimulation is related to strengthening of the stimulated spastic muscle and inhibition of the antagonist. A 26-year-old man with familial spastic paraparesis presented with gait dysfunction and bilateral lower limb spastic muscle tone. Clinically, muscle strength and sensation were normal. He was considered appropriate for a trial of therapeutic electrical stimulation following failed trials of physical therapy and baclofen. No other treatment was used concurrent with the electrical stimulation. Before treatment, quantitative gait analysis revealed 63% of normal velocity and a crouched gait pattern, associated with excessive electromyographic activity in the hamstrings and gastrocnemius muscles. Based on these findings, bilateral stimulation of the quadriceps and anterior compartment musculature was performed two to three times per week for three months. Repeat gait analysis was conducted three weeks after the cessation of stimulation treatment. A 27% increase in velocity was noted associated with an increase in both cadence and right step length. Right hip and bilateral knee stance motion returned to normal (rather than "crouched"). No change in the timing of dynamic electromyographic activity was seen. These findings suggest a role for the use of electrical stimulation for rehabilitation of spasticity. The specific mechanism of this improvement remains uncertain.

  13. Correlation between two methods of florbetapir PET quantitative analysis.

    PubMed

    Breault, Christopher; Piper, Jonathan; Joshi, Abhinay D; Pirozzi, Sara D; Nelson, Aaron S; Lu, Ming; Pontecorvo, Michael J; Mintun, Mark A; Devous, Michael D

    2017-01-01

    This study evaluated performance of a commercially available standardized software program for calculation of florbetapir PET standard uptake value ratios (SUVr) in comparison with an established research method. Florbetapir PET images for 183 subjects clinically diagnosed as cognitively normal (CN), mild cognitive impairment (MCI) or probable Alzheimer's disease (AD) (45 AD, 60 MCI, and 78 CN) were evaluated using two software processing algorithms. The research method uses a single florbetapir PET template generated by averaging both amyloid positive and amyloid negative registered brains together. The commercial software simultaneously optimizes the registration between the florbetapir PET images and three templates: amyloid negative, amyloid positive, and an average. Cortical average SUVr values were calculated across six predefined anatomic regions with respect to the whole cerebellum reference region. SUVr values were well correlated between the two methods (r2 = 0.98). The relationship between the methods computed from the regression analysis is: Commercial method SUVr = (0.9757*Research SUVr) + 0.0299. A previously defined cutoff SUVr of 1.1 for distinguishing amyloid positivity by the research method corresponded to 1.1 (95% CI = 1.098, 1.11) for the commercial method. This study suggests that the commercial method is comparable to the published research method of SUVr analysis for florbetapir PET images, thus facilitating the potential use of standardized quantitative approaches to PET amyloid imaging.

  14. 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.

  15. Inside Single Cells: Quantitative Analysis with Advanced Optics and Nanomaterials

    PubMed Central

    Cui, Yi; Irudayaraj, Joseph

    2014-01-01

    Single cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single cell activity. In order to obtain quantitative information (e.g. molecular quantity, kinetics and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single cell studies both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live cell analysis. Although a considerable proportion of single cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single cell analysis. PMID:25430077

  16. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    SciTech Connect

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-02

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

  17. Quantitative evaluation of midpalatal suture maturation via fractal analysis

    PubMed Central

    Kwak, Kyoung Ho; Kim, Yong-Il; Kim, Yong-Deok

    2016-01-01

    Objective The purpose of this study was to determine whether the results of fractal analysis can be used as criteria for midpalatal suture maturation evaluation. Methods The study included 131 subjects aged over 18 years of age (range 18.1–53.4 years) who underwent cone-beam computed tomography. Skeletonized images of the midpalatal suture were obtained via image processing software and used to calculate fractal dimensions. Correlations between maturation stage and fractal dimensions were calculated using Spearman's correlation coefficient. Optimal fractal dimension cut-off values were determined using a receiver operating characteristic curve. Results The distribution of maturation stages of the midpalatal suture according to the cervical vertebrae maturation index was highly variable, and there was a strong negative correlation between maturation stage and fractal dimension (−0.623, p < 0.001). Fractal dimension was a statistically significant indicator of dichotomous results with regard to maturation stage (area under curve = 0.794, p < 0.001). A test in which fractal dimension was used to predict the resulting variable that splits maturation stages into ABC and D or E yielded an optimal fractal dimension cut-off value of 1.0235. Conclusions There was a strong negative correlation between fractal dimension and midpalatal suture maturation. Fractal analysis is an objective quantitative method, and therefore we suggest that it may be useful for the evaluation of midpalatal suture maturation. PMID:27668195

  18. A Computational Tool for Quantitative Analysis of Vascular Networks

    PubMed Central

    Zudaire, Enrique; Gambardella, Laure; Kurcz, Christopher; Vermeren, Sonja

    2011-01-01

    Angiogenesis is the generation of mature vascular networks from pre-existing vessels. Angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. Several murine experimental systems are well suited for studying developmental and pathological angiogenesis. They include the embryonic hindbrain, the post-natal retina and allantois explants. In these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. Nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. Non-automated protocols are being used widely and they are, in general, time - and labour intensive, prone to human error and do not permit computation of complex spatial metrics. We have developed a light-weight, user friendly software, AngioTool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. AngioTool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. In addition, AngioTool calculates the so-called “branching index” (branch points / unit area), providing a measurement of the sprouting activity of a specimen of interest. We have validated AngioTool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. AngioTool is open source and can be downloaded free of charge. PMID:22110636

  19. Quantitative analysis of triple-mutant genetic interactions.

    PubMed

    Braberg, Hannes; Alexander, Richard; Shales, Michael; Xu, Jiewei; Franks-Skiba, Kathleen E; Wu, Qiuqin; Haber, James E; Krogan, Nevan J

    2014-08-01

    The quantitative analysis of genetic interactions between pairs of gene mutations has proven to be effective for characterizing cellular functions, but it can miss important interactions for functionally redundant genes. To address this limitation, we have developed an approach termed triple-mutant analysis (TMA). The procedure relies on a query strain that contains two deletions in a pair of redundant or otherwise related genes, which is crossed against a panel of candidate deletion strains to isolate triple mutants and measure their growth. A central feature of TMA is to interrogate mutants that are synthetically sick when two other genes are deleted but interact minimally with either single deletion. This approach has been valuable for discovering genes that restore critical functions when the principal actors are deleted. TMA has also uncovered double-mutant combinations that produce severe defects because a third protein becomes deregulated and acts in a deleterious fashion, and it has revealed functional differences between proteins presumed to act together. The protocol is optimized for Singer ROTOR pinning robots, takes 3 weeks to complete and measures interactions for up to 30 double mutants against a library of 1,536 single mutants.

  20. Involvement of aurantiactinomyxon in the life cycle of Thelohanellus testudineus (Cnidaria: Myxosporea) from allogynogenetic gibel carp Carassius auratus gibelio, with morphological, ultrastructural, and molecular analysis.

    PubMed

    Zhao, Dan Dan; Zhai, Yan Hua; Liu, Yang; Wang, Si Jia; Gu, Ze Mao

    2017-07-13

    During the investigation of actinosporean fauna diversity from commercial fish ponds in Hubei Province, China, a novel aurantiactinomyxon type was found from Branchiura sowerbyi. Spore body of the aurantiactinomyxon was ellipsoidal in side view and triangular in apical view, 15.5 ± 0.5 (14.5-16.4) μm in diameter; three leaf-like caudal processes were approximately equal, measuring 13.2 ± 0.9 (11.5-16.2) μm long and 7.4 ± 0.4 (6.7-8.0) μm wide at the base; three polar capsules were located at the apex of spore body, globular in apical view, 2.2 ± 0.1 (2.0-2.3) μm in diameter, and pyriform in side view, 2.5 ± 0.2 (2.3-2.9) μm in length and 2.0 ± 0.2 (1.8-2.4) μm in width; a total of 32 germ cells were observed within the sporoplasm. Ultrastructural analysis showed that the development was asynchronous between pansporocysts but synchronous within a pansporocyst. The formation of sporoblast and the development of sporogonic stage were also described and discussed. The 18S ribosomal DNA sequences of the current aurantiactinomyxon type corresponded to that of a previously reported Thelohanellus testudineus, suggesting that the newly identified aurantiactinomyxon type is the actinosporean stage in the life cycle of T. testudineus.

  1. Medial prefrontal cortical estradiol rapidly alters memory system bias in female rats: ultrastructural analysis reveals membrane-associated estrogen receptors as potential mediators.

    PubMed

    Almey, Anne; Cannell, Elizabeth; Bertram, Kyla; Filardo, Edward; Milner, Teresa A; Brake, Wayne G

    2014-11-01

    High plasma levels of estradiol (E2) are associated with use of a place memory system over a response memory system. We examined whether infusing estradiol into the medial prefrontal cortex (mPFC) or anterior cingulate cortex (AC) could affect memory system bias in female rats. We also examined the ultrastructural distribution of estrogen receptor (ER)-α, ERβ, and G protein-coupled estrogen receptor 1 (GPER1) in the mPFC of female rats as a mechanism for the behavioral effects of E2 in the mPFC. Each rat was infused bilaterally with either E2 (0.13 μg) or vehicle into the mPFC or AC. The majority of E2 mPFC rats used place memory. In contrast, the majority of mPFC vehicle rats and AC E2 or vehicle rats used response memory. These data show that mPFC E2 rapidly biases females to use place memory. Electron microscopic analysis demonstrated that ERα, ERβ, and GPER1 are localized in the mPFC, almost exclusively at extranuclear sites. This is the first time that GPER1 has been localized to the mPFC of rats and the first time that ERα and ERβ have been described at extranuclear sites in the rat mPFC. The majority of receptors were observed on axons and axon terminals, suggesting that estrogens alter presynaptic transmission in the mPFC. This provides a mechanism via which ERs could rapidly alter transmission in the mPFC to alter PFC-dependent behaviors, such as memory system bias. The discrete nature of immunolabeling for these membrane-associated ERs may explain the discrepancy in previous light microscopy studies.

  2. Medial Prefrontal Cortical Estradiol Rapidly Alters Memory System Bias in Female Rats: Ultrastructural Analysis Reveals Membrane-Associated Estrogen Receptors as Potential Mediators

    PubMed Central

    Cannell, Elizabeth; Bertram, Kyla; Filardo, Edward; Milner, Teresa A.

    2014-01-01

    High plasma levels of estradiol (E2) are associated with use of a place memory system over a response memory system. We examined whether infusing estradiol into the medial prefrontal cortex (mPFC) or anterior cingulate cortex (AC) could affect memory system bias in female rats. We also examined the ultrastructural distribution of estrogen receptor (ER)-α, ERβ, and G protein-coupled estrogen receptor 1 (GPER1) in the mPFC of female rats as a mechanism for the behavioral effects of E2 in the mPFC. Each rat was infused bilaterally with either E2 (0.13 μg) or vehicle into the mPFC or AC. The majority of E2 mPFC rats used place memory. In contrast, the majority of mPFC vehicle rats and AC E2 or vehicle rats used response memory. These data show that mPFC E2 rapidly biases females to use place memory. Electron microscopic analysis demonstrated that ERα, ERβ, and GPER1 are localized in the mPFC, almost exclusively at extranuclear sites. This is the first time that GPER1 has been localized to the mPFC of rats and the first time that ERα and ERβ have been described at extranuclear sites in the rat mPFC. The majority of receptors were observed on axons and axon terminals, suggesting that estrogens alter presynaptic transmission in the mPFC. This provides a mechanism via which ERs could rapidly alter transmission in the mPFC to alter PFC-dependent behaviors, such as memory system bias. The discrete nature of immunolabeling for these membrane-associated ERs may explain the discrepancy in previous light microscopy studies. PMID:25211590

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

    NASA Technical Reports Server (NTRS)

    Shortle, John F.; Allocco, Michael

    2005-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Shortle, John F.; Allocco, Michael

    2005-01-01

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

  5. Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

    PubMed

    Kerepesi, Csaba; Grolmusz, Vince

    2016-05-01

    DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet--a webserver implementation of AMPHORA2--, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under

  6. Qualitative and quantitative analysis of atmospheric organosulfates in Centreville, Alabama

    NASA Astrophysics Data System (ADS)

    Hettiyadura, Anusha P. S.; Jayarathne, Thilina; Baumann, Karsten; Goldstein, Allen H.; de Gouw, Joost A.; Koss, Abigail; Keutsch, Frank N.; Skog, Kate; Stone, Elizabeth A.

    2017-01-01

    Organosulfates are components of secondary organic aerosols (SOA) that form from oxidation of volatile organic compounds (VOCs) in the presence of sulfate. In this study, the composition and abundance of organosulfates were determined in fine particulate matter (PM2.5) collected from Centreville, AL, during the Southern Oxidant and Aerosol Study (SOAS) in summer 2013. Six organosulfates were quantified using hydrophilic interaction liquid chromatography (HILIC) with triple quadrupole mass spectrometry (TQD) against authentic standards. Among these, the three most abundant species were glycolic acid sulfate (0.5-52.5 ng m-3), lactic acid sulfate (0.5-36.7 ng m-3), and hydroxyacetone sulfate (0.5-14.3 ng m-3). These three species were strongly inter-correlated, suggesting similar precursors and/or formation pathways. Further correlations with sulfate, isoprene, and isoprene oxidation products indicate important roles for these precursors in organosulfate formation in Centreville. Positive filter sampling artifacts associated with these organosulfates due to gas adsorption or reaction of gas phase precursors of organosulfates with sulfuric acid were assessed for a subset of samples and were less than 7.8 % of their PM2.5 concentrations. Together, the quantified organosulfates accounted for < 0.3 % of organic carbon mass in PM2.5. To gain insights into other organosulfates in PM2.5 collected from Centreville, semi-quantitative analysis was employed by way of monitoring characteristic product ions of organosulfates (HSO4- at m/z 97 and SO4- ṡ at m/z 96) and evaluating relative signal strength by HILIC-TQD. Molecular formulas of organosulfates were determined by high-resolution time-of-flight (TOF) mass spectrometry. The major organosulfate signal across all samples corresponded to 2-methyltetrol sulfates, which accounted for 42-62 % of the total bisulfate ion signal. Conversely, glycolic acid sulfate, the most abundant organosulfate quantified in this study, was 0

  7. The Measles Vaccination Narrative in Twitter: A Quantitative Analysis

    PubMed Central

    Radzikowski, Jacek; Jacobsen, Kathryn H; Croitoru, Arie; Crooks, Andrew; Delamater, Paul L

    2016-01-01

    Background The emergence of social media is providing an alternative avenue for information exchange and opinion formation on health-related issues. Collective discourse in such media leads to the formation of a complex narrative, conveying public views and perceptions. Objective This paper presents a study of Twitter narrative regarding vaccination in the aftermath of the 2015 measles outbreak, both in terms of its cyber and physical characteristics. We aimed to contribute to the analysis of the data, as well as presenting a quantitative interdisciplinary approach to analyze such open-source data in the context of health narratives. Methods We collected 669,136 tweets referring to vaccination from February 1 to March 9, 2015. These tweets were analyzed to identify key terms, connections among such terms, retweet patterns, the structure of the narrative, and connections to the geographical space. Results The data analysis captures the anatomy of the themes and relations that make up the discussion about vaccination in Twitter. The results highlight the higher impact of stories contributed by news organizations compared to direct tweets by health organizations in communicating health-related information. They also capture the structure of the antivaccination narrative and its terms of reference. Analysis also revealed the relationship between community engagement in Twitter and state policies regarding child vaccination. Residents of Vermont and Oregon, the two states with the highest rates of non-medical exemption from school-entry vaccines nationwide, are leading the social media discussion in terms of participation. Conclusions The interdisciplinary study of health-related debates in social media across the cyber-physical debate nexus leads to a greater understanding of public concerns, views, and responses to health-related issues. Further coalescing such capabilities shows promise towards advancing health communication, thus supporting the design of more

  8. The Measles Vaccination Narrative in Twitter: A Quantitative Analysis.

    PubMed

    Radzikowski, Jacek; Stefanidis, Anthony; Jacobsen, Kathryn H; Croitoru, Arie; Crooks, Andrew; Delamater, Paul L

    2016-01-01

    The emergence of social media is providing an alternative avenue for information exchange and opinion formation on health-related issues. Collective discourse in such media leads to the formation of a complex narrative, conveying public views and perceptions. This paper presents a study of Twitter narrative regarding vaccination in the aftermath of the 2015 measles outbreak, both in terms of its cyber and physical characteristics. We aimed to contribute to the analysis of the data, as well as presenting a quantitative interdisciplinary approach to analyze such open-source data in the context of health narratives. We collected 669,136 tweets referring to vaccination from February 1 to March 9, 2015. These tweets were analyzed to identify key terms, connections among such terms, retweet patterns, the structure of the narrative, and connections to the geographical space. The data analysis captures the anatomy of the themes and relations that make up the discussion about vaccination in Twitter. The results highlight the higher impact of stories contributed by news organizations compared to direct tweets by health organizations in communicating health-related information. They also capture the structure of the antivaccination narrative and its terms of reference. Analysis also revealed the relationship between community engagement in Twitter and state policies regarding child vaccination. Residents of Vermont and Oregon, the two states with the highest rates of non-medical exemption from school-entry vaccines nationwide, are leading the social media discussion in terms of participation. The interdisciplinary study of health-related debates in social media across the cyber-physical debate nexus leads to a greater understanding of public concerns, views, and responses to health-related issues. Further coalescing such capabilities shows promise towards advancing health communication, thus supporting the design of more effective strategies that take into account the complex

  9. Nanotechnology patents in the automotive industry (a quantitative & qualitative analysis).

    PubMed

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

    The aim of the article is to present a trend in patent filings for application of nanotechnology to the automobile sector across the world, using the keyword-based patent search. Overviews of the patents related to nano technology in the automobile industry have been provided. The current work has started from the worldwide patent search to find the patents on nanotechnology in the automobile industry and classify the patents according to the various parts of an automobile to which they are related and the solutions which they are providing. In the next step various graphs have been produced to get an insight into various trends. In next step, analysis of patents in various classifications, have been performed. The trends shown in graphs provide the quantitative analysis whereas; the qualitative analysis has been done in another section. The classifications of patents based on the solution they provide have been performed by reading the claims, titles, abstract and full texts separately. Patentability of nano technology inventions have been discussed in a view to give an idea of requirements and statutory bars to the patentability of nanotechnology inventions. Another objective of the current work is to suggest appropriate framework for the companies regarding use of nano technology in the automobile industry and a suggestive strategy for patenting of the inventions related to the same. For example, US Patent, with patent number US2008-019426A1 discusses the invention related to Lubricant composition. This patent has been studied and classified to fall under classification of automobile parts. After studying this patent, it is deduced that, the problem of friction in engine is being solved by this patent. One classification is the "automobile part" based while other is the basis of "problem being solved". Hence, two classifications, namely reduction in friction and engine were created. Similarly, after studying all the patents, a similar matrix has been created.

  10. Quantitative assessment of hip osteoarthritis based on image texture analysis.

    PubMed

    Boniatis, I S; Costaridou, L I; Cavouras, D A; Panagiotopoulos, E C; Panayiotakis, G S

    2006-03-01

    A non-invasive method was developed to investigate the potential capacity of digital image texture analysis in evaluating the severity of hip osteoarthritis (OA) and in monitoring its progression. 19 textural features evaluating patterns of pixel intensity fluctuations were extracted from 64 images of radiographic hip joint spaces (HJS), corresponding to 32 patients with verified unilateral or bilateral OA. Images were enhanced employing custom developed software for the delineation of the articular margins on digitized pelvic radiographs. The severity of OA for each patient was assessed by expert orthopaedists employing the Kellgren and Lawrence (KL) scale. Additionally, an index expressing HJS-narrowing was computed considering patients from the unilateral OA-group. A textural feature that quantified pixel distribution non-uniformity (grey level non-uniformity, GLNU) demonstrated the strongest correlation with the HJS-narrowing index among all extracted features and utilized in further analysis. Classification rules employing GLNU feature were introduced to characterize a hip as normal or osteoarthritic and to assign it to one of three severity categories, formed in accordance with the KL scale. Application of the proposed rules resulted in relatively high classification accuracies in characterizing a hip as normal or osteoarthritic (90.6%) and in assigning it to the correct KL scale category (88.9%). Furthermore, the strong correlation between the HJS-narrowing index and the pathological GLNU (r = -0.9, p<0.001) was utilized to provide percentages quantifying hip OA-severity. Texture analysis may contribute in the quantitative assessment of OA-severity, in the monitoring of OA-progression and in the evaluation of a chondroprotective therapy.

  11. Quantitative texture analysis of talc in mantle hydrated mylonites

    NASA Astrophysics Data System (ADS)

    Benitez-Perez, J. M.; Gomez Barreiro, J.; Wenk, H. R.; Vogel, S. C.; Soda, Y.; Voltolini, M.; Martinez-Catalan, J. R.

    2014-12-01

    A quantitative texture analysis of talc-serpentinite mylonites developed in highly deformed ultramafic rocks from different orogenic contexts have been done with neutorn diffraction at HIPPO (Los Álamos National Laboratory). Mineral assemblage, metamorphic evolution and deformative fabric of these samples could be correlated with those verified along the shallow levels (<100km; <5GPa) of a subduction zone. The hydration of mantle (ultramafic) rocks at those levels it is likely to occur dynamically, with important implications on seismogenesis. Given the high anisotropy of the major phases in the samples (i.e. talc and antigorite) it is expected to influence seismic anisotropy of the whole system, in the presence of texture. However to date there was no data on the crystallographic preferred orientation of talc and examples of antigorite textures are very limited. We explore the contribution of talc texture to the seismic anisotropy of mantle hydrated mylonites. Acknowledgements: This work has been funded by research project CGL2011-22728 of Spanish Ministry of Economy and Competitiveness. JGB and JMBP are grateful to the Ramón y Cajal and FPI funding programs. Access to HIPPO (LANSCE) to conduct diffraction experiments is kindly acknowledged.

  12. Quantitative analysis of dynamic association in live biological fluorescent samples.

    PubMed

    Ruusuvuori, Pekka; Paavolainen, Lassi; Rutanen, Kalle; Mäki, Anita; Huttunen, Heikki; Marjomäki, Varpu

    2014-01-01

    Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells.

  13. Quantitative analysis of brain magnetic resonance imaging for hepatic encephalopathy

    NASA Astrophysics Data System (ADS)

    Syh, Hon-Wei; Chu, Wei-Kom; Ong, Chin-Sing

    1992-06-01

    High intensity lesions around ventricles have recently been observed in T1-weighted brain magnetic resonance images for patients suffering hepatic encephalopathy. The exact etiology that causes magnetic resonance imaging (MRI) gray scale changes has not been totally understood. The objective of our study was to investigate, through quantitative means, (1) the amount of changes to brain white matter due to the disease process, and (2) the extent and distribution of these high intensity lesions, since it is believed that the abnormality may not be entirely limited to the white matter only. Eleven patients with proven haptic encephalopathy and three normal persons without any evidence of liver abnormality constituted our current data base. Trans-axial, sagittal, and coronal brain MRI were obtained on a 1.5 Tesla scanner. All processing was carried out on a microcomputer-based image analysis system in an off-line manner. Histograms were decomposed into regular brain tissues and lesions. Gray scale ranges coded as lesion were then brought back to original images to identify distribution of abnormality. Our results indicated the disease process involved pallidus, mesencephalon, and subthalamic regions.

  14. A quantitative analysis of cardiac myocyte relaxation: a simulation study.

    PubMed

    Niederer, S A; Hunter, P J; Smith, N P

    2006-03-01

    The determinants of relaxation in cardiac muscle are poorly understood, yet compromised relaxation accompanies various pathologies and impaired pump function. In this study, we develop a model of active contraction to elucidate the relative importance of the [Ca2+]i transient magnitude, the unbinding of Ca2+ from troponin C (TnC), and the length-dependence of tension and Ca2+ sensitivity on relaxation. Using the framework proposed by one of our researchers, we extensively reviewed experimental literature, to quantitatively characterize the binding of Ca2+ to TnC, the kinetics of tropomyosin, the availability of binding sites, and the kinetics of crossbridge binding after perturbations in sarcomere length. Model parameters were determined from multiple experimental results and modalities (skinned and intact preparations) and model results were validated against data from length step, caged Ca2+, isometric twitches, and the half-time to relaxation with increasing sarcomere length experiments. A factorial analysis found that the [Ca2+]i transient and the unbinding of Ca2+ from TnC were the primary determinants of relaxation, with a fivefold greater effect than that of length-dependent maximum tension and twice the effect of tension-dependent binding of Ca2+ to TnC and length-dependent Ca2+ sensitivity. The affects of the [Ca2+]i transient and the unbinding rate of Ca2+ from TnC were tightly coupled with the effect of increasing either factor, depending on the reference [Ca2+]i transient and unbinding rate.

  15. Quantitative and graphic acoustic analysis of phonatory modulations: the modulogram.

    PubMed

    Buder, Eugene H; Strand, Edythe A

    2003-04-01

    A method is presented for analyzing phonatory instabilities that occur as modulations of fundamental frequency (f0) and sound pressure level (SPL) on the order of 0.2 to 20 cycles per second. Such long-term phonatory instabilities, including but not limited to traditional notions of tremor, are distinct from cycle-to-cycle perturbation such as jitter or shimmer. For each of the 2 parameters (f0, in Hz, and SPL, in dB), 3 frequency domains are proposed: (a) flutter (10-20 Hz), (b) tremor (2-10 Hz), and (c) wow (0.2-2.0 Hz), yielding 6 types of instability. Analyses were implemented using fast Fourier transforms (FFTs) with domain-specific analysis parameters. Outputs include a graphic display in the form of a set of low-frequency spectrograms (the "modulogram") and quantitative measures of the frequencies, magnitudes, durations, and sinusoidal form of the instabilities. An index of a given instability is developed by combining its duration and average modulation magnitude into a single quantity. Performance of the algorithms was assessed by analyzing test signals with known degrees of modulation, and a range of applications was reviewed to provide a rationale for use of modulograms in phonatory assessment.

  16. Quantitative SERS sensors for environmental analysis of naphthalene.

    PubMed

    Péron, O; Rinnert, E; Toury, T; Lamy de la Chapelle, M; Compère, C

    2011-03-07

    In the investigation of chemical pollutants, such as PAHs (Polycyclic Aromatic Hydrocarbons) at low concentration in aqueous medium, Surface-Enhanced Raman Scattering (SERS) stands for an alternative to the inherent low cross-section of normal Raman scattering. Indeed, SERS is a very sensitive spectroscopic technique due to the excitation of the surface plasmon modes of the nanostructured metallic film. The surface of quartz substrates was coated with a hydrophobic film obtained by silanization and subsequently reacted with polystyrene (PS) beads coated with gold nanoparticles. The hydrophobic surface of the SERS substrates pre-concentrates non-polar molecules such as naphthalene. Under laser excitation, the SERS-active substrates allow the detection and the identification of the target molecules localized close to the gold nanoparticles. The morphology of the SERS substrates based on polystyrene beads surrounded by gold nanoparticles was characterized by scanning electron microscopy (SEM). Furthermore, the Raman fingerprint of the polystyrene stands for an internal spectral reference. To this extent, an innovative method to detect and to quantify organic molecules, as naphthalene in the range of 1 to 20 ppm, in aqueous media was carried out. Such SERS-active substrates tend towards an application as quantitative SERS sensors for the environmental analysis of naphthalene.

  17. Quantitative Financial Analysis of Alternative Energy Efficiency Shareholder Incentive Mechanisms

    SciTech Connect

    Cappers, Peter; Goldman, Charles; Chait, Michele; Edgar, George; Schlegel, Jeff; Shirley, Wayne

    2008-08-03

    Rising energy prices and climate change are central issues in the debate about our nation's energy policy. Many are demanding increased energy efficiency as a way to help reduce greenhouse gas emissions and lower the total cost of electricity and energy services for consumers and businesses. Yet, as the National Action Plan on Energy Efficiency (NAPEE) pointed out, many utilities continue to shy away from seriously expanding their energy efficiency program offerings because they claim there is insufficient profit-motivation, or even a financial disincentive, when compared to supply-side investments. With the recent introduction of Duke Energy's Save-a-Watt incentive mechanism and ongoing discussions about decoupling, regulators and policymakers are now faced with an expanded and diverse landscape of financial incentive mechanisms, Determining the 'right' way forward to promote deep and sustainable demand side resource programs is challenging. Due to the renaissance that energy efficiency is currently experiencing, many want to better understand the tradeoffs in stakeholder benefits between these alternative incentive structures before aggressively embarking on a path for which course corrections can be time-consuming and costly. Using a prototypical Southwest utility and a publicly available financial model, we show how various stakeholders (e.g. shareholders, ratepayers, etc.) are affected by these different types of shareholder incentive mechanisms under varying assumptions about program portfolios. This quantitative analysis compares the financial consequences associated with a wide range of alternative incentive structures. The results will help regulators and policymakers better understand the financial implications of DSR program incentive regulation.

  18. Quantitative analysis of plasma interleiukin-6 by immunoassay on microchip

    NASA Astrophysics Data System (ADS)

    Abe, K.; Hashimoto, Y.; Yatsushiro, S.; Yamamura, S.; Tanaka, M.; Ooie, T.; Baba, Y.; Kataoka, M.

    2012-03-01

    Sandwich enzyme-linked immunoassay (ELISA) is one of the most frequently employed assays for clinical diagnosis, since this enables the investigator to identify specific protein biomarkers. However, the conventional assay using a 96-well microtitration plate is time- and sample-consuming, and therefore is not suitable for rapid diagnosis. To overcome these drawbacks, we performed a sandwich ELISA on a microchip. We employed the piezoelectric inkjet printing for deposition and fixation of 1st antibody on the microchannnel surface (300 μm width and 100 μm depth). Model analyte was interleukin-6 (IL-6) which was one of the inflammatory cytokine. After blocking the microchannel, antigen, biotin-labeled 2nd antibody, and avidin-labeled peroxidase were infused into the microchannel and incubated for 20 min, 10 min, and 5 min, respectively. This assay could detect 2 pg/ml and quantitatively measure the range of 0-32 pg/ml. Liner regression analysis of plasma IL-6 concentration obtained by microchip and conventional methods exhibited a significant relationship (R2 = 0.9964). This assay reduced the time for the antigen-antibody reaction to 1/6, and the consumption of samples and reagents to 1/50 compared with the conventional method. This assay enables us to determine plasma IL-6 with accuracy, high sensitivity, time saving ability, and low consumption of sample and reagents, and thus will be applicable to clinic diagnosis.

  19. Separation and quantitative analysis of alkyl sulfate ethoxymers by HPLC.

    PubMed

    Morvan, Julien; Hubert-Roux, Marie; Agasse, Valérie; Cardinael, Pascal; Barbot, Florence; Decock, Gautier; Bouillon, Jean-Philippe

    2008-01-01

    Separation of alkyl sulfate ethoxymers is investigated on various high-performance liquid chromatography (HPLC) stationary phases: Acclaim C18 Surfactant, Surfactant C8, and Hypercarb. For a fixed alkyl chain length, ethoxymers are eluted in the order of increasing number of ethoxylated units on Acclaim C18 Surfactant, whereas a reversed elution order is observed on Surfactant C8 and Hypercarb. Moreover, on an Acclaim C18 Surfactant column, non-ethoxylated compounds are eluted in their ethoxymers distribution and the use of sodium acetate additive in mobile phase leads to a co-elution of ethoxymers. HPLC stationary phases dedicated to surfactants analysis are evaluated by means of the Tanaka test. Surfactant C8 presents a great silanol activity whereas Acclaim C18 Surfactant shows a high steric selectivity. For alkyl sulfates, linearity of the calibration curve and limits of detection and quantitation are evaluated. The amount of sodium laureth sulfate raw material found in commercial body product is in agreement with the specification of the manufacturer.

  20. Quantitative analysis of regulatory flexibility under changing environmental conditions

    PubMed Central

    Edwards, Kieron D; Akman, Ozgur E; Knox, Kirsten; Lumsden, Peter J; Thomson, Adrian W; Brown, Paul E; Pokhilko, Alexandra; Kozma-Bognar, Laszlo; Nagy, Ferenc; Rand, David A; Millar, Andrew J

    2010-01-01

    The circadian clock controls 24-h rhythms in many biological processes, allowing appropriate timing of biological rhythms relative to dawn and dusk. Known clock circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation, which was analysed by comparison with three contrasting models. A simple, quantitative measure, Dusk Sensitivity, was introduced to compare the behaviour of clock models with varying loop complexity. Evening-expressed clock genes showed photoperiod-dependent dusk sensitivity, as predicted by the three-loop model, whereas the one- and two-loop models tracked dawn and dusk, respectively. Output genes for starch degradation achieved dusk-tracking expression through light regulation, rather than a dusk-tracking rhythm. Model analysis predicted which biochemical processes could be manipulated to extend dusk tracking. Our results reveal how an operating principle of biological regulators applies specifically to the plant circadian clock. PMID:21045818

  1. Quantitative analysis of 3-OH oxylipins in fermentation yeast.

    PubMed

    Potter, Greg; Xia, Wei; Budge, Suzanne M; Speers, R Alex

    2017-02-01

    Despite the ubiquitous distribution of oxylipins in plants, animals, and microbes, and the application of numerous analytical techniques to study these molecules, 3-OH oxylipins have never been quantitatively assayed in yeasts. The formation of heptafluorobutyrate methyl ester derivatives and subsequent analysis with gas chromatography - negative chemical ionization - mass spectrometry allowed for the first determination of yeast 3-OH oxylipins. The concentration of 3-OH 10:0 (0.68-4.82 ng/mg dry cell mass) in the SMA strain of Saccharomyces pastorianus grown in laboratory-scale beverage fermentations was elevated relative to oxylipin concentrations in plant tissues and macroalgae. In fermenting yeasts, the onset of 3-OH oxylipin formation has been related to fermentation progression and flocculation initiation. When the SMA strain was grown in laboratory-scale fermentations, the maximal sugar consumption rate preceded the lowest concentration of 3-OH 10:0 by ∼4.5 h and a distinct increase in 3-OH 10:0 concentration by ∼16.5 h.

  2. Quantitative analysis of cellular metabolic dissipative, self-organized structures.

    PubMed

    de la Fuente, Ildefonso Martínez

    2010-09-27

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life.

  3. Quantitative image analysis of HIV-1 infection in lymphoid tissue

    SciTech Connect

    Haase, A.T.; Zupancic, M.; Cavert, W.

    1996-11-08

    Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy. A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productivity infected cells. Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment. 22 refs., 2 figs., 2 tabs.

  4. Assessment of hair surface roughness using quantitative image analysis.

    PubMed

    Park, K H; Kim, H J; Oh, B; Lee, E; Ha, J

    2017-07-19

    Focus on the hair and hair cuticle is increasing. The hair cuticle is the first layer to be exposed to damage and the area of primary protection. For such reasons, hair product manufacturers consider cuticle protection important. However, previous studies used only visual assessment to examine the cuticle. This study aimed to obtain the changes in cuticles and measure hair roughness using a HIROX microscope. A total of 23 female subjects used the same products daily for 4 weeks. Three hair samples per subject were collected from three different areas of the head. Measurements were taken before and after 4 weeks of daily product use. The hair surface changes were clearly observed on the captured images. Moreover, hair surface roughness was observed using various parameters on HIROX software. After 4 weeks of daily product use, the roughness parameter value of the hair surface was significantly decreased. Our result suggests that the hair roughness analytical method using HIROX can be a new paradigm for high-quality quantitative analysis of the hair cuticle. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

    PubMed Central

    de la Fuente, Ildefonso Martínez

    2010-01-01

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

  6. Quantitative analysis of biomedical samples using synchrotron radiation microbeams

    NASA Astrophysics Data System (ADS)

    Ektessabi, Ali; Shikine, Shunsuke; Yoshida, Sohei

    2001-07-01

    X-ray fluorescence (XRF) using a synchrotron radiation (SR) microbeam was applied to investigate distributions and concentrations of elements in single neurons of patients with neurodegenerative diseases. In this paper we introduce a computer code that has been developed to quantify the trace elements and matrix elements at the single cell level. This computer code has been used in studies of several important neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD) and parkinsonism-dementia complex (PDC), as well as in basic biological experiments to determine the elemental changes in cells due to incorporation of foreign metal elements. The substantial nigra (SN) tissue obtained from the autopsy specimens of patients with Guamanian parkinsonism-dementia complex (PDC) and control cases were examined. Quantitative XRF analysis showed that neuromelanin granules of Parkinsonian SN contained higher levels of Fe than those of the control. The concentrations were in the ranges of 2300-3100 ppm and 2000-2400 ppm respectively. On the contrary, Zn and Ni in neuromelanin granules of SN tissue from the PDC case were lower than those of the control. Especially Zn was less than 40 ppm in SN tissue from the PDC case while it was 560-810 ppm in the control. These changes are considered to be closely related to the neuro-degeneration and cell death.

  7. High throughput, quantitative analysis of human osteoclast differentiation and activity.

    PubMed

    Diepenhorst, Natalie A; Nowell, Cameron J; Rueda, Patricia; Henriksen, Kim; Pierce, Tracie; Cook, Anna E; Pastoureau, Philippe; Sabatini, Massimo; Charman, William N; Christopoulos, Arthur; Summers, Roger J; Sexton, Patrick M; Langmead, Christopher J

    2017-02-15

    Osteoclasts are multinuclear cells that degrade bone under both physiological and pathophysiological conditions. Osteoclasts are therefore a major target of osteoporosis therapeutics aimed at preserving bone. Consequently, analytical methods for osteoclast activity are useful for the development of novel biomarkers and/or pharmacological agents for the treatment of osteoporosis. The nucleation state of an osteoclast is indicative of its maturation and activity. To date, activity is routinely measured at the population level with only approximate consideration of the nucleation state (an 'osteoclast population' is typically defined as cells with ≥3 nuclei). Using a fluorescent substrate for tartrate-resistant acid phosphatase (TRAP), a routinely used marker of osteoclast activity, we developed a multi-labelled imaging method for quantitative measurement of osteoclast TRAP activity at the single cell level. Automated image analysis enables interrogation of large osteoclast populations in a high throughput manner using open source software. Using this methodology, we investigated the effects of receptor activator of nuclear factor kappa-B ligand (RANK-L) on osteoclast maturation and activity and demonstrated that TRAP activity directly correlates with osteoclast maturity (i.e. nuclei number). This method can be applied to high throughput screening of osteoclast-targeting compounds to determine changes in maturation and activity.

  8. Quantitative produced water analysis using mobile 1H NMR

    NASA Astrophysics Data System (ADS)

    Wagner, Lisabeth; Kalli, Chris; Fridjonsson, Einar O.; May, Eric F.; Stanwix, Paul L.; Graham, Brendan F.; Carroll, Matthew R. J.; Johns, Michael L.

    2016-10-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1-30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

  9. Communication about vaccinations in Italian websites: a quantitative analysis.

    PubMed

    Tafuri, Silvio; Gallone, Maria S; Gallone, Maria F; Zorico, Ivan; Aiello, Valeria; Germinario, Cinzia

    2014-01-01

    Babies' parents and people who look for information about vaccination often visit anti-vaccine movement's websites, blogs by naturopathic physicians or natural and alternative medicine practitioners. The aim of this work is to provide a quantitative analysis on the type of information available to Italian people regarding vaccination and a quality analysis of websites retrieved through our searches. A quality score was created to evaluate the technical level of websites. A research was performed through Yahoo, Google, and MSN using the keywords "vaccine" and "vaccination," with the function "OR" in order to identify the most frequently used websites. The 2 keywords were input in Italian, and the first 15 pages retrieved by each search engine were analyzed. 149 websites were selected through this methodology. Fifty-three per cent of the websites belonged to associations, groups, or scientific companies, 32.2% (n = 48) consisted of a personal blog and 14.8% (n = 22) belonged to some of the National Health System offices. Among all analyzed websites, 15.4% (n = 23) came from anti-vaccine movement groups. 37.6% reported webmaster name, 67.8% webmaster e-mail, 28.6% indicated the date of the last update and 46.6% the author's name. The quality score for government sites was higher on average than anti-vaccine websites; although, government sites don't use Web 2.0 functions, as the forums.: National Health System institutions who have to promote vaccination cannot avoid investing in web communication because it cannot be managed by private efforts but must be the result of Public Health, private and scientific association, and social movement synergy.

  10. Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria

    PubMed Central

    Moolman, M. Charl; Kerssemakers, Jacob W.J.; Dekker, Nynke H.

    2015-01-01

    Fluorescence microscopy has revolutionized in vivo cellular biology. Through the specific labeling of a protein of interest with a fluorescent protein, one is able to study movement and colocalization, and even count individual proteins in a live cell. Different algorithms exist to quantify the total intensity and position of a fluorescent focus. Although these algorithms have been rigorously studied for in vitro conditions, which are greatly different than the in-homogenous and variable cellular environments, their exact limits and applicability in the context of a live cell have not been thoroughly and systematically evaluated. In this study, we quantitatively characterize the influence of different background subtraction algorithms on several focus analysis algorithms. We use, to our knowledge, a novel approach to assess the sensitivity of the focus analysis algorithms to background removal, in which simulated and experimental data are combined to maintain full control over the sensitivity of a focus within a realistic background of cellular fluorescence. We demonstrate that the choice of algorithm and the corresponding error are dependent on both the brightness of the focus, and the cellular context. Expectedly, focus intensity estimation and localization accuracy suffer in all algorithms at low focus to background ratios, with the bacteroidal background subtraction in combination with the median excess algorithm, and the region of interest background subtraction in combination with a two-dimensional Gaussian fit algorithm, performing the best. We furthermore show that the choice of background subtraction algorithm is dependent on the expression level of the protein under investigation, and that the localization error is dependent on the distance of a focus from the bacterial edge and pole. Our results establish a set of guidelines for what signals can be analyzed to give a targeted spatial and intensity accuracy within a bacterial cell. PMID:26331246

  11. Quantitative analysis of technological innovation in minimally invasive surgery.

    PubMed

    Hughes-Hallett, A; Mayer, E K; Pratt, P J; Vale, J A; Darzi, A W

    2015-01-01

    In the past 30 years surgical practice has changed considerably owing to the advent of minimally invasive surgery (MIS). This paper investigates the changing surgical landscape chronologically and quantitatively, examining the technologies that have played, and are forecast to play, the largest part in this shift in surgical practice. Electronic patent and publication databases were searched over the interval 1980-2011 for ('minimally invasive' OR laparoscopic OR laparoscopy OR 'minimal access' OR 'key hole') AND (surgery OR surgical OR surgeon). The resulting patent codes were allocated into technology clusters. Technology clusters referred to repeatedly in the contemporary surgical literature were also included in the analysis. Growth curves of patents and publications for the resulting technology clusters were then plotted. The initial search revealed 27,920 patents and 95,420 publications meeting the search criteria. The clusters meeting the criteria for in-depth analysis were: instruments, image guidance, surgical robotics, sutures, single-incision laparoscopic surgery (SILS) and natural-orifice transluminal endoscopic surgery (NOTES). Three patterns of growth were observed among these technology clusters: an S-shape (instruments and sutures), a gradual exponential rise (surgical robotics and image guidance), and a rapid contemporaneous exponential rise (NOTES and SILS). Technological innovation in MIS has been largely stagnant since its initial inception nearly 30 years ago, with few novel technologies emerging. The present study adds objective data to the previous claims that SILS, a surgical technique currently adopted by very few, represents an important part of the future of MIS. © 2015 BJS Society Ltd. Published by John Wiley & Sons Ltd.

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

    PubMed

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

    2013-06-01

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

  13. Mineralization of elastic fibers and alterations of extracellular matrix in pseudoxanthoma elasticum. Ultrastructure, immunocytochemistry, and X-ray analysis

    SciTech Connect

    Walker, E.R.; Frederickson, R.G.; Mayes, M.D.

    1989-01-01

    Histologic paraffin sections of pseudoxanthoma elasticum (PXE)-involved skin of forearm and axilla were used for histochemistry and immunohistochemical and analytical electron microscopy to study the progressive mineralization in the dermis of patients with PXE. The von Kossa technique identified mineral deposits throughout the reticular PXE dermis. X-ray analysis revealed patterns of calcium and phosphorus deposition in the von Kossa-positive areas, and the immunohistochemical staining using monoclonal antibodies identified increased chondroitin-6-sulfate in these areas when compared with normal skin. Scanning transmission electron microscopy observation combined with X-ray dot mapping show calcium and phosphorus to be codistributed within the mineralized area. This study confirms by new methods the increase in chondroitin-6-sulfate, alterations in elastin and collagen, and a high calcium and phosphorus elemental distribution matching the mineralized area in the PXE dermis.

  14. Column precipitation chromatography: an approach to quantitative analysis of eigencolloids.

    PubMed

    Breynaert, E; Maes, A

    2005-08-01

    A new column precipitation chromatography (CPC) technique, capable of quantitatively measuring technetium eigencolloids in aqueous solutions, is presented. The CPC technique is based on the destabilization and precipitation of eigencolloids by polycations in a confined matrix. Tc(IV) colloids can be quantitatively determined from their precipitation onto the CPC column (separation step) and their subsequent elution upon oxidation to pertechnetate by peroxide (elution step). A clean-bed particle removal model was used to explain the experimental results.

  15. Quantitative analysis of flavanones and chalcones from willow bark.

    PubMed

    Freischmidt, A; Untergehrer, M; Ziegler, J; Knuth, S; Okpanyi, S; Müller, J; Kelber, O; Weiser, D; Jürgenliemk, G

    2015-09-01

    Willow bark extracts are used for the treatment of fever, pain and inflammation. Recent clinical and pharmacological research revealed that not only the salicylic alcohol derivatives, but also the polyphenols significantly contribute to these effects. Quantitative analysis of the European Pharmacopoeia still focuses on the determination of the salicylic alcohol derivatives. The objective of the present study was the development of an effective quantification method for the determination of as many flavanone and chalcone glycosides as possible in Salix purpurea and other Salix species as well as commercial preparations thereof. As Salix species contain a diverse spectrum of the glycosidated flavanones naringenin, eriodictyol, and the chalcone chalconaringenin, a subsequent acidic and enzymatic hydrolysis was developed to yield naringenin and eriodictyol as aglycones, which were quantified by HPLC. The 5-O-glucosides were cleaved with 11.5% TFA before subsequent hydrolysis of the 7-O-glucosides with an almond β-glucosidase at pH 6-7. The method was validated with regard to LOD, LOQ, intraday and interday precision, accuracy, stability, recovery, time of hydrolysis, robustness and applicability to extracts. All 5-O- and 7-O-glucosides of naringenin, eriodictyol and chalconaringenin were completely hydrolysed and converted to naringenin and eriodictyol. The LOD of the HPLC method was 0.77 μM of naringenin and 0.45 μM of eriodictyol. The LOQ was 2.34 μM of naringenin and 1.35 μM for eriodictyol. The method is robust with regard to sample weight, but susceptible concerning enzyme deterioration. The developed method is applicable to the determination of flavanone and chalcone glycosides in willow bark and corresponding preparations.

  16. A qualitative and quantitative analysis of vegetable pricing in supermarket

    NASA Astrophysics Data System (ADS)

    Miranda, Suci

    2017-06-01

    The purpose of this study is to analyze the variables affecting the determination of the sale price of vegetable which is constant over time in a supermarket qualitatively and quantitavely. It focuses on the non-organic vegetable with a fixed selling price over time such as spinach, beet, and parsley. In qualitative analysis, the sale price determination is influenced by the vegetable characteristics: (1) vegetable segmentation (low to high daily consumed); (2) vegetable age (how long it can last related to freshness); which both characteristic relates to the inventory management and ultimately to the sale price in supermarket. While quantitatively, the vegetables are divided into two categories: the leaf vegetable group that the leaves are eaten as a vegetable with the aging product (a) = 0 and the shelf life (t) = 0, and the non-leafy vegetable group with the aging group (a) = a+1 and the shelf life (t) = t+1. The vegetable age (a) = 0 means they only last for one day when they are ordered then they have to terminate. Whereas a+1 is that they have a longer life for more than a day such as beet, white radish, and string beans. The shelf life refers to how long it will be placed in a shelf in supermarket in line with the vegetable age. According to the cost plus pricing method using full price costing approach, production costs, non-production costs, and markup are adjusted differently for each category. There is a holding cost added to the sale price of the non-leafy vegetable, yet it is assumed a 0 holding cost for the leafy vegetable category. The amount of expected margin of each category is correlated to the vegetable characteristics.

  17. Quantitative analysis of harmonic convergence in mosquito auditory interactions

    PubMed Central

    Aldersley, Andrew; Champneys, Alan; Robert, Daniel

    2016-01-01

    This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the ‘harmonic convergence’ phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male–female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male–male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry. PMID:27053654

  18. Hydrocarbons on Phoebe, Iapetus, and Hyperion: Quantitative Analysis

    NASA Technical Reports Server (NTRS)

    Cruikshank, Dale P.; MoreauDalleOre, Cristina; Pendleton, Yvonne J.; Clark, Roger Nelson

    2012-01-01

    We present a quantitative analysis of the hydrocarbon spectral bands measured on three of Saturn's satellites, Phoebe, Iaperus, and Hyperion. These bands, measured with the Cassini Visible-Infrared Mapping Spectrometer on close fly-by's of these satellites, are the C-H stretching modes of aromatic hydrocarbons at approximately 3.28 micrometers (approximately 3050 per centimeter), and the are four blended bands of aliphatic -CH2- and -CH3 in the range approximately 3.36-3.52 micrometers (approximately 2980- 2840 per centimeter) bably indicating the presence of polycyclic aromatic hydrocarbons (PAH), is unusually strong in comparison to the aliphatic bands, resulting in a unique signarure among Solar System bodies measured so far, and as such offers a means of comparison among the three satellites. The ratio of the C-H bands in aromatic molecules to those in aliphatic molecules in the surface materials of Phoebe, NAro:NAliph approximately 24; for Hyperion the value is approximately 12, while laperus shows an intermediate value. In view of the trend of the evolution (dehydrogenation by heat and radiation) of aliphatic complexes toward more compact molecules and eventually to aromatics, the relative abundances of aliphatic -CH2- and -CH3- is an indication of the lengths of the molecular chain structures, hence the degree of modification of the original material. We derive CH2:CH3 approximately 2.2 in the spectrum of low-albedo material on laperus; this value is the same within measurement errors to the ratio in the diffuse interstellar medium. The similarity in the spectral signatures of the three satellites, plus the apparent weak trend of aromatic/aliphatic abundance from Phoebe to Hyperion, is consistent with, and effectively confirms that the source of the hydrocarbon-bearing material is Phoebe, and that the appearance of that material on the other two satellites arises from the deposition of the inward-spiraling dust that populates the Phoebe ring.

  19. A quantitative analysis of optimal treatment capacity for perinatal asphyxia.

    PubMed

    Geva, Alon; Gray, James

    2012-01-01

    In centers electing to offer therapeutic hypothermia for treating hypoxic-ischemic encephalopathy (HIE), determining the optimal number of cooling devices is not straightforward. The authors used computer-based modeling to determine the level of service as a function of local HIE caseload and number of cooling devices available. The authors used discrete event simulation to create a model that varied the number of HIE cases and number of cooling devices available. Outcomes of interest were percentage of HIE-affected infants not cooled, number of infants not cooled, and percentage of time that all cooling devices were in use. With 1 cooling device, even the smallest perinatal center did not achieve a cooling rate of 99% of eligible infants. In contrast, 2 devices ensured 99% service in centers treating as many as 20 infants annually. In centers averaging no more than 1 HIE infant monthly, the addition of a third cooling device did not result in a substantial reduction in the number of infants who would not be cooled. Centers electing to offer therapeutic hypothermia with only a single cooling device are at significant risk of being unable to provide treatment to eligible infants, whereas 2 devices appear to suffice for most institutions treating as many as 20 annual HIE cases. Three devices would rarely be needed given current caseloads seen at individual institutions. The quantitative nature of this analysis allows decision makers to determine the number of devices necessary to ensure adequate availability of therapeutic hypothermia given the HIE caseload of a particular institution.

  20. Quantitative analysis of harmonic convergence in mosquito auditory interactions.

    PubMed

    Aldersley, Andrew; Champneys, Alan; Homer, Martin; Robert, Daniel

    2016-04-01

    This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the 'harmonic convergence' phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male-female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male-male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry.

  1. Quantitative image analysis of cell colocalization in murine bone marrow.

    PubMed

    Mokhtari, Zeinab; Mech, Franziska; Zehentmeier, Sandra; Hauser, Anja E; Figge, Marc Thilo

    2015-06-01

    Long-term antibody production is a key property of humoral immunity and is accomplished by long-lived plasma cells. They mainly reside in the bone marrow, whose importance as an organ hosting immunological memory is becoming increasingly evident. Signals provided by stromal cells and eosinophils may play an important role for plasma cell maintenance, constituting a survival microenvironment. In this joint study of experiment and theory, we investigated the spatial colocalization of plasma cells, eosinophils and B cells by applying an image-based systems biology approach. To this end, we generated confocal fluorescence microscopy images of histological sections from murine bone marrow that were subsequently analyzed in an automated fashion. This quantitative analysis was combined with computer simulations of the experimental system for hypothesis testing. In particular, we tested the observed spatial colocalization of cells in the bone marrow against the hypothesis that cells are found within available areas at positions that were drawn from a uniform random number distribution. We find that B cells and plasma cells highly colocalize with stromal cells, to an extent larger than in the simulated random situation. While B cells are preferentially in contact with each other, i.e., form clusters among themselves, plasma cells seem to be solitary or organized in aggregates, i.e., loosely defined groups of cells that are not necessarily in direct contact. Our data suggest that the plasma cell bone marrow survival niche facilitates colocalization of plasma cells with stromal cells and eosinophils, respectively, promoting plasma cell longevity. © 2015 International Society for Advancement of Cytometry.

  2. Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

    PubMed Central

    De la Fuente, Ildefonso M.; Cortes, Jesus M.

    2012-01-01

    The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis. PMID:22393350

  3. Transcriptome Analysis and Ultrastructure Observation Reveal that Hawthorn Fruit Softening Is due to Cellulose/Hemicellulose Degradation

    PubMed Central

    Xu, Jiayu; Zhao, Yuhui; Zhang, Xiao; Zhang, Lijie; Hou, Yali; Dong, Wenxuan

    2016-01-01

    Softening, a common phenomenon in many fruits, is a well coordinated and genetically determined process. However, the process of flesh softening during ripening has rarely been described in hawthorn. In this study, we found that ‘Ruanrou Shanlihong 3 Hao’ fruits became softer during ripening, whereas ‘Qiu JinXing’ fruits remained hard. At late developmental stages, the firmness of ‘Ruanrou Shanlihong 3 Hao’ fruits rapidly declined, and that of ‘Qiu JinXing’ fruits remained essentially unchanged. According to transmission electron microscopy, the middle lamella of ‘Qiu JinXing’ and ‘Ruanrou Shanlihong 3 Hao’ fruit flesh was largely degraded as the fruits matured. Microfilaments in ‘Qiu JinXing’ flesh were arranged close together and were deep in color, whereas those in ‘Ruanrou Shanlihong 3 Hao’ fruit flesh were arranged loosely, partially degraded and light in color. RNA-Seq analysis yielded approximately 46.72 Gb of clean data and 72,837 unigenes. Galactose metabolism and pentose and glucuronate interconversions are involved in cell wall metabolism, play an important role in hawthorn texture. We identified 85 unigenes related to the cell wall between hard- and soft-fleshed hawthorn fruits. Based on data analysis and real-time PCR, we suggest that β-GAL and PE4 have important functions in early fruit softening. The genes Ffase, Gns,α-GAL, PE63, XTH, and CWP, which are involved in cell wall degradation, are responsible for the different textures of hawthorn fruits. Thus, we hypothesize that the different textures of ‘Qiu JinXing’ and ‘Ruanrou Shanlihong 3 Hao’ fruits at maturity mainly result from cellulose/hemicelluloses degradation rather than from lamella degradation. Overall, we propose that different types of hydrolytic enzymes in cells interact to degrade the cell wall, resulting in ultramicroscopic Structure changes in the cell wall and, consequently, fruit softening. These results provide fundamental insight

  4. Ultrastructural analysis of the root canal walls after preparation with two rotary nickel-titanium endodontic instruments

    PubMed Central

    Poggio, Claudio; Dagna, Alberto; Chiesa, Marco; Beltrami, Riccardo; Colombo, Marco

    2014-01-01

    Background: Root canal preparation may produce a large quantity of smear layer that covers canal walls. Aims: The aim of this study was to evaluate by Scanning Electron Microscope (SEM) the root canal dentine after instrumentation with nickel-titanium rotary files, in order to evaluate the presence/absence of smear layer and the presence/absence of open tubules on the root canal walls at the coronal, middle, and apical third of each sample. Materials and Methods: A total of 20 single-rooted freshly extracted teeth were selected and divided into two groups. For each group, root canals were shaped with Mtwo and Revo-S instruments under irrigation with Sodium hypochlorite and 17% ethylenediaminetetraacetic acid. Specimens were fractured longitudinally and SEM analyzed at standard magnification of ×1000 and ×5000. The presence/absence of smear layer and the presence/absence of open tubules at the coronal, middle, and apical third of each canal were evaluated using a three-step scale for scores. Statistical Analysis Used: Numeric data were analyzed using the Kruskall-Wallis and Mann-Whitney U-Statistical tests and significance was pre-determined at P < 0.05. Results and Conclusions: This study did not reveal differences among the two groups. Mtwo and Revo-S showed no significant difference between them and both presented very low smear layer scores and open tubules scores, with no significant difference among coronal, middle, and apical third. Mtwo and Revo-S rotary instruments seem to be effective in removing smear layer from canal walls. PMID:25191073

  5. Ultrastructural Analysis of the Foreskin in Patients With True Phimosis Treated or Not Treated With Topical Betamethasone and Hyaluronidase Ointment.

    PubMed

    Favorito, Luciano Alves; Gallo, Carla B M; Costa, Waldemar S; Sampaio, Francisco J B

    2016-12-01

    To evaluate, by using scanning electron microscopy (SEM), the possible alterations of the foreskin connective tissue in patients with true phimosis submitted to topical treatment with betamethasone and hyaluronidase ointment. We studied 15 patients (mean 5.3 years old) submitted or not to topical application of betamethasone 0.2% and hyaluronidase cream. For qualitative analysis of the connective tissue, we studied 5 samples from each foreskin, with 2 mm length. The samples were submitted to fixation for SEM by immersing tissue fragments in a modified Karnovsky solution for 48 hours at 4°C. The obtained acellular preparations were then processed for high-vacuum SEM, and observations were performed on a LEO 435 (Zeiss, Oberkochen, Germany) scanning electron microscope with an acceleration voltage of 15 to 20 kV. Parents of 7 children did not agree with the clinical treatment and opted for circumcision directly. These patients served as the control group (nontreated). Eight patients submitted to topical treatment could not expose the glans and were referred for circumcision. In SEM, with a magnification of 5000×, we observed important differences in the organization of the collagen and elastic system fibers when comparing treated and nontreated patients with betamethasone and hyaluronidase. Treated patients presented a different organization of collagen with a clear decrease in the elastic system fibers. The treatment of phimosis with betamethasone + hyaluronidase showed changes in the structure of the foreskin with a decrease of elastic system fibers, which is characteristic of the healing processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Quantitative PCR analysis of salivary pathogen burden in periodontitis

    PubMed Central

    Salminen, Aino; Kopra, K. A. Elisa; Hyvärinen, Kati; Paju, Susanna; Mäntylä, Päivi; Buhlin, Kåre; Nieminen, Markku S.; Sinisalo, Juha; Pussinen, Pirkko J.

    2015-01-01

    Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9 ± 9.2 years) with coronary artery disease (CAD) diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR (qPCR). Median salivary concentrations of Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary Aggregatibacter actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4–5 mm periodontal pockets, ≥6 mm pockets, and alveolar bone loss (ABL). High level of T. forsythia was associated also with bleeding on probing (BOP). The combination of the four bacteria, i.e., the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR) of 2.40 (95% CI 1.39–4.13). When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51–4.52). The highest OR 3.59 (95% CI 1.94–6.63) was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and

  7. Quantitative PCR analysis of salivary pathogen burden in periodontitis.

    PubMed

    Salminen, Aino; Kopra, K A Elisa; Hyvärinen, Kati; Paju, Susanna; Mäntylä, Päivi; Buhlin, Kåre; Nieminen, Markku S; Sinisalo, Juha; Pussinen, Pirkko J

    2015-01-01

    Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9 ± 9.2 years) with coronary artery disease (CAD) diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR (qPCR). Median salivary concentrations of Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary Aggregatibacter actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4-5 mm periodontal pockets, ≥6 mm pockets, and alveolar bone loss (ABL). High level of T. forsythia was associated also with bleeding on probing (BOP). The combination of the four bacteria, i.e., the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR) of 2.40 (95% CI 1.39-4.13). When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51-4.52). The highest OR 3.59 (95% CI 1.94-6.63) was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and T

  8. Universal platform for quantitative analysis of DNA transposition.

    PubMed

    Pajunen, Maria I; Rasila, Tiina S; Happonen, Lotta J; Lamberg, Arja; Haapa-Paananen, Saija; Kiljunen, Saija; Savilahti, Harri

    2010-11-26

    Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. The established universal papillation assay platform should be widely applicable to a variety of mobile elements. It can be used for mechanistic

  9. Immunophenotypic and Ultrastructural Analysis of Mast Cells in Hermansky-Pudlak Syndrome Type-1: A Possible Connection to Pulmonary Fibrosis

    PubMed Central

    Kirshenbaum, Arnold S.; Cruse, Glenn; Desai, Avanti; Bandara, Geethani; Leerkes, Maarten; Lee, Chyi-Chia R.; Fischer, Elizabeth R.; O’Brien, Kevin J.; Gochuico, Bernadette R.; Stone, Kelly; Gahl, William A.; Metcalfe, Dean D.

    2016-01-01

    Hermansky-Pudlak Syndrome type-1 (HPS-1) is an autosomal recessive disorder caused by mutations in HPS1 which result in reduced expression of the HPS-1 protein, defective lysosome-related organelle (LRO) transport and absence of platelet delta granules. Patients with HPS-1 exhibit oculocutaneous albinism, colitis, bleeding and pulmonary fibrosis postulated to result from a dysregulated immune response. The effect of the HPS1 mutation on human mast cells (HuMCs) is unknown. Since HuMC granules classify as LROs along with platelet granules and melanosomes, we set out to determine if HPS-1 cutaneous and CD34+ culture-derived HuMCs have distinct granular and cellular characteristics. Cutaneous and cultured CD34+-derived HuMCs from HPS-1 patients were compared with normal cutaneous and control HuMCs, respectively, for any morphological and functional differences. One cytokine-independent HPS-1 culture was expanded, cloned, designated the HP proMastocyte (HPM) cell line and characterized. HPS-1 and idiopathic pulmonary fibrosis (IPF) alveolar interstitium showed numerous HuMCs; HPS-1 dermal mast cells exhibited abnormal granules when compared to healthy controls. HPS-1 HuMCs showed increased CD63, CD203c and reduced mediator release following FcɛRI aggregation when compared with normal HuMCs. HPM cells also had the duplication defect, expressed FcɛRI and intracytoplasmic proteases and exhibited less mediator release following FcɛRI aggregation. HPM cells constitutively released IL-6, which was elevated in patients’ serum, in addition to IL-8, fibronectin-1 (FN-1) and galectin-3 (LGALS3). Transduction with HPS1 rescued the abnormal HPM morphology, cytokine and matrix secretion. Microarray analysis of HPS-1 HuMCs and non-transduced HPM cells confirmed upregulation of differentially expressed genes involved in fibrogenesis and degranulation. Cultured HPS-1 HuMCs appear activated as evidenced by surface activation marker expression, a decrease in mediator content and

  10. Quantitative proton nuclear magnetic resonance for the structural and quantitative analysis of atropine sulfate.

    PubMed

    Shen, Shi; Yao, Jing; Shi, Yaqin

    2014-02-01

    This study assessed a general method of quantitative nuclear magnetic resonance (qNMR) for the calibration of atropine sulfate (Active Pharmaceutical Ingredient, API) as reference standard. The spectra were acquired in D2O using maleic acid as the internal standard. Conformational behaviors of tropane ring were observed and studied by means of NMR and ROESY experiments at different temperature, which showed that the azine methyl group was at equilibrium for axial and equatorial conformations at room temperature. Signal delay and monitor signals of qNMR experimentation were optimized for quantification. The study reported here validated the method's linearity, range, limit of quantification, stability and precision. The results were consistent with the results obtained from mass balance approach.

  11. A Quantitative Analysis of the Behavioral Checklist of the Movement ABC Motor Test

    ERIC Educational Resources Information Center

    Ruiz, Luis Miguel; Gomez, Marta; Graupera, Jose Luis; Gutierrez, Melchor; Linaza, Jose Luis

    2007-01-01

    The fifth section of the Henderson and Sugden's Movement ABC Checklist is part of the general Checklist that accompanies The Movement ABC Battery. The authors maintain that the analysis of this section must be mainly qualitative instead of quantitative. The main objective of this study was to employ a quantitative analysis of this behavioural…

  12. The Utility of Quantitative Methods for Political Intelligence Analysis. A Case Study in Latin America

    DTIC Science & Technology

    1995-10-20

    The paper examines the suitability of current intelligence analysis developed during the Cold War era and finds a lack of quantitative techniques...that are prevalent in academic social science research. Several areas where quantitative research might be applied successfully to intelligence analysis are

  13. [Bibliometric analysis of bacterial quantitative proteomics in English literatures].

    PubMed

    Zhang, Xin; She, Danyang; Liu, Youning; Wang, Rui; Di, Xiuzhen; Liang, Beibei; Wang, Yue

    2014-07-01

    To analyze the worldwide advances on bacterial quantitative proteomics over the past fifteen years with bibliometric approach. Literature retrieval was conducted throughout the databases of Pubmed, Embase and Science citation index (SCI), using "bacterium" and "quantitative proteomics" as the key words. The deadline is July 2013. We sorted and analyzed these articles with Endnote X6 from the aspects of published year, the first author, name of journal, published institution, cited frequency and publication type. 932 English articles were included in our research after deleting the duplicates. The first article on bacterial quantitative proteomics was reported in 1999. The maximal publications were 163 related articles in 2012. Up till July 2013, authors from more than 23 countries and regions have published articles in this field. China ranks the fourth. The main publication type is original articles. The most frequently cited article is entitled with "Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition" by Silva JC, Gorenstein MV, Li GZ, et al in Mol Cell Proteomics 2006. The most productive author is Smith RD from Biological Sciences Division, Pac. Northwest National Laboratory. The top journal publishing bacterial quantitative proteomics is Proteomics. More and more researchers pay attention to quantitative proteomics which will be widely used in bacteriology.

  14. Geographical classification of Epimedium based on HPLC fingerprint analysis combined with multi-ingredients quantitative analysis.

    PubMed

    Xu, Ning; Zhou, Guofu; Li, Xiaojuan; Lu, Heng; Meng, Fanyun; Zhai, Huaqiang

    2017-05-01

    A reliable and comprehensive method for identifying the origin and assessing the quality of Epimedium has been developed. The method is based on analysis of HPLC fingerprints, combined with similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and multi-ingredient quantitative analysis. Nineteen batches of Epimedium, collected from different areas in the western regions of China, were used to establish the fingerprints and 18 peaks were selected for the analysis. Similarity analysis, HCA and PCA all classified the 19 areas into three groups. Simultaneous quantification of the five major bioactive ingredients in the Epimedium samples was also carried out to confirm the consistency of the quality tests. These methods were successfully used to identify the geographical origin of the Epimedium samples and to evaluate their quality. Copyright © 2016 John Wiley & Sons, Ltd.

  15. Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

    ERIC Educational Resources Information Center

    Hill, Devon W.; And Others

    1988-01-01

    Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

  16. Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

    ERIC Educational Resources Information Center

    Hill, Devon W.; And Others

    1988-01-01

    Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

  17. Quantitative analysis of norfloxacin by 1H NMR and HPLC.

    PubMed

    Frackowiak, Anita; Kokot, Zenon J

    2012-01-01

    1H NMR and developed previously HPLC methods were applied to quantitative determination of norfloxacin in veterinary solution form for pigeon. Changes in concentration can lead to significant changes in the 1H chemical shifts of non-exchangeable aromatic protons as a result of extensive self-association phenomena. This chemical shift variation of protons was analyzed and applied in the quantitative determination of norfloxacin. The method is simple, rapid, precise and accurate, and can be used for quality control of this drug.

  18. Quantitative Analysis of Circular Symmetry of Venus Coronae and Craters

    NASA Astrophysics Data System (ADS)

    Stoddard, P. R.; Jurdy, D. M.

    2007-12-01

    The origin of craters has long been debated: Exogenic or endogenic? Impact or volcanic? While for the craters of the Earth and Moon the issue has been largely resolved, it has flared anew in recent papers by Hamilton (2005, 2007), Vita-Finzi et al. (2005), and Jurdy and Stoddard (2005, 2007). We weigh in with a quantitative technique to differentiate between these possible mechanisms. Craters by their nature are circular. They are excavated by a roughly hemispherical shock wave, and thus almost regardless of impact angle, will be round rim-and-basin structures (Melosh, 1989). Although underlying structural features, such as faults, and later tectonic deformation can affect crater shape we suggest that the strongest test of an impact origin for coronae is the circularity of these features. Here we introduce an approach for the assessment of a feature's circular symmetry. Using altimetry data we compare, by cross-correlation, multiple profiles across a single feature. Jurdy and Stoddard (2005) provided an example in which Mead crater and two coronae were analyzed. They found that for each corona, profiles cross- correlated at only 25-30% of perfect cross-correlation. Profiles for Mead crater, however, correlated at a much higher level, 80%. Here, we perform an expanded study of features generally classified as craters, and others whose classification as coronae has been questioned by Hamilton (2007). We choose only the largest craters, since altimetry data are too coarse to allow enough data points for analyses of smaller features, and also because they are of similar size to the coronae in our study. For each feature, 36 profiles are extracted from the altimetry data, de-sloped, and averaged together. For each feature, the individual profiles are correlated against the average, and the correlations themselves were averaged to give an assessment of circular symmetry. Results indicate accepted craters have the highest correlation averages (are most circular) and

  19. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    PubMed

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-05-03

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  20. Microchromatography of hemoglobins. VIII. A general qualitative and quantitative method in plastic drinking straws and the quantitative analysis of Hb-F.

    PubMed

    Schroeder, W A; Pace, L A

    1978-03-01

    The microchromatographic procedure for the quantitative analysis of the hemoglobin components in a hemolysate uses columns of DEAE-cellulose in a plastic drinking straw with a glycine-KCN-NaCl developer. Not only may the method be used for the quantitative analysis of Hb-F but also for the analysis of the varied components in mixtures of hemoglobins.

  1. The effect of age on mitochondrial ultrastructure.

    PubMed

    Wilson, P D; Franks, L M

    1975-01-01

    The ultrastructure of perfused livers and of mitochondrial fractions from 6-month-old and 30-month-old C57/BL mice were studied. In old mice the liver cell mitochondria were enlarged and rounded with a light 'foamy', vacuolated matrix, short cristae and a loss of dense granules. Quantitative studies showed a 60% increase in the mean size and an increased proportion of larger mitochondria in intact 30-month-old perfused livers. Endothelial and Kupffer cell mitochondria were smaller than those of the parenchymal cells. Mitochondria in pellets prepared from 6- and 30-month-old livers were rounded and condensed, although there were a few larger and 'foamy' mitochondria in the preparations from old mice. Up to 47% of large mitochondria in the old livers were lost during cell fractionation.

  2. [Quantitative cartilage analysis with magnetic resonance tomography (qMRI)--a new era in arthrosis diagnosis?].

    PubMed

    Eckstein, F; Englmeier, K H; Reiser, M

    2002-06-01

    Magnetic resonance imaging (MRI) is a new and very powerful method for the diagnostics and monitoring of osteoarthritis. Its advantage is that all articular tissues can be visualized directly and are accessible for three-dimensional analysis. This article reviews qualitative, semi-quantitative, and quantitative studies on articular cartilage with MRI. In particular we discuss pulse sequences and three-dimensional postprocessing methods for quantitative analysis of cartilage volume and thickness, along with their accuracy and precision in healthy volunteers and patients with osteoarthritis. It addition, we present approaches for quantitative analyses of structural/biochemical parameters and for the deformational behavior of cartilage in vivo.

  3. MOLD SPECIFIC QUANTITATIVE PCR: THE EMERGING STANDARD IN MOLD ANALYSIS

    EPA Science Inventory

    Today I will talk about the use of quantitative or Real time PCR for the standardized identification and quantification of molds. There are probably at least 100,000 species of molds or fungi. But there are actually about 100 typically found indoors. Some pose a threat to human...

  4. Teaching Quantitative Research Methods: A Quasi-Experimental Analysis.

    ERIC Educational Resources Information Center

    Bridges, George S.; Gillmore, Gerald M.; Pershing, Jana L.; Bates, Kristin A.

    1998-01-01

    Describes an experiment designed to introduce aspects of quantitative reasoning to a large, substantively-focused class in the social sciences. Reveals that participating students' abilities to interpret and manipulate empirical data increased significantly, independent of baseline SAT verbal and mathematics scores. Discusses implications for…

  5. Quantitative proteomic analysis by accurate mass retention time pairs.

    PubMed

    Silva, Jeffrey C; Denny, Richard; Dorschel, Craig A; Gorenstein, Marc; Kass, Ignatius J; Li, Guo-Zhong; McKenna, Therese; Nold, Michael J; Richardson, Keith; Young, Phillip; Geromanos, Scott

    2005-04-01

    Current methodologies for protein quantitation include 2-dimensional gel electrophoresis techniques, metabolic labeling, and stable isotope labeling methods to name only a few. The current literature illustrates both pros and cons for each of the previously mentioned methodologies. Keeping with the teachings of William of Ockham, "with all things being equal the simplest solution tends to be correct", a simple LC/MS based methodology is presented that allows relative changes in abundance of proteins in highly complex mixtures to be determined. Utilizing a reproducible chromatographic separations system along with the high mass resolution and mass accuracy of an orthogonal time-of-flight mass spectrometer, the quantitative comparison of tens of thousands of ions emanating from identically prepared control and experimental samples can be made. Using this configuration, we can determine the change in relative abundance of a small number of ions between the two conditions solely by accurate mass and retention time. Employing standard operating procedures for both sample preparation and ESI-mass spectrometry, one typically obtains under 5 ppm mass precision and quantitative variations between 10 and 15%. The principal focus of this paper will demonstrate the quantitative aspects of the methodology and continue with a discussion of the associated, complementary qualitative capabilities.

  6. Teaching Quantitative Reasoning for Nonscience Majors through Carbon Footprint Analysis

    ERIC Educational Resources Information Center

    Boose, David L.

    2014-01-01

    Quantitative reasoning is a key intellectual skill, applicable across disciplines and best taught in the context of authentic, relevant problems. Here, I describe and assess a laboratory exercise that has students calculate their "carbon footprint" and evaluate the impacts of various behavior choices on that footprint. Students gather…

  7. Teaching Quantitative Reasoning for Nonscience Majors through Carbon Footprint Analysis

    ERIC Educational Resources Information Center

    Boose, David L.

    2014-01-01

    Quantitative reasoning is a key intellectual skill, applicable across disciplines and best taught in the context of authentic, relevant problems. Here, I describe and assess a laboratory exercise that has students calculate their "carbon footprint" and evaluate the impacts of various behavior choices on that footprint. Students gather…

  8. Quantitative and Qualitative Analysis of Biomarkers in Fusarium verticillioides

    USDA-ARS?s Scientific Manuscript database

    In this study, a combination HPLC-DART-TOF-MS system was utilized to identify and quantitatively analyze carbohydrates in wild type and mutant strains of Fusarium verticillioides. Carbohydrate fractions were isolated from F. verticillioides cellular extracts by HPLC using a cation-exchange size-excl...

  9. MOLD SPECIFIC QUANTITATIVE PCR: THE EMERGING STANDARD IN MOLD ANALYSIS

    EPA Science Inventory

    Today I will talk about the use of quantitative or Real time PCR for the standardized identification and quantification of molds. There are probably at least 100,000 species of molds or fungi. But there are actually about 100 typically found indoors. Some pose a threat to human...

  10. A new quantitative method for gunshot residue analysis by ion beam analysis.

    PubMed

    Christopher, Matthew E; Warmenhoeven, John-William; Romolo, Francesco S; Donghi, Matteo; Webb, Roger P; Jeynes, Christopher; Ward, Neil I; Kirkby, Karen J; Bailey, Melanie J

    2013-08-21

    Imaging and analyzing gunshot residue (GSR) particles using the scanning electron microscope equipped with an energy dispersive X-ray spectrometer (SEM-EDS) is a standard technique that can provide important forensic evidence, but the discrimination power of this technique is limited due to low sensitivity to trace elements and difficulties in obtaining quantitative results from small particles. A new, faster method using a scanning proton microbeam and Particle Induced X-ray Emission (μ-PIXE), together with Elastic Backscattering Spectrometry (EBS) is presented for the non-destructive, quantitative analysis of the elemental composition of single GSR particles. In this study, the GSR particles were all Pb, Ba, Sb. The precision of the method is assessed. The grouping behaviour of different makes of ammunition is determined using multivariate analysis. The protocol correctly groups the cartridges studied here, with a confidence >99%, irrespective of the firearm or population of particles selected.

  11. Structural and Quantitative Analysis of Three C-Glycosylflavones by Variable Temperature Proton Quantitative Nuclear Magnetic Resonance

    PubMed Central

    Liu, Yang; Dai, Zhong

    2017-01-01

    Quantitative nuclear magnetic resonance is a powerful tool in drug analysis because of its speed, precision, and efficiency. In present study, the application of variable temperature proton quantitative nuclear magnetic resonance (VT-1H-qNMR) for the calibration of three C-glycosylflavones including orientin, isoorientin, and schaftoside as reference substances was reported. Since there was conformational equilibrium due to the restricted rotation around the C(sp3)-C(sp2) bond in C-glycosylflavones, the conformational behaviors were investigated by VT-NMR and verified by molecular mechanics (MM) calculation. The VT-1H-qNMR method was validated including the linearity, limit of quantification, precision, and stability. The results were consistent with those obtained from mass balance approach. VT-1H-qNMR can be deployed as an effective tool in analyzing C-glycosylflavones. PMID:28243484

  12. Ultrastructural demonstration of Cx43 gap junctions in induced pluripotent stem cells from human cord blood.

    PubMed

    Beckmann, Anja; Schubert, Madline; Hainz, Nadine; Haase, Alexandra; Martin, Ulrich; Tschernig, Thomas; Meier, Carola

    2016-11-01

    Gap junction proteins are essential for direct intercellular communication but also influence cellular differentiation and migration. The expression of various connexin gap junction proteins has been demonstrated in embryonic stem cells, with Cx43 being the most intensely studied. As Cx43 is the most prominent gap junction protein in the heart, cardiomyocyte-differentiated stem cells have been studied intensely. To date, however, little is known about the expression and the subcellular distribution of Cx43 in undifferentiated stem cells or about the structural arrangement of channels. We, therefore, here investigate expression of Cx43 in undifferentiated human cord-blood-derived induced pluripotent stem cells (hCBiPS2). For this purpose, we carried out quantitative real-time PCR and immunohistochemistry. For analysis of Cx43 ultrastructure and protein assembly, we performed freeze-fracture replica immunogold labeling (FRIL). Cx43 expression was detected at mRNA and protein level in hCBIPS2 cells. For the first time, ultrastructural data are presented on gap junction morphology in induced pluripotent stem (iPS) cells from cord blood: Our FRIL and electron microscopical analysis revealed the occurrence of gap junction plaques in undifferentiated iPS cells. In addition, these gap junctions were shown to contain the gap junction protein Cx43.

  13. Quantitative analysis of immobilized metalloenzymes by atomic absorption spectroscopy.

    PubMed

    Opwis, Klaus; Knittel, Dierk; Schollmeyer, Eckhard

    2004-12-01

    A new, sensitive assay for the quantitative determination of immobilized metal containing enzymes has been developed using atomic absorption spectroscopy (AAS). In contrast with conventionally used indirect methods the described quantitative AAS assay for metalloenzymes allows more exact analyses, because the carrier material with the enzyme is investigated directly. As an example, the validity and reliability of the method was examined by fixing the iron-containing enzyme catalase on cotton fabrics using different immobilization techniques. Sample preparation was carried out by dissolving the loaded fabrics in sulfuric acid before oxidising the residues with hydrogen peroxide. The iron concentrations were determined by flame atomic absorption spectrometry after calibration of the spectrometer with solutions of the free enzyme at different concentrations.

  14. Quantitative sectioning and noise analysis for structured illumination microscopy

    PubMed Central

    Hagen, Nathan; Gao, Liang; Tkaczyk, Tomasz S.

    2011-01-01

    Structured illumination (SI) has long been regarded as a nonquantitative technique for obtaining sectioned microscopic images. Its lack of quantitative results has restricted the use of SI sectioning to qualitative imaging experiments, and has also limited researchers’ ability to compare SI against competing sectioning methods such as confocal